Preface

Population genetics is a prominent area in biology, as it is a basis for the comprehension of the evolution of living beings. There are several applications of population genetics ranging from the analysis of gene frequencies of a population to the genetic improvement of plants and animals.

This book provides a comprehensive review of population genetics over four sections.

Section 1, "Population Genetics and Main Driving Forces of Evolution", includes chapters on natural selection, derivation, and selection flow.

Section 2, "Population Genetics and Conservation", includes a chapter on phylogeography, biodiversity, molecular markers, and conservation.

Section 3, "Genetic Diversity and Animal Breeding" includes a chapter on the genetic diversity and evolution of Yunnan chicken breeds in China.

Section 4, "Genetic Diversity and Population Structure of Plant Crops", includes a chapter on morpho-nutraceutical diversity of jute and related fiber crops such as vegetables.

> **Rafael Trindade Maia**  Semi-Arid Sustainable Development Center, Federal University of Campina Grande, Sumé, Brazil

> > **Magnólia Campos de Araújo** Federal University of Campina Grande, Sumé, Brazil

**1**

Section 1

Population Genetics and Main

Driving Forces of Evolution

Section 1

## Population Genetics and Main Driving Forces of Evolution

### **Chapter 1**

### Introductory Chapter: Population Genetics

*Rafael Trindade Maia and Magnólia Campos de Araújo*

### **1. Introduction**

Population genetics is a science that studies the genetic composition and distribution, as well as its effects, through mathematical formulas and indicators for measuring genetic diversity. It aims to evaluate allele, phenotypic and genotypic frequencies in populations of living beings; allowing to understand the origin and dynamics of genetic variation, making it possible to make predictions about the influences of one or more evolutionary processes on these compositions over generations. In this context, population genetics seeks to find an evolutionary meaning to explain genetic variation in living beings and better understand the evolutionary mechanisms that act on it.

Understanding the genetic diversity of populations has several uses, such as monitoring pathogens and vectors, conservation studies and species management, genetic improvement of plants and animals, genetic counselling, monitoring of hereditary diseases, etc. The mechanisms associated with changes in allelic and genotypic frequencies are 1) Mutation; 2) Natural selection; 3) Migration (with gene flow); 4) Genetic drift [1].

### **2. Mutation**

Mutations are the primary sources of genetic variation, responsible for avoiding genetic homogeneity between populations, as they result in new alleles. By definition, mutations are changes in the DNA sequence, which may result from spontaneous errors in DNA replication during cell division or due to external factors such as exposure to mutagenic chemicals, radiation and viral infections [2].

### **3. Natural selection**

Natural selection, initially proposed by Darwin, advocated that those with characteristics that increased the chance of survival or reproduction of individuals tended to settle in populations. In this context, it can be said that natural selection works favouring the advantageous alleles, genotypes and phenotypes and eliminating the unfavourable ones. There are two types of natural selection: positive or Darwinian selection, which acts on an adaptive mutation by increasing its frequency in the population; and negative or purifying selection, which acts in the opposite direction, reducing the frequency or even eliminating deleterious mutations from populations [3].

### **4. Migration (with gene flow)**

The migration of individuals between different populations with consequent reproductive success results in gene flow, which is the transfer of alleles between populations. The outcome of these gene transfers depends on the difference between allelic frequencies in populations and the number and proportion of migrant individuals. It is a crucial evolutionary mechanism for conservation geneticists since gene flow is essential to minimise the effects of inbreeding and genetic drift on natural populations [4].

### **5. Genetic drift**

Of all the evolutionary mechanisms, genetic drift is the one that most randomly alters the gene and allelic frequencies of populations. As it is a completely stochastic process, it is impossible, at first, to predict the allelic frequencies in the face of a drift event. This mechanism is associated with the loss of genetic variation in populations, which may make them more vulnerable in subsequent generations. Genetic drift is a consequence of a drastic alteration of natural and casual order, such as earthquakes, tsunamis, tornadoes, floods, fires, avalanches and other processes, affecting a large population contingent [5].

### **6. Hardy–Weinberg equilibrium**

The Hardy–Weinberg equilibrium is one of the fundamental principles of population genetics. Assuming that a population is panmictic and mated at random and that there is no interference from evolutionary mechanisms (Mutation, Natural Selection, Migration and Drift), allelic and genotypic frequencies remain the same across generations. The Hardy–Weinberg theorem can be applied mathematically to a pair of alleles (a gene) through Newton's binomial, according to the following expression in Eq. (1):

$$p^2 + 2pq + q^2 = 1 \tag{1}$$

Where:

*p* is the frequency of the *A* allele. *q* is the frequency of the *a* allele. *p*2 is a frequency of *AA* homozygotes. *q*2 is a frequency of *aa* homozygotes. *2pq* is the frequency of *Aa* heterozygotes.

When populations are not in Hardy–Weinberg equilibrium, it means that evolutionary forces are acting and changing their allele and genotypic frequencies [6].

Analysing population genetics, through scientific investigations, is one of the best ways to understand the evolutionary history of living beings, with diverse applications in various sectors (health, agriculture, genetic improvement, biotechnology, etc.). In this sense, population genetics is an integrative and challenging science, with great discoveries and challenges to be achieved and a great and promising future in the post-genomic era.

*Introductory Chapter: Population Genetics DOI: http://dx.doi.org/10.5772/intechopen.104879*

### **Author details**

Rafael Trindade Maia1,2\* and Magnólia Campos de Araújo2

1 Federal University of Campina Grande, Center for Sustainable Development of the Semiarid Region, Sumé, Paraíba State, Brazil

2 Federal University of Campina Grande, Center of Education and Health, Postgraduate Program in Natural Sciences and Biotechnology, Cuité, Paraíba State, Brazil

\*Address all correspondence to: rafael.rafatrin@gmail.com

© 2022 The Author(s). Licensee IntechOpen. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

### **References**

[1] Okazaki A, Yamazaki S, Inoue I, et al. Population genetics: Past, present, and future. Human Genetics. 2021;**140**:231- 240. DOI: 10.1007/s00439-020-02208-5

[2] Hershberg R. Mutation—The engine of evolution: Studying mutation and its role in the evolution of bacteria. Cold Spring Harbor Perspectives in Biology. 2015;**7**(9):a018077

[3] Gregory TR. Understanding natural selection: Essential concepts and common misconceptions. Evolution: Education and Outreach. 2009;**2**:156-175

[4] Ellstrand NC, Rieseberg LH. When gene flow really matters: Gene flow in applied evolutionary biology. Evolutionary Applications. 2016;**9**(7): 833-836

[5] Lynch M, Ackerman M, Gout JF, et al. Genetic drift, selection and the evolution of the mutation rate. Nature Review Genetics. 2016;**17**:704-714. DOI: 10.1038/ nrg.2016.104

[6] Salanti G, Amountza G, Ntzani E, et al. Hardy–Weinberg equilibrium in genetic association studies: An empirical evaluation of reporting, deviations, and power. European Journal of Human Genetics. 2005;**13**:840-848

Section 2

## Population Genetics and Conservation

### **Chapter 2**

## Perspective Chapter: Molecular Approach for the Study of Genetic Diversity and Conservation Prioritization of Fish Population

*Shahnawaz Ali and Chinnathangam Siva*

### **Abstract**

Fishes are the most abundant vertebrates in the animal kingdom. They play important biological and ecological roles. Various anthropogenic and climatic factors have led to the decline of natural population and increased the risk of extinction. CBD emphasized the conservation of biodiversity at all levels from genes to ecosystems. However, little attention paid to genetic considerations in restoration efforts. Estimation of genetic diversity and population structure is inevitable for effective implementation of conservation management program. Available DNA markers like mitochondrial and microsatellite markers provide useful insight into understanding the genetic diversity status of fish population in the wild. The present chapter highlights the importance of genetic diversity and its determinants. Utility of mitochondrial and microsatellite markers shown through a case study of a threatened cyprinid species *Neolissochilus hexagonolepis* known as chocolate mahseer that is widely distributed in the North-eastern part of India. Presence of low genetic diversity confirmed its threatened status and further analysis based on various genetic parameters revealed the status of different stocks as well as the population structure of this species. The results obtained could be helpful in rehabilitation and conservation planning and prioritization for the maintenance of a viable population of this species.

**Keywords:** biodiversity, conservation, population genetics, molecular markers, phylogeography

### **1. Introduction**

Fishes are cold-blooded aquatic vertebrates, and over half of the living vertebrates are fishes. The estimated total number of fishes is more than 35,934 species, and it is higher than the combined total of other vertebrates [1]. Among all known fish species, more than 15,000 are found in freshwater, which is less than 0.3% of available global water, while more than 16,000 species are marine, which is 70% of the earth's surface [2]. The incredible diversity of fishes is astounding that is evident from their morphology, the habitat they occupy, their physiological adaptation, and

behavior [3]. They have a long evolutionary history of origin and diversification that began in the Cambrian Period at least 520 million years ago [4]. They occupy all types of the aquatic environment, and to survive and colonize in different habitats, fishes have developed various types of anatomical, physiological, behavioral, and ecological adaptation and plays different types of biological and ecological roles [5]. Fishes are also critically important for the food security and nutrition of everincreasing human population, and more than 4.5 billion people get at least 15% of their average per capita intake of animal protein from fish. They have unique nutritional properties and are one of the efficient feed converters into high quality food therefore, widely exploited from natural water bodies as well as produced through aquaculture production systems [6].

However, due to various anthropogenic and climatic factors, fish stocks both in marine as well as freshwater are continuously declining and are under severe threats. The unfulfilled demand for resources has resulted in cumulative pressure on the marine ecosystem from a range of human activities. As a result, both marine species and habitat are experiencing detrimental impacts due to different human interference [7–8]. It is estimated that humans have impacted almost 90% of the global ocean surface [9], and marine fish abundances have declined by 38% in last three decades [10]. Loss of coral habitats, overfishing, dredging activities, and damage caused by bottom trawling all have led to the significant decline of marine fish stocks, its recruitment, and yields, and even after continuous efforts recovery has not yet been achieved [11].

On the other side, freshwater ecosystem has been assessed as the most impacted and endangered ecosystem on the planet [12]. The decline in biodiversity is much greater in freshwater than in terrestrial and marine ecosystems [13, 14]. The major threats to global freshwater biodiversity include overexploitation; water pollution; flow modification; destruction or degradation of habitat; invasion by exotic species; infectious diseases, and the combined and interacting influences of these threats have resulted in population declines and range reduction of freshwater biodiversity worldwide [12, 15, 16]. Therefore, direct and indirect anthropogenic impacts have resulted in global decline of biodiversity [7, 17].

In addition, global climate change also poses many threats to biodiversity and alters the physical, chemical, and biological characteristics of freshwater and marine biodiversity and habitats [18, 19]. According to recent estimates, around 50% of global freshwater fish species are potentially threatened due to climate change [20]. The effects of climate change have been recorded and predicted in terms of changes in species phenology, range, and physiology [21], thus accelerating the risk of extinction [22–24]. It is increasingly recognized that the scales of different anthropogenic impacts are greater than natural drivers for the earth system and hence coined the name of a new geological epoch, the "Anthropocene" where human-induced changes dominate over natural cycles [25, 26]. The loss of global biodiversity is now comparable to previous global-scale mass extinction events, and we are now witnessing the "sixth mass extinction" event [27, 28]. It is further shown that the sixth mass extinction is more severe than perceived in terms of species extinction [29].

In its assessment, the Convention on Biological Diversity (CBD) has emphasized the conservation of biodiversity at all levels from genes, population, species, and ecosystems [30, 31]. As discussed above, the threat to freshwater biodiversity is far greater than other ecosystems, and the fish species are becoming either vulnerable or endangered, and their numbers are continuously increasing every year (**Figure 1**), and around 37% of freshwater fishes are threatened with the risk of extinction [20]. The loss of habitat and invasion of non-native species in major riverine systems of

*Perspective Chapter: Molecular Approach for the Study of Genetic Diversity and Conservation... DOI: http://dx.doi.org/10.5772/intechopen.102018*

**Figure 1.**

*Changes in numbers of species in the threatened categories (CR: Critical; EN: Endangered; VU: Vulnerable) from 2000 to 2021 (IUCN Red List version 2021–3) for the fish species on the Red List (Accessed on November 17, 2021; https://www.iucnredlist.org/).*

the world has reduced not only the species diversity but also caused similarity among species assemblages. This has led to the "taxonomic homogenization" on a regional and global scale [32]. The overall aim of conservation is to protect biological diversity and the underlying processes that sustain it in the face of perturbation caused by human activities. The strategies for conservation need prioritization that maximizes both representation and persistence of diversity [33]. It is known that all organisms are endowed with a genetic blueprint and thus contribute to genetic diversity, which is the foundation of all biological diversity. Earlier works demonstrated that loss of genetic diversity might lead to the collapse of population and even species that are present in the wild [34, 35]. While comparing threatened and non-threatened taxa, it was revealed that the genetic factors such as heterozygosities reduced to a considerable level in the threatened taxa before a species driven to the risk of extinction [36]. Although CBD agreed on the conservation of genetic diversity, little attention has been paid to genetic considerations in restoration efforts, and it remained largely neglected [37]. Therefore, it is necessary to document genetic diversity at the population and species level so that a comprehensive conservation strategy can be implemented for the rehabilitation and restoration of species.

### **2. Determinants of genetic diversity and its measurement**

The vast and varied population of fishes inherit different genetic traits and thus shows remarkable genetic diversity both at spatial and temporal scales [38, 39]. The genetic composition defines the form and functionality of the organism. The presence of genetic variation in the population and species contributes to the ability to respond to environmental changes [40]. The loss of species and their distributional range are detrimental to the genetic diversity, which the species inherited and accumulated over millions of years of evolutionary processes. Thus documenting the genetic variation in populations is important to understand the forces that change their genetic composition over time, and thus their evolutionary relationship is described through the study of population genetics [41]. It is also important to understand that each individual of a species might have a similar phenotype but distinct genetic makeup. These differences arise due to the difference in their nucleotide sequences (e.g. DNA sequences) which is called "polymorphism." Genetic diversity provides the raw material for the survival, evolution, and natural selection of the organism [42]. One of the important phenomenons, which contribute towards the genetic variation among individuals at species or population level, is "mutation." In other words, it is a base pair substitution in the DNA sequences (either coding or non-coding region) during the replication, and this is an essential requirement for the evolution [41]. Mutation in non-coding sequences evolves faster than coding sequences since it does not directly affect the gene functions. Thus these genetic variants or "alleles" appear or added at each generation due to random mutation or may disappear due to loss of alleles under the influence of "genetic drift" (i.e., a random change in gene frequencies). The other important evolutionary force responsible for high genetic variation is the "Natural selection" that can change gene frequencies in the population and leads toward the relative fitness in the population. However, for natural selection to affect the allele frequency, the locus must be in the coding region [43]. In contrast to this, "Neutral Theory of Molecular Evolution" proposed by "Kimura" [44] argues that most allelic variations and substitutions in proteins and DNA are neutral. According to this theory, gene frequencies may change by "genetic drift" without the influence of natural selection, and in a large panmictic population (i.e., where species show random mating within a population), and it is inversely proportional to the effective population size [45].

The detection and measurements of genetic diversity and population structure are essentially required for the development of the appropriate strategies for the implementation of conservation programs [46, 47]. Furthermore, molecular phylogenetics and genetic diversity analysis help in ascertaining the taxonomic identity and evolutionary relationship of the wild species. There are certain population genetic parameters that are measured for the evaluation of genetic variability at individual and population levels. These measures are essential for the comprehensive assessment of genetic structure within and among the population. Among such important population genetic parameters are the percentage of polymorphic loci; the number of alleles per locus; the effective number of alleles per locus; observed and expected heterozygosity; estimates of effective population size; and assessment of linkage disequilibrium. Further, for estimating variations between population it is essentially required to measure different types of variances (*Fst, G*ST, *R*ST), genetic distances, and correlation between genetic distance and geographic distance [43, 48]. These population genetic parameters provide important data to draw any plausible conclusion about the status of the stock and its genetic structure.

### **3. Application of molecular technology and fisheries genetics**

The advent of molecular techniques in the last seven decades has provided significant insights into the population structure and its genetic diversity. Initially, the technique of protein gel electrophoresis to several allozyme loci was applied to measure the genetic variation in the species [49] and assessment of the fish genetic stock. The use of allozyme remained a dominant method until the development of

*Perspective Chapter: Molecular Approach for the Study of Genetic Diversity and Conservation... DOI: http://dx.doi.org/10.5772/intechopen.102018*

DNA amplification using the PCR (Polymerase Chain Reaction) technique [50]. The arrival of PCR-based techniques revolutionized the field of molecular genetics and led to the emergence of fish genomics by the use of DNA-based markers technology. A genetic or molecular marker is a gene or DNA sequence with a known location on a chromosome and associated with a particular gene or trait. The popular genetic markers widely used for genetic diversity assessment include allozymes, mitochondrial DNA, RFLP, RAPD, AFLP, microsatellite, SNP, and EST markers. Genetic markers have been applied to three areas of fisheries in particular; stock structure analysis, aquaculture, and taxonomy/systematics [51] with varying degrees of success [52].

Among the different available DNA markers, mitochondrial DNA (mtDNA) has been widely and effectively used for the assessment of population structure and phylogenetic study [53, 54]. Mitochondrial DNA (mtDNA), as the name suggests, is contained in the mitochondria of the cell and is generally maternally inherited. The general features of mitochondrial DNA include predominantly female inheritance, lack of recombination, selectively neutral, high rate of evolution, relatively simple structure, and multiple copies in the cell [55, 56]. Therefore, different mtDNA gene sequences have proved to be a good marker for analyzing variation at interspecific and intraspecific levels in fishes. Mitochondrial DNA marker (mtDNA) is widely used to study the gene flow, hybrid zones, population structure, phylogenetics, phylogeography, molecular evolution, and conservation genetics [57]. Another type of marker, which is known as satellite DNA is increasingly used for the investigation of genetic variability and divergence between the species [58]. Microsatellite, also known as Simple Sequence Repeats (SSRs), has widely been utilized for studies in population genetics, evolutionary and conservation biology of species and therefore considered as the most significant genetic marker [59]. A microsatellite is tandem repeated motifs of 1–6 bases found in all prokaryotic and eukaryotic genomes. They are present in both coding and non-coding regions and are usually characterized by a high degree of length polymorphism. Further, microsatellites featured with codominant inheritance, inheritance in a mendelian fashion, wide distribution, high stability, and repeatability signify their usage for the assessment of genetic diversity within and between populations and provide significant genetic information [60]. Hence, species-specific microsatellite markers are extensively developed and studied in different fish populations [61, 62].

Recently, with the advent of next-generation sequencing (NGS) platforms, the SSR markers in the non-model organism can be developed rapidly and efficiently compared to the conventional methods [63, 64]. The random sequencing based approach also facilitates the genotyping of a high number of loci at moderate costs [65]. Among the different NGS platforms available, the Illumina sequencing method is a powerful tool for the discovery of SSRs and delivers the highest yield of error-free data for the most sensitive or complex sequencing samples [66].

### **4. Conservation prioritization of fish population: a case study**

The use of molecular markers based technology has immensely contributed to different aspects of conservation genetics of species, such as resolving the taxonomic ambiguity; designing captive and marker assisted breeding programs; detecting diversity within and among geographical populations; estimating gene flow, and understanding the factors contributing to fitness [67]. Therefore, management of the species must include information on the extent and organization of genetic diversity in populations to suggest sustainable conservation strategies. This becomes more relevant when we are dealing with endangered species [46]. The fundamental aim of the conservation of species is to minimize genetic deterioration of endangered stock and maintain a viable population to avoid the bottleneck and risk of extinction. The parameters such as genetic divergence among populations and gene flow rate are helpful in characterizing populations, species, and subspecies in different conservation units [68]. Here we have briefly discussed the use of mitochondrial and microsatellite markers in conservation prioritization of a threatened cyprinid species *Neolissochilus hexagonolepis* known as chocolate mahseer that is widely distributed in the north-eastern part of India.

Mahseer is the common name used for three carp genera, *viz*. *Tor*, *Neolissochilus*, and *Naziritor* (family Cyprinidae). *N. hexagonolepis* has been widely reported from southeast Asia and is abundantly available in the Brahmaputra river basin of Northeast India [69]. The species is enjoyed as food as well as sports fish and also identified as a candidate species for aquaculture [70]. However, the natural population is rapidly declining due to various anthropogenic reasons such as degradation of natural habitat, hydro development projects, and angling demands of the species and therefore categorized as threatened species by IUCN [71, 72]. For the implementation of any effective conservation program it is inevitable to obtain basic genetic information of this species. Therefore, we used mitochondrial and microsatellite DNA markers to study the genetic structure, population history, and genetic diversity of geographically isolated populations of the *N. hexagonolepis* from Northeast India. The information provided to identify genetically diverse stocks as well as delineation of conservation units that can be utilized to optimize the conservation of the chocolate mahseer.

In the experimental setup, 200 fish samples were collected from different geographically isolated drainages from Northeast India. First, we evaluated the targeted genetic parameters using three mitochondrial markers, namely ATPase6/8, cytochrome oxidase I (CO-I) and cytochrome b (Cytb). For amplification of these mitochondrial genes, total genomic DNA from fin samples was used and amplified using standard primer pairs designed from the whole mitochondrial genome sequence. Further, PCR products were column purified and sequenced in both directions using an ABI 3130 Genetic Analyzer (Applied Biosystem, Carlsbad, CA) with Big Dye Terminator cycle sequencing kit v.3.1 with the help of the same primers used for amplification of the target genes. Robust statistical analysis was performed using suitable computer programs to estimate the population genetic parameter, mainly polymorphic sites (S), haplotype diversity (Hd), nucleotide diversity (p), and haplotype number. Molecular variance (AMOVA), molecular diversity indices, and genetic differentiation (FST) were also calculated. Moreover, the phylogenetic relationship among individuals of different populations was constructed by implementing the maximum likelihood tree method (MLM) based on the best-predicted model [73]. Mean genetic distances between the populations for all the three genes were also calculated. Geographical distances were simulated with haplotypes to determine the optimal number of population groups (K = 2–8). Possible correlation between pairwise genetic differentiation and geographical distances among nine populations was estimated by applying the Mantel test [74].

The analysis revealed the genetic diversity status of different populations based on their haplotype and nucleotide diversity pattern. In comparison, some populations has undergone a reduction in size or recent colonization events whereas, other

### *Perspective Chapter: Molecular Approach for the Study of Genetic Diversity and Conservation... DOI: http://dx.doi.org/10.5772/intechopen.102018*

populations showed a high level of divergence between haplotypes, indicating a long historical evolutionary pattern [75]. Analysis of molecular variance revealed a high level of genetic structuring among populations. Five major groups and one paraphyletic intermediate group were obtained by phylogenetic analysis. Overall results indicated a positive correlation between geographical distances and genetic divergence [76]. The analysis of different genetic parameters clearly indicated that most of the variation in genetic differentiation is present among population groups, and genetic variations in the chocolate mahseer population might be due to specific habitat conditions that influence population genetic structure. Further, the study also confirmed the threatened status of the population being low in genetic diversity. Thus, information generated by the study would be helpful for developing stockspecific strategies for

### *N. hexagonolepis* breeding, conservation, and management.

Further, microsatellite markers were developed, and population genetics, evolutionary, and conservation biology of *N. hexagonolepis* were studied. Here we used NGS technology (Illumina Miseq) to develop 25 novel SSR markers and further used these markers for assessing the genetic diversity and population structure of this species from Northeast India. Different population genetic parameters such as a number of polymorphic loci, numbers of alleles per locus, observed and expected heterozygosity, and pairwise genetic diversity were estimated using available computer programs. Population structure and bottleneck were estimated as well as migration pattern was studied using appropriate statistical methods.

In *N. hexagonolepis* we found tetra-nucleotides as the most frequent microsatellite motifs that were opposed to what is observed for other cyprinids where di-nucleotide is the most abundant [77]. All the loci were highly polymorphic and thus used for the analysis. In certain population, observed heterozygosity was lower than expected heterozygosity (He) which indicated the inbreeding effect within the populations [78]. Analysis of molecular variance (AMOVA) and high *F*st indicated relatively low gene flow among the population. Migration analysis also revealed that there is no active migration among the studied populations of *N. hexagonolepis*. The STRUCTURE analysis identified five subgroups that substantiate the result of cluster analysis and factorial correspondence analysis (FCA). Based on the estimation of different genetic parameters through statistical analysis, we could successfully identify the genetic status of different stocks as well as the population structure of this species [79]. The identified major groups can be considered as different conservation units when applying any management measures. Thus both the markers were extremely useful in genetic stock assessment of the species under study and provided critical information regarding conservation prioritization.

### **5. Conclusion**

Although freshwater ecosystems is under severe threat due to various anthropogenic and climatic factors, little attention and effort have been paid towards its conservation. Identification of fish stock structure and assessment of their genetic diversity should be an important component of any conservation planning. Available molecular tools are quite useful for the estimation of species diversity at individual to population levels. Further, it becomes more important when we deal with species of endangered categories. The present study clearly indicated that the use of mitochondrial and microsatellite markers has provided a great deal of information related to the fish population under study. We could develop novel microsatellite markers, which will be further useful for stock characterization as well as any marker-assisted breeding program in aquaculture. Apart from these, molecular techniques are commonly used as bio-monitoring tools for assessing the genetic diversity status of the species that help in rehabilitation and conservation planning and prioritization for the maintenance of a sustainable ecosystem.

### **Acknowledgements**

The authors acknowledge the financial assistance provided by Indian Council of Agricultural Research (ICAR) New Delhi, India for carrying out this research work under the project "Fish Genetic Stock—An outreach activity". The authors express thanks to Director, ICAR-Directorate of Coldwater Fisheries Research, Bhimtal, India for providing all necessary support.

### **Conflict of interest**

The authors declare no conflict of interest.

### **Author details**

Shahnawaz Ali\* and Chinnathangam Siva ICAR-Directorate of Coldwater Fisheries Research, Bhimtal, Uttarakhand, India

\*Address all correspondence to: alicife@gmail.com

© 2022 The Author(s). Licensee IntechOpen. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

*Perspective Chapter: Molecular Approach for the Study of Genetic Diversity and Conservation... DOI: http://dx.doi.org/10.5772/intechopen.102018*

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Section 3

## Genetic Diversity and Animal Breeding

### **Chapter 3**

## Status of World's Unique Animal Genetic Resource of Ladakh

*Feroz Din Sheikh*

### **Abstract**

Ladakh is the only typical cold arid zone of our country with extreme climate and hostile condition, the area makes its flora and fauna a unique one and distinct from rest of the country. Around 60% of the farmers of Ladakh are Pastoralist and 40% of the farmers are agriculturist and the majority of the economic income comes from animal rearing in Ladakh. It has some of the world's best animal genetic resource in the form of Changthangi Pashmina goats, Changthangi Sheep, Malra Goat, Malluk and Purig Sheep, Semi domesticated Yak and its crosses, Bactrian (Double Humped Camel) Zanskari horse, Ladakhi Cattle and Changthangi Dog. All these livestock contributes a lot to the income of the farmers of Ladakh especially the Changthang nomads who are completely dependent on livestock rearing. The livestock in Changthang is reared on extensive system on high altitude pastureland. During the past few decades these unique germplasms are facing several threats for its ecofriendly existence with the human populations. These threats and constraints are figured with possible recommendation and solution in the present study. Ladakh has been deprived of basic research facilities in animal science sector for so many years due to which this unique genetic resources are declining in terms of numbers as well as in production. Another reason is shifting of Ladakh economy from agro pastoralist to tourism business. If necessary steps are not taken immediately a time will reach that all this precious animal will be lost forever. The present article describes the present status and critical issues pertaining to animal genetic resource of Ladakh.

**Keywords:** Ladakh, Changthang, animals, population, livestock

### **1. Introduction**

Nature has its own role to play in selecting the best germplasm which can thrive and which are adapted to extreme type environment. The process of selection though it takes thousands of year but the result is a birth of a perfect organism, one such unique example is the highly diverse and unique domestic and wild animals of Ladakh. Ladakh meaning "Land of Passes" covers around 45,000 square miles (117,000 sq.km) and contains the Ladakh range, which is south-eastern extension of the Karakoram Range and upper Himalayan Range. It is administratively divided between Pakistan (northwest), as part of Gilgit Baltistan, and India (southeast), as part of Ladakh Union Territory (until October 31, 2019, part of Jammu Kashmir State; in addition, China administers portion of north-eastern part of Ladakh. Ladakh has

**Figure 1.** *Map of Union Territory of Ladakh.*

two main districts Leh and Kargil and it is the only typical cold arid zone of our country. The total land area of Leh district alone is 45,110 km<sup>2</sup> and along with Kargil district it forms more than 70% area of erstwhile Jammu & Kashmir state (**Figure 1**). The geographical location with an altitude extending from 11,000 to 16,000 ft asl and typical climatic condition with temperature ranging from +40°C in summer to 40°C of the area makes its floura and fauna a unique place on mother earth. Around 60% of the farmers of Ladakh are Pastoralist and 40% of the farmers are agriculturist and the majority of the economic income comes from animal rearing in Ladakh [1]. It has some of the world's best animal genetic resource in the form of Changthangi Pashmina goats, Changthangi Sheep, Malra Goat, Malluk Sheep, Semi domesticated Yak and its crosses, Bactrian (Double Humped Camel) Zanskari horse, Ladakhi Cattle and Changthangi Dog. These livestock are the main source of income for Ladakhi people and in the case of Changthang people, they are completely dependent on livestock rearing. The present status of each of this unique species are presented below:

### **2. Changthangi Pashmina goat**

The Pashmina internationally known as "Cashmere", a fine luxury fibre, is the prince of the specialty fibres obtained from domestic goats known as "*capra ibex*". The word "pashmina" comes from "pashm" meaning wool in Persian language and it is also known as 'tivit'sometimes. The cashmere breeds of goats (**Figure 2**) are found throughout the world and some of the important breeds are, Vatani of Afghanistan, Don, Orenberg and Altai mountain of Russia, Tan goats of China, Markhore and Raini of Iran, Kurdi of Iraq, Feral goats of Australia, Chegu and Changthangi goats of India. The three major producers of cashmere wool are China (60–70%), Mongolia (30–40%) and Iran, Afghanistan, Nepal etc (10–20%). Ladakh is a world leader in producing the

**Figure 2.** *Changthangi Pashmina Goat.*

finest Pashmina (fibre diameter less than 12μ) and a store house of the best germplasm with potential to exploit the superior genetic material for improvement of a whole range of pashmina producing goats in the world [2]. Changthangi goats also called as 'Changra' goats is primarily used for Pashmina production and secondarily used for meat production purpose, they also produce some amount of milk used by the nomads for making butter, cheese and curd for domestic use. These Pashmina goats are of great importance for vitalizing the economy of poverty stricken region of Changthang region of Leh districts of Ladakh (**Table 1**). In our country the Changthang region produces around 45,000 kgs of raw Pashmina fibre every year from about 2.03 lacs of Changthangi goats [3], which forms 99% of the total Pashmina production of India with 1% from Chegu breed of goat from Himachal Pradesh state. These goats are reared by Changpa Nomads on vast pastureland of Changthang region of Ladakh India (**Figure 3**). Compared to rest of the world the Pashmina fibre produced from this goats are relatively longer and finer, which aids the Kashmiri weavers to spin easily for preparing various high quality winter garments. This fibre has three times insulating values of the finest wool on a comparable weight basis and also possess 90% of the strength of merino wool and 60% strength of mohair [4]. The importance of this valuable fibre was discovered by the people of Europe during 17th century. It is believed that emperor Napoleon presented a shawl to Empress Josephine and there is a rumor that pashmina garments are as soft as baby skin and provide warm to hatch an egg. The craftsmen in Kashmir developed their own technique to process the raw material and used it for the manufacture of shawls. Thousands of artisans get involved in Kashmir for preparing shawls and pashmina business sustained the economy of thousands of artisan families in Kashmir and thousands of Changpa families in Ladakh as the possibilities for agriculture farming in Changthang is quite low [5]. The People of Changthang rear huge herds of goats and remained in migration in specific routes in search of better pasture


#### **Table 1.**

*Average income statement of each family from different livestock product (INR).*

**Figure 3.** *Flock of Changthangi Pashmina Goat.*

### **Figure 4.** *Pashmina Goats at High Land Pasture.*

for their livestock (**Figure 4**). The available pasture was sufficient for the number of livestock reared in Changthang by the Changpas till 1959, but during Chinese invasion in 1962 a lot of people from western Tibet migrated to Changthang side along with their livestock. They settled in Changthang and ultimately extra stocking of livestock on limited pastures caused damage to the pastureland due to overgrazing. Regarding pashmina production and its role in the economics of Changthangi people, the analyzed data shows that the highest average income at individual family level is fetched from Changthangi goats, which comes to around Rs 79,886.98, followed by Sheep Rs 33,412.88 and Yak, Rs 2621.63 annually. The overall average income of each family comes to Rs 116,021.49, in which Rs 79,886.98 is solely contributed by Changthangi goats, showing 68.85% of the total income annually. This result indicates that pashmina goats add to majority of the total income. The contribution of sheep is followed by pashmina goat represents 28.8% of the total income from livestock [1]. These results give a clear picture that the income generated from Changthangi goat in the form of Pashmina fibres, chevon, milk and manure forms the basis of their livelihood (**Figure 5**). In some villages like Koyul, Kharnak, Anlay, Korzok, Tsaga the income from pashmina goat contribute more than 90% of the total income.

### **2.1 Population status**

The number of Changthangi goats in the year 2000 was 163,663 with a sudden increase to 223,093 in 2001. The populations remain static till 2004. In 2005 a sharp decline to 187,299 was noticed with marginal increasing trend to 208,611 in 2009 [6, 7]. The population of Changthangi goat was 217,771 in 2014 and has shown a slight increase to present 219,198 in 2019 [3, 8]. The Population status of pashmina is static for the past two decade, however the population of local goat (Malra) has drastically reduced from 68,838 in the year 2006 to 3162 in 2014 [8, 9] and now to slight increase to 16,199 in 2019 [3] which is a concern. The detail population status of pashmina goat is given in **Tables 2** and **3**.

### **2.2 Diversity study**

Genetic diversity study in Changthangi goats of Ladakh was done by this institute in 2020. The genetic distance analyzed based on the microsatellite allele variability between different clusters shows genetic nearness and farness between the Changthangi goats of different subpopulations, which could be very useful for


**Table 2.**

*Sheep and goat population as per livestock census/departmental survey.*


### **Table 3.**

*Sheep husbandry estimated production.*

### *Status of World's Unique Animal Genetic Resource of Ladakh DOI: http://dx.doi.org/10.5772/intechopen.103767*

formulating future breeding plans in these goats. The Diversity study was done using highly polymorphic 15 microsatellites as recommended by FAO. The microsatellite are good candidates for breed characterization and diversity study. The study proved very useful for genetic investigations and assessing admixture in this goat populations. Bottleneck analysis revealed no recent bottleneck in Changthangi goats of Ladakh [10]. The strong inference that the Changthang breed of goat has not undergone bottleneck is important for goat breeders and conservationists, as it indicates that any unique alleles present in this breed may not have been lost. Therefore, it can be recommended that within breed diversity is actively maintained to enable these extensively unmanaged stocks to adapt to future demands and conditions and there is ample scope for further improvement in its productivity through appropriate breeding strategies. The substantial genetic variation and polymorphism observed across studied loci in the Changthangi Goats of Ladakh and the inference drawn from this study could be used for formulating future breeding plan and overall genetic improvement of this goat for Cashmere and meat production in whole of Ladakh.


### **2.3 Constraints and solutions**


### **2.4 Future strategies**


### **3. Changthangi sheep**

Changthang region of Ladakh is the home tract for a potent dual purpose breed of sheep 'Changthangi' also known as "Changluk" locally. These breed of sheep is famous throughout the Ladakh region for its quality wool and mutton production (**Figure 6**). A total of about 113,554 of Changthangi sheep population sustain the economy of Changthangi people in the year 2003 which has drastically reduced to 49,654 in 2009 [7, 11]. Presently the population of Changluk is less than 70,000. This sudden reduction in the sheep population may be attributed to low income from sheep rearing compared to Pashmina goats, whose population is increasing year by year [12]. The low income return from sheep rearing is due to lay man approach for maintaining this breed as till date no specific breeding policy has been adopted for up gradation of

**Figure 6.** *Changthangi Sheep.*

these sheep in the field and no effort has been made even by the state govt, which is clear from the fact that no such established farm of these sheep exist in the whole of Ladakh division. Low income from sheep is also attributed to religious belief as these people prefer other source of income from livestock other than meat production. A scientific approach in managing and rearing this Changthangi sheep is need of the time as the cost of rearing this animal is getting higher than its production. Also the required growth rate of the sector is possible only through selection based on important production traits. Among many of the constraints to sheep production in Ladakh, scarcity of feed, lack of breeding policy and high mortality has been the major limiting factors [13]. This is partly because sheep breeding in Ladakh is non-controlled, and health and nutrition management are very poor. Diminutive breeding efforts attempted as early as 1960s focused on crossbreeding of the indigenous breeds with exotic breeds (Russian Merino, Karakul) to improve growth and wool yield. Currently, exotic and crossbred's sheep in Ladakh constitute little proportion (<10%) of the total sheep population. The crossbreeding programme suffered from poor planning, not involving livestock owners and stakeholders in decision making and ownership of the initiatives on top of low regard to the potential of indigenous breeds. Studies made on Changthangi sheep breeds revealed within breed variation for growth and indicated feasibility for productivity improvement of indigenous sheep breeds through genetic means [12]. In the present situation owing to the importance of livestock in cold arid region of Ladakh, a framework for sheep breeding is seriously needed.

As per the recommendations of National commission on Agriculture from time to time, Northern Temperate Region of India including J&K has been earmarked for propagation of fine wool germ plasm. Big strides have been made in fine wool sector by the state. The production potential of the indigenous stock has been increased by more than double. However, till date Changthangi goat has been deprived of basic research for breed upgradation. Further, sheep breeding policy in the Union Territory of J&K and Ladakh should not be mono-cultured only for fine wool production because of its diverse agro- climatic conditions but it should be region specific and diversified.

### **3.1 Population status**

On the contrary to the population trend of Pashmina goats in Ladakh the Changthangi sheep shows an initial sharp inclining trend from 66,822 in the year 2000 to 113,544 in 2004 with a subsequent declining trend to 49,652 in 2009 [7, 14, 15]. The population is somewhat static with 55,353 Changluk in 2014 [8]. However, the population of local Malluk has increased to 48,124 during the past few years making a total district sheep population of 103,477 in 2014. Presently the Changthangi Sheep population is 67,521 mostly restricted to Changthang region [3]. If suitable measures are not adopted, then the precious germplasm of Changthangi sheep may be lost during the coming years. The detail population status is given in **Table 4**.

### **3.2 Wool production**

During our recent study at this institute, Changthangi sheep is one of the unique breeds having double coat with marked difference in fibre diameter and surface characteristics fibres. One of the striking observation reported in Changthangi sheep was that unlike other sheep breeds, Changthangi sheep produces double coat with marked difference in fibre diameter. The average fibre diameter of fine fibres was 14.35 0.50 μm which was significantly lower (*p* < 0.05) than that of coarse fibres (40.04 1.4 μm). The fibre diameter of fine fibres is comparable to that of pashmina growing from the Changthangi goats whose diameter range between 11–15 μm. The reason for presence of double coat and finer fibres may be attributed to the sub-zero temperature (even goes down up to <sup>40</sup><sup>o</sup> C) of the Changthang belt of Ladakh. Like Pashmina goats, Changthangi sheep might have adapted themselves to produce down


### **Table 4.**

*Livestock population as per livestock census/Departmental survey.*

*Status of World's Unique Animal Genetic Resource of Ladakh DOI: http://dx.doi.org/10.5772/intechopen.103767*

fibres which help to protect them against the extreme cold conditions [16]. The production scale of finer fibre in Changthangi sheep should be studied further so that it can be used for improving the income of the livestock rearer of Ladakh. Till date the Changthangi sheep has been under rated for its quality wool production. The Quality of Changthangi sheep wool is categorized as carpet wool but our study indicates that it is medium type wool and have scope of good market by developing a fine textured apparels. Further, the undercoat produced from secondary follicle can be utilized for the development of fine textured fabrics with smooth and warmth which in turn will fetch more prices only next to pashmina.

### **3.3 Important features of breed**


**Figure 7.** *Changthangi Sheep on winter pasture.*


### **3.4 Constraints and solutions**



### **3.5 Future strategies**


### **4. Yak**

The yak species (*Bos grunniens*) represents a unique bovine species adapted to the Tibetan plateau of China and India at an altitudes of 3000 m above sea level where oxygen content is only 33% of that at sea level and intensity of ultraviolet radiation is 3–4 times that in lowland areas [17]. Consequently, yak adapted to this environment likely have special physiological mechanisms to protect their central nervous systems against hypoxic and oxidative injury. Semi-domestic Yak is commonly known as "the Ships of the Plateau" has been domesticated under hostile climates of high altitude in the Ladakh plateau and adjoining regions of greater Himalayas also (**Figures 8** and **9**). Apart from being pack and draught animal it provides milk, meat, fibre, hide. It is best

**Figure 8.** *Male Yak at High Land Grazing.*

**Figure 9.** *Yaks at High Land Grazing.*

known for its hardiness and resistant to extreme cold climate and hypoxic conditions. Yaks of Ladakh are very hardy and they rarely need any health care and its very rare to find any health issues in Yaks.

In India, Union Territory of Ladakh has the highest population of Yaks and its hybrids distributed in both Kargil and Leh districts. But, the National Research Centre on Yak was established at Dirang Arunachal Pradesh and till date Ladakh is devoid of any kind of support from NRC yak and Govt. of India leaving this precious germplasm to perish in times to come. The other areas, where Yaks are found include Drass valley and Doda district of Jammu & Kashmir, North-Western Himalayan region mainly Spiti Valley, Pangi Valley in Chamba and Sangla Valley in tribal district of Kinnaur, Pithoragarh district of Garhwal hills, Sikkim and Arunachal Pradesh. The base line data on the Yak of Ladakh is not available, whatsoever meager information available is based on few Yaks; therefore, status of real production, reproduction and other potential of this animal are wanting. The animal besides having agricultural utility has religious utility for the Buddhist community of Ladakh. No scientific improvement programme is in force to improve this animal, and the biggest hurdle in it is the lack of systematic and sufficient information about the species.

Yak when hybridize with domestic cow exhibit great degree of heterosis. The popularity of these hybrids among the farmer can be gauzed from the specific name to each back cross and hybrid. The real heterosis exhibited is not documented because of lack of information on potential of Yak.

In the cold arid zone of Ladakh the precious species of livestock viz. Yak (Bos *grunniens*) needs to be documented and improved by adopting the technologies which are already in vogue for cattle and buffalo improvement. To exploit the benefits of species hybridization by crossing Yak with cattle, the performance of different levels of inheritance of Yak with cattle germ-plasm needs to be studied in depth to harvest maximum benefits.

### **4.1 Population status**

In India, the Yak population decreased drastically to about 30,000 in 1987 from 130,000 in the late seventies. The highest Yak population was about 21,400 in Arunachal Pradesh in 1972 and this population has shown sharp decline since & about 8921 Yaks had been estimated in 1997–98. These sharp declines in Yak population may be due to large scale cross breeding of Yak dams with local cattle to produce the hybrid Dzo and Dzomo, which is more useful and easily manageable than Yak due to its docile nature.

Likewise, in Ladakh also the same pattern of decline in Yak population has existed and at present it is very difficult to find elite Yaks in the population. The yak population has a sharp decline from 18,904 in 2007 to 13,420 in 2008 in Leh district similar pattern is also noticed in Kargil district [1, 18]. Presently the Yak population of Leh has slightly increased to 18,877 in 2019 [3]. However, the crosses like Dzo & Dzomo has increased abruptly from 9495 in 2008 to 34,174 in 2019 [3, 19]. This is mainly due to uncontrolled crossing with local cattle.


### **4.2 Constraints and solution**


### **4.3 Future strategies**


### **5. Zanskari horse**

Zanskari and Chumurti breeds are the two main horse breed of Ladakh area, the Zanskari horse are found mainly in the Zanskar region of Ladakh and Chumurti being

### *Status of World's Unique Animal Genetic Resource of Ladakh DOI: http://dx.doi.org/10.5772/intechopen.103767*

lesser and found mainly towards Chumur village of Changthang bordering China. The majority of the horses in Ladakh are Zanskari (**Figure 10**). These horses are very well adapted to run in hypoxic and freezing condition of Ladakh. The main utility of Zanskari horse is as a draught and sport animal. In some far flung village this horses are traditionally used for ploughing the agriculture field and for thrashing the crops (**Figure 11**). The famous traditional game of Ladakh 'Stapolok' (Polo) of Ladakh from ancient times is played using these horses. These horses are very hardy and was of great importance in earlier times for trades and transportation. In eighties owing to conserve this horse State Govt has opened a Zanskari horse breeding farm at Chuchot

**Figure 10.** *Zanskari Horse at Zanskar.*

**Figure 11.** *Zanskari Horse at field work.*

which is presently at critical stage due to lack of efficient breeding policy. Further, due to mechanization and development of road system, Zanskari horse, one of the precious germplasm adapted to the hypoxic conditions of high altitudes of Ladakh, is already endangered and needs immediate attention for its conservation. Though presently it has found its new way of income through tourism in trekking routes. Presently the population of Zanskari horse is 5534 which is almost equal to local donkey population of 5296 [3].

### **5.1 Constraints and solution**


### **5.2 Future strategies**


### **6. Bactrian (Double Humped) camel**

Another important livestock species of Ladakh region is Bactrian camel, which has played a great role in silk route trading transportation connecting China and Central Asia via Ladakh during 18th century. The present camel has been raised from a base population 18–22 camel since from 1937 when Ladakh was open for silk route trading,

**Figure 12.** *Double Humped Camel at Leh.*

**Figure 13.** *Double Humped Camel Safari at Hundar.*

since then no importation of Camel has been done due to border restriction. These camel had a critical population of hardly about 125 in 2008 [18] and presently increased to 189 [3]. In early 20th century these animals were abandoned by the local farmers due to lack of its use in day to day life. However, after opening of the Nubra village (Habitat) for tourism sector the business of Camel riding flourishes thereby increasing the economy of farmers. Presently, and Nubra valley becomes a centre of attraction for both national and international tourists (**Figures 12** and **13**). A total active business of camel riding for around 4 months from June to October was able to purchase feed and fodder for this camel for 12 months along with lots of extra savings to the Camel breeders. Though this Camel can be reared for milk, meat and wool, but the farmers rear it for tourism related business only, the reason being easy management and profitable income. It must be conserved on scientific lines with complete registration of all the available animals and maintenance of their breeding plan for extra income through its milk, meat and wool production.


### **6.1 Constraints and solution**

### **6.2 Future strategies**


### **7. Cattle**

The local cattle which is a non-descriptive breed was registered as a Ladakhi Cattle breed recently in 2019 by National Bureau of Animal Genetics Resource Karnal, Govt of India. The Ladakhi Cattle is very well adapted to the hypoxic condition of Ladakh, it can thrive very well on meagre feed and highly resistant to most of the contagious disease (**Figures 14** and **15**). Certain reports on the local cattle indicate it to the Bos *taurus* species. In Ladakh the performance of Jersey crossed with these local cattle is very much appreciated by the farmers and more than 80% of the Ladakhi cattle are cross between Jersey and Local with an overall average milk production of 5–6 litres per day. There is complete trend of increase in cattle population of Leh district since from the year 1992 (24,836 Nos) to 2008 (36,231 Nos) leading to a sharp increase in total milk production of the district. The cattle population of Leh district in 2014 was 12977 with a static milk production. Presently there are 47,151 of Ladakhi cattle [3, 8].

**Figure 14.** *A Ladakhi Cow.*

This data reveals that after breed registration its number has increased drastically. The Ladakhi Cattle produce around 1–2 litres of milk (7–8% fat) per day with no input expenditure on feed and medicines and under improved managemental system its production goes to 5–6 litres of milk per day. The milk and colostrum of these cattle are explored for biomolecules having high medicinal values in humans. Presently, these local cattle which are adapted to Ladakh condition are being replaced by Jersey cattle which have many managemental and health issues regarding their adaptation in Ladakh. If this trend continues then this local genetic resource in future will be lost forever.


### **7.1 Constraints and solution**


### **7.2 Future strategies**


### **8. Poultry**

Like other states of India with the pace of time there is great demand for poultry meat and eggs in Ladakh also, and all the demands are made by suppliers from Punjab and Kashmir. In the past there used to be a local poultry layer bird, very well adapted in every village house of farmers with broodiness. But due to lack of any policy the local birds of Ladakh has extinct and for the past 4–5 years it is very hard to find any local bird with broodiness. Though there is an increase in birds numbers mostly Vanraja Breed (dual purpose breed) from 6093 in 2007–08 and 20,829 in 2014 but the real poultry germplasm of the area is already lost. Normal Hatchery unit doesn't work well in Ladakh and hatching is a major problem in Ladakh condition due to cold, arid and high altitude of the region. Hence a hatchery suitable for Ladakh needs to be developed. Till date no research has been done to establish a broiler or layer line fit for cold arid zone of Ladakh, though DRDO claims to have done it but there is nothing to see at farmers/village level. Though a broiler business is not a profitable business in Ladakh condition but revival of age old backyard poultry has a great scope.


### **8.1 Constraints and solution**

### **8.2 Other non-descriptive native livestock**


**Figure 16.** *Purig Sheep at Turtuk.*

around 600–700 in numbers and declining every year due to crossing with Changthangi, Karakul and Marino Sheep. If proper action is not taken this germplasm may be lost in years to come.

3.*Malra goat*: The Malra name has been derived from local word meaning 'Local Goat', it is a medium size goat (**Figure 17**) commonly found in Khaltse

**Figure 17.** *Malra Goat at Lamayuru.*

Lamayuru, Lingshet, Photoksar, Skiu, Markha, villages of Leh District. The goat produces a small amount of Cashmere fibre (50–100 gm/animal) and mainly used for chevon production. Their number is also declining and presently estimated to be around 700–800, and the figure of Malra given under the Census includes all types of non-pashmina goat breeds found in Leh.


**Figure 18.** *Changthangi Dog.*

The above mentioned livestock needs to characterised and conserved on priority and the first step in this is the registration of all these non-descriptive animals as proper Breed. Krishi Vigyan Kendra -Leh SKUAST-K in collaboration with National Bureau of Animal Genetics Resource-Karnal Govt of India has started the process of Characterization and Registration of all this precious germplasm in the year 2021 and it will be completed by the end of the year 2024.

### **8.3 Conclusions and recommendations**


### **Acknowledgements**

The author is very thankful to Indian Council of Agriculture Research for funding various research projects run by SKUAST-K in Union Territory of Ladakh. The author also acknowledge the contribution of SERB-DST Govt of India for funding the project genetic improvement of Changthangi Sheep.

### **Author details**

Feroz Din Sheikh Krishi Vigyan Kendra-Leh I, Sher-e Kashmir University of Agricultural Sciences and Technology of Kashmir, Leh, India

\*Address all correspondence to: aizar22@gmail.com

© 2022 The Author(s). Licensee IntechOpen. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

*Status of World's Unique Animal Genetic Resource of Ladakh DOI: http://dx.doi.org/10.5772/intechopen.103767*

### **References**

[1] Sheikh FD, Azmat S, Ganai TAS, Misra SS, Azmat S. Socio-economic role of Pashmina goat on Changthang people. Indian Journal of Animal Science. 2008; **78**(11):1298-1301

[2] Ganai T.A.S., Kirmani M.A., Ganai N. A. and Tundup T. 2004; Pashmina production in Changthangi goats beyond the period of longest and shortest day. Proceedings of conference of Indian Society of Animal Genetics and Breeding-India

[3] Ladakh Autonomous Hill Development Council. 2019; District Census, Leh Ladakh.

[4] Von Bergen W. Wool Handbook. 3rd ed. Vol. Volume I. London, New York: John Wiley & Sons; 1963. pp. 343-365

[5] Sheikh FD, Bhattacharya TK, Misra SS, Kumar P, Sharma A. DRB3.2 gene polymorphism and its association with Pashmina production in Changthangi goat. International Journal of Immunogenetics. 2006;**33**:271-276

[6] Ladakh Autonomous Hill Development Council. 2005; District Census, Leh Ladakh

[7] Ladakh Autonomous Hill Development Council. 2009; District Census, Leh Ladakh

[8] Ladakh Autonomous Hill Development Council. 2014; District Census, Leh Ladakh

[9] Ladakh Autonomous Hill Development Council. 2006; District Census, Leh Ladakh

[10] Sheikh FD, Ganai TAS, Ganai AM, Alam S, Asmat S. Exploring genetic diversity in Cashmere goats of Ladakh

for enhancing production. Small Rumina nt Research. 2021;**201**:106409

[11] Ladakh Autonomous Hill Development Council. 2003; District Census, Leh Ladakh

[12] Ganai TAS, Misra SS, Sheikh FD. Description of Changthangi Sheep of Ladakh. Indian Journal of Small Ruminants. 2010;**17**(1):32-40

[13] F.D. Sheikh, T.A.S. Ganai, T. Tsewang, S.S. Misra and S. Azmat, 2010; Changthangi sheep: A Valuable Genetic Resource. Agro-Animal Resources of Higher Himalayas, 365

[14] Ladakh Autonomous Hill Development Council. 2000; District Census, Leh Ladakh

[15] Ladakh Autonomous Hill Development Council. 2004; District Census, Leh Ladakh

[16] Malik AA, Khan HM, Sofi AH, Mir MS, Farooq J, Sheikh FD, et al. Wool characteristics of Changthangi Sheep. Small Ruminant Research. 2021;**199**: 106364

[17] Sheikh FD. Indian Wild Life Year Book. Dong: The Wild Yak of Ladakh; 2009. pp. 15-23

[18] Ladakh Autonomous Hill Development Council. 2007; District Census, Leh Ladakh

[19] Ladakh Autonomous Hill Development Council. 2008; District Census, Leh Ladakh

## Genetic Diversity and Evolution of Yunnan Chicken Breeds of China

*Mohammed Alsoufi and Ge Changrong*

### **Abstract**

Chickens are the first type of bird that was domesticated and spread widely in the world to cover the growing demand for animal protein from meat and eggs, and it was cultivated from a wild ancestor known Red junglefowl (Gallus gallus). Yunnan Province is considered the most diverse in culture and biology among all the provinces of China. There are a total of more than 24 chicken breeds in Yunnan Province. These chickens are characterized by good quality of their meat and eggs, a good immune system against diseases, and the ability to adapt to various environmental and administrative conditions. Yunnan Province is one of the centers of domestication and evolutionary of chickens in the world. There are many studies that have been conducted to evaluate and study the genetic diversity and evolutionary relationship within and among chicken breeds in Yunnan Province and their relationship with wild chicken species and other chicken breeds using phenotypic markers, protein polymorphisms, SNPs marker, microsatellite marker, and mitochondrial DNA marker. However, there is no review that summarizes these studies, and most of these studies were authored in the Chinese language. Therefore, we have reviewed all studies that have been conducted on Yunnan chicken breeds diversity in Yunnan Province.

**Keywords:** genetic diversity, Yunnan chicken breeds, molecular studies, phenotypic studies

### **1. Introduction**

Poultry at the present time is called the domesticated birds and is used in the production of meat and eggs, and includes the following—chicken, ostrich, duck, turkey, goose, quail, pheasant, peacocks, and guinea fowl [1, 2]. Chickens are the first type of bird that was domesticated and spread widely in the world to cover the growing demand for animal protein from meat and eggs and it was cultivated from a wild ancestor known Red junglefowl (Gallus gallus) regarding since more than eight thousand years [3, 4]. Currently, the scientific and technological advancement across the globe was reflected in the production and domestication of poultry, which led to the existence of many breeds resulting from breeding, genetic improvement programs, and natural selection. Moreover, the production system, modern chicken, and the focus of countries on obtaining the largest possible amount of animal protein with the lowest possible loss led to loss of genetic diversity, a decrease of genetic variation, and disappearance of many local breeds, so that many research centers have sounded the alarm about the necessity of preserving local chicken breeds as an indispensable genetic resource [5].

During the last decades, commercial chicken breeds were imported in into China, and then a crossbreeding process was carried out with local breeds to cover the growing demand for chicken products. The total number of chickens in China about 10 billion birds in 2015 representing all types of chicken, of which 44%, 37%, 9.5% and 9.5% broilers, yellow chicken, layer and hybrid broiler [6]. Although approximately 107 local chicken breeds have been registered in China by the research centers, most of them are raised in small groups and the rural area, and some of them are at risk, as there are about six breeds at risk of extinction and due to the hybridization process with commercial strains, the number of local breeds adapted to hard environmental conditions in Yunnan, like to the rest of China, is constantly declining, in addition to the decrease in genetic diversity, which will negatively affect the ability of local chickens to withstand harsh environments, resist diseases, and losing the characteristics of high-quality meat. From all the above, we note that it is needed to maintain the highest genetic variation of local breeds as a national genetic resource and globally, for the purpose of breeding and genetic improvement programs that we will need in the future [5, 7, 8]. In this article, we have reviewed all the studies that were conducted previously on the genetic variation of chicken breeds in Yunnan Province.

### **2. Yunnan Province as a center of animal domestication**

Yunnan Province is located in Southern China, sharing borders with Myanmar, Laos, and Vietnam at (21°8′32″–29°15′8"N, 97°31′39″–106°11′47″E). Most of the Yunnan landscape is classed as a mountainous region with the Tropic of Cancer, which runs across the southern region. The province of Yunnan is an incredibly different geographical location that comprises mountains, valleys, lakes, and rivers. The climate in Yunnan ranges from the tropical oceanic monsoon in summers and dry interior monsoon in winters, combined with adequate sunshine, long frost-free periods, and abundant rainfall. In combination with these highly diversified geographic conditions, Yunnan exemplifies a vital biological diversity center of worldwide importance. Yunnan is the center of about half of China's varieties of greater vertebrate and plant types and various species of rare, widespread, and wild animals. Yunnan is also the territory for feral descendants of many species of livestock and has been suggested to be a center domesticated of prevalent animals, such as the pig, chicken, and the dog [3, 9]. Yunnan Province is considered the most diverse in culture and biology among all the provinces of China. Its varied environment, from snow-covered mountains to tropical environments, enabled it to possess many species of plants and animals that have no equivalent in the whole world. The wide range of topographical along with a tropical humidity has made Yunnan Province extremely diverse biology and with a high degree of endemicity of species, as it has become one of the richest areas in the world in terms of plant and animal resources with 17 thousand species of plants and the equivalent of the northern hemisphere combined [10]. Although the area of Yunnan Province does not exceed 4% of the total area of China, it contains about 42.6% of plants species protected and 72.5% of wild animals protected that are found

### *Genetic Diversity and Evolution of Yunnan Chicken Breeds of China DOI: http://dx.doi.org/10.5772/intechopen.102915*

throughout the country [11], and is also considered as a home of many animals, the most important of which is the South Asian Gorge, Indochina tiger, Asian elephant [12], box turtle, the Yunnan monkey [13], and red forest chickens species, in addition to it contains 11 national and nature reserves [14], moreover, Yunnan province has about 650 species of freshwater fish with 580 species are natives, this equates to 40% of freshwater fish in China [15]. Yunnan Province possesses many local poultry breeds with a large variety of various traits [16].

### **3. Yunnan chicken breeds and their phenotypic characteristics and location of domestication**

According to the report of Yunnan provincial animal and poultry genetic resources committee [17], there are a total of more than 24 breeds, and these breeds are located and distributed across all regions of Yunnan Province (**Figure 1**), named Nixi chicken, Wuding chicken, Xishuangbanna game chicken, Chahua chicken, Dali chicken, Xichou black bone chicken, Yanjin black bone chicken, Daweishan mini chicken, Yunlong short led chicken, Yangbi Hang chicken, Dulong chicken, Lanping chicken, Taliu black bone chicken, Dehong chicken, Labai high leg chicken, Lanping silky chicken, Mengzi game chicken, Poya chicken, Tengchong white chicken, Wuliangshan black boned chicken (Puer feathered feet chicken, Nanjiang green and black boned chicken), Weixin chicken, Wenshan chicken, and Piao chicken. These chickens are characterized by the good quality of their meat, a good immune system against diseases, and the ability to adapt to various environmental and administrative conditions. Because of the introduction of commercial strains, the number of these local breeds is decreasing, therefore, measures must be created to conserve these genetic supplies [19]. Furthermore, there are many breeds living in villages and mountains in Yunnan Province that have not been recorded or unknown until now, according to Kun et al. [20], in their study, that has reported three new breeds; Frizzle chicken, Naked-neck chicken, and YN chicken (YN) in Nujiang Prefecture in Yunnan Province (**Table 1**). Moreover, these domestic breeds when compared to broiler or layer chicken breeds mostly still not yet extensively bred and selected and possess a poorer performance, therefore some of them are not financially useful as broilers and layer breeds. However, it will continue to be a resource of genetic materials for the reason that they have been synthetically selected and bred throughout a lengthy history of reproduction and breeding using standards and methods that are completely different from those used with commercial chickens breeding [29].

There are many breeds of chickens that have been formed during thousands of years in Yunnan Province, and they can be divided according to their production purpose into the following: Entertainment type, meat type, dual type, and eggs type [17, 18].

Entertainment type: These chicken breeds are similar to wild chicken breeds (Red Junglefowl) that still live wild in the forests of Yunnan Province and are characterized by their low production of eggs and meat and their small size (**Figure 2**).

Xishuangbanna game chicken: Entertainment type, an ancient breed with history 2000 years. Large body size (2.5 kg male and 1.7 kg female), the annual production of eggs is 100–120 egg, white skin, variable plumage color (mostly grayish-green mixed with golden red) long neck, small walnut comb, and red earlobe [30]. This breed is distributed in Xishuangbanna prefecture (Southwest of Yunnan Province), (21°09'N–22°36'N and 90°56′E–101°50′E, ∼2429 m above sea

### **Figure 1.**

*Map of China and Yunnan Province indicating the location of domestication and distribution of chicken breed in Yunnan Province, [17, 18].*

level); yearly average temperature 18.6–21.9°C, rainfall of 1200 mm–1700 mm, and humidity of 81–85% [17, 31].


*Genetic Diversity and Evolution of Yunnan Chicken Breeds of China DOI: http://dx.doi.org/10.5772/intechopen.102915*

### **Table 1.**

*Haplotype diversity and nucleotide diversity in some Yunnan chicken breeds from previous studies.*

Chahua chicken: Primitive type, good for running and flying, small body size (1.27 kg male and 1.07 kg female), yielding 100–140 eggs per year, the color of plumage is mixed gray, green, black, and yellow, the wattle and comb are red, and the skin color is white with some chicken is yellow. This breed is domesticated and distributed in Xishuangbanna and Licang, Puer, Dehong prefecture (Southwestern and Western Yunnan), (21°09'N–22°36'N and 90°56′E–101°50′E, ∼2429 m above sea level); yearly average temperature 18.6–21.9°C ¬, rainfall of 1200 mm–1700 mm, and humidity of 81–85% [17, 23].

Dehong chicken: wild breed, small size (0.93 kg male and 0.67 kg female), the yielding eggs production is 8–12 eggs under natural conditions and 80 eggs per year in the farm. Single red comb, the skin color is white, the color of plumages is mainly mixed red with white, yellow with black, and black with white. This breed is mainly located and distributed in Mangshi, Longchun, and another county in Dehong prefecture (west of Yunnan Province), (23°50'N–25°20'N and 97°31′E–98°43′E, ∼893 m–1200 m above sea level); rainfall of 1400 mm–1700 mm [17].

Mengzi game chicken: Entertainment type, large body size, tall, thick bones and strong (3 kg male and 2 kg female), the annual production of eggs is 50–80 egg, hard feeding, and strong resistance to diseases. White yellow skin color, red meat color, variable plumage color (mainly dark green, red with black, yellow with black) long neck, small walnut comb, and red earlobe. This breed is located and lived in Mengzi

#### **Figure 2.**

*The morphology of entertainment type native breeds in Yunnan Province in China, [17, 18].*

County, Honghe prefecture (Southeast of Yunnan Province), (23°01'N–23°34'N and 103°13′E–103°49′E, ∼200 m–2567 m above sea level); yearly average temperature 18.6°C, rainfall of 1200 mm–1700 mm, and humidity of 72% [17].

Dulong chicken: Dual type with minimal production costs, hard feeding, and strong resistance to diseases. Small body size (0.97 kg male and 1.15 kg female), the yielding eggs production is 55–75 eggs. The skin color is white, the color of plumages is mainly mixed red with white, yellow with black, and black with white. This breed is distributed in Gongshan County, Nujiang prefecture (Northwest Yunnan), (27°40'N–28°45'N and 98°45′E–98°30′E, ∼4964 m above sea level); yearly average temperature 16°C, rainfall of 2932 mm–4000 mm, and humidity of 90% [32].

Daweishan mini chicken: This breed is a slow growing, small size (0.85 kg male and 0.68 kg female), aggressive, pectoral muscles, and thighs are combined with strong, thin bones, yielding about 60 eggs per year, The color of plumages are mainly white, yellow, red flowers, the comb is red and multiple [27]. This breed is distributed in Pingbian County, Honghe prefecture (Southeastern of Yunnan Province), (22°49'N–23°23'N and 103°24′E–103°58′E, ∼154 m–2590 m above sea level): yearly average temperature 16°C, rainfall of 1450 mm–1700 mm, and humidity of 33.5– 80.9% [17, 22].

*Genetic Diversity and Evolution of Yunnan Chicken Breeds of China DOI: http://dx.doi.org/10.5772/intechopen.102915*

**Figure 3.**

*The morphology of eggs production type native breeds in Yunnan Province in China, [17, 18].*

Egg production type: These breeds are mostly characterized by their small size and producing many eggs in year (**Figure 3**), which are the following:

Nixi chicken: Egg production type, its egg production reaches 156–221 eggs annually, the body size is small (1.6 kg male and 1.2 kg female), single red comb, long tail, gray shank, most of them white skin and some are black, variable plumage (mixed red and yellow and black for male and most of the black color with some white color for female and mixed yellow with black color). The regions of domestication and distribution of this breed are lives and are Shangri La County, Diqing prefecture county (Northwestern Yunnan), (26°52'N–28°52'N and 99°23′E–100°19′E, ∼2800 m above sea level); yearly average temperature 7.4–13.5°C, rainfall of 270 mm–500 mm [16, 17].

Yunlong short-leg chicken: Yunlong chicken is a type of eggs production (160–190 eggs per year), small size (1.9 kg male and 1.6 kg female), good meat quality, unique flavor features, strong adaptability, the skin color is black or white and the color of plumages are mainly red and yellow. This breed is located and lives in Yunlong County, Dali prefecture (Central Yunnan plateau), (25°28'N–26°23'N and 99°52′E–99°46′E, ∼730 m–3663 m above sea level); yearly average temperature 15.9°C, rainfall of 730 mm [17, 27].

Poya chicken: This breed is a type of eggs production (150–210 eggs per year), small size (1.4 kg male and 1.3 kg female). This breed has a red and single type of comb, the plumage color is red, white, black, and yellow. The skin color is white. Funingxian County, Wenshan prefecture (Southeast of Yunnan province), is the location of domesticated of this breed, (23°41'N–23°52'N and 105°53′E–106°10′E, ∼823 m above sea level); yearly average temperature 19.3°C, rainfall of 1200 mm [17].

Dual type: These breeds are of medium size, and their production of eggs and meat is acceptable (**Figure 4**), and the most important of them are the following:

### **Figure 4.**

*The morphology of dual production types native breeds in Yunnan Province in China, [17, 18].*

Xichou black bone chicken: Dual-type, aggressive and vigilant, bodyweight is medium (2 kg and 1.7 kg for female), the number of eggs produced is about 100–130 annually, the shank, skin, and bone are black, a varied plumage color, comb, wattle, earlobe, and beak are red and black. This breed has domesticated and distributed in Xichou County, Wenshan prefecture (Southeastern of Yunnan Province), (23°05'N–23°37'N and 104°22′E–104°58′E, ∼667–1962.9 m above sea level); yearly average temperature 15.5°C, rainfall of 1100 mm–1600 mm, and humidity of 78% [16, 17].

Wuding chicken: Dual type (meat and eggs production). The body size of this chicken breed has small and large types (3 kg for male large type, 2.1 for male small type, and 1.7 kg for female), the number of eggs produced reaches 90–130 eggs per year. The color of plumages, skin, and bone is varied, the comb is red and single. Some of these breed chickens have feathered feet. This breed is located in Wuding

County, Chuxiong prefecture (Central Yunnan plateau), (25°19'N–26°11'N and 101°56′E–102°29′E, ∼862 m–2956 m above sea level); yearly average temperature 15.1°C, rainfall of 959 mm [16, 17].

Piao chicken: The common name is Piao chicken, this breed has no pygostyle, tail bones, tail fat gland, tail feathers, caudal vertebra, and uropygial gland. Medium size, the bodyweight is reached to 2 kg for male and 1.7 kg for female, the number of eggs produced reaches 100–130 eggs per year, the skin, meat, and shank color mostly black and some skin is white, a varied plumage color (reddish-brown, black, white, yellow with flower color, single red comb. The location and distributions of this breed are Zhenyuan County, Puer prefecture (Southwestern of Yunnan), (23°24'N–24°22'N and 100°21′E–101°31′E, ∼774 m–3137 m above sea level); yearly average temperature 18.5°C, rainfall of 1284 mm, and humidity of 78% [17, 33].

Taliu black bone chicken: Dual type (meat and eggs production). Large size (2.4 kg male and 2 kg female), the yielding eggs production is 90–120 eggs, with strong black skin, black bones, black meat, good meat quality, plumages colors are two types, red mixed with yellow, black color and white color. The location of this breed is Yongsheng County, Lijiang prefecture (Northwestern Yunnan), (25°59'N–27°04'N and 100°22′E–101°11′E, ∼2890 m above sea level); yearly average temperature 13.5°C, rainfall of 936 mm [17, 24].

Lanping silky chicken: Dual type (meat and eggs production), medium size (1.9 kg male and 1.6 kg female), the production of eggs is about 110–120 eggs annually, the meat flavor is superior and unique, the tail is very short, the colors are mainly red meat, white skin, black shank, the plumage color is yellow with black tail and wings. This breed is located and lives in Lanping County, Nujiang prefecture (Northwestern Yunnan), (26°06'N–27°04'N and 98°58′E–99°38′E, ∼1350 m–4435 m above sea level); yearly average temperature 13.7°C, rainfall of 1002 mm [17, 24].

Tengchong white chicken: Dual type (meat and eggs production), the body size is a medium (2.1 kg male and 1.7 kg female). The production of eggs reaches 100–150 eggs per year. This breed has a red and single type of comb, the plumage color is white. The color of shanks, skin, bone is black. This breed is distributed in Tenchong County, Baoshan prefecture (western Yunnan), (24°38'N–25°52'N and 98°05′E–98°46′E, ∼930 m–3780 m above sea level); yearly average temperature 14.8°C, rainfall of 1469 mm, and humidity of 81.7% [16, 17].

Nanjiang black-boned chicken: Dual type (meat and eggs production), the body size is a medium (2.9 kg male and 2.2 kg female). Small head, green ear, the color of skin, meat, and bone is black. This breed has a red and single type of comb, the plumage male color is red, in addition to whit color, the female color manly is yellow and some chicken color is white. This breed is located and lives in Wuliangshan County, Dali prefecture (Western Yunnan province), (24°32'N–25°10'N and 100°06′E–100°41′E, ∼994 m–3061 m above sea level); yearly average temperature 19.2°C, rainfall of 770 mm, and humidity of 68% [17].

Meat production type: These breeds are mostly characterized by their large size and high efficiency in the production of meat (**Figure 5**), which are the following:

Yanjin black bone chicken: Meat production type, large body size (3.1 kg male and 2.4 kg female), yielding 120–160 eggs per year. The skin, eyes wattle, face, ear, and comb are black, also the beak, toes, and shanks are black, a variable plumage color (mostly white or black), the location and distribution of this breed are Yanjin County, Zhaotong prefecture county (Northeast of Yunnan Province), (26°34'N–28°40'N and

### **Figure 5.**

*The morphology of meat production types native breeds in Yunnan Province in China, [17, 18].*

102°52′E–105°19′E, ∼267 m–4040 m above sea level); yearly average temperature 6.2–21°C, rainfall of 1100 mm [16, 30].

Labai high leg chicken: Meat production type, the meat is tender and unique, tall body, long greenshank, large size (2.7 kg male and 2.3 kg female), the yielding eggs production is 90–120 eggs, the skin color is white, and the color of male plumages are mainly yellow, with black wings and tail and yellow and black for female. Ninglang County, Lijiang prefecture (Northwestern Yunnan), is the region of domestication and distribution of this breed, (26°36'N–27°56'N and 100°22′E–101°15′E, ∼1350 m–4510 m above sea level); yearly average temperature 12.7°C, rainfall of 918 mm, and humidity of 69% [17, 27].

Puer feathered feet chicken: Meat production type, this breed has a feather on feet, large size (3 kg male and 2.4 kg female), the production of eggs reaches 90–130 eggs per year. The skin color is mostly black and some of them are white, the plumage *Genetic Diversity and Evolution of Yunnan Chicken Breeds of China DOI: http://dx.doi.org/10.5772/intechopen.102915*

color is reddish-brown or yellowish-brown, and the color of the tail is black, in addition to some females is white or black. This breed is located and distributed in Puer County, Puer prefecture (Southwestern of Yunnan), (23°56'N–24°29'N and 100°22′E–101°15′E, ∼795 m–3371 m above sea level); yearly average temperature 18.3°C, rainfall of 1086 mm, and humidity of 77% [17].

Weixin chicken: Meat production type, the bodyweight is large (4.3 kg for male and 3.5 kg for female), The production of eggs reaches 128 eggs per year. The legs are tall and thick, this breed has a red and single type of comb, white skin, the plumage color mostly is a black female and red or red with black for male. Weixin County, Zhaotong prefecture (Northeast of Yunnan Province), is the location and distributions of this breed, (27°42′30"N–28°07′30"N and 104°41′15″E–105°18′45″E, ∼480 m–1902 m above sea level); yearly average temperature 13.3°C, rainfall of 1060 mm, and humidity of 84–89% [17].

Wenshan chicken: Meat production type, large size (2.6 kg male and 2 kg female). The production of eggs reaches 90–120 eggs per year. This breed has a red and single type of comb, the plumage color is brown for female and reddish-brown for male. This breed is located and has domesticated in Wenshan city and Maguan County, Wenshan prefecture (Southeastern of Yunnan Province), (22°34'N–24°28'N and 103°30′E–106°11′E, ∼123 m–2991 m above sea level); yearly average temperature 15.8–19.3°C, rainfall of 1224 mm, and humidity of 76.7-86% [17, 18].

### **4. Genetic diversity molecular studies of Yunnan chicken breeds**

Yunnan Chicken breeds are mainly reared in remote mountainous areas. But what is disturbing is that these breeds are less affected by the outside world, but it is being bred in a traditional selection by farmers, nevertheless, in recent periods, the genetic resources of poultry have received strong support from the Ministry of Agriculture and the provincial government to preserve these genetic resources and expand production for many breeds [34].

During the past 30 years and assuming that Yunnan Province is one of the centers of domestication and evolutionary of chickens in the world, there are many studies that have been conducted to evaluate and study the genetic diversity and evolutionary relationship within and among chicken breeds in Yunnan province and their relationship with wild chicken species and other chicken breeds using phenotypic markers [35], protein polymorphisms [36], and mitochondrial DNA marker [20, 22–24, 27, 31, 37].

### **4.1 Mitochondrial DNA marker studies**

Jia et al. [22] studied the origin and genetic variation of 30 Daweishan Mini chickens breed and compared them with five species of red jungle fowl (G.g. bankiva, G.g. gallus, G.g. murghi, G.g. jabouill, and G.g. spadiceus) sequence that downloads from previously published data (GenBank) using mtDNA. They identified 18 variable sites and observed six haplotypes. Their conclusion has indicated multiple origins for the Daweishan breed and the subspecies G.g. spadiceus is more contributed of Daweishan Mini chickens breed evolution. Similarly, the conclusion has obtained by LU et al. [23] revealed that multiple origins for Chahua chicken and Daweishan breed, and the subspecies G.g. spadiceus is more contributed of Daweishan Mini chicken breed and Chahua chicken breed evolution. This study has conducted on 30 Daweishan Mini

and 30 Chahua chicken breeds to assess the origin and genetic variety of these breeds using mtDNA marker.

Furthermore, Gongpan et al. [25] in their study that conducted on 50 chickens of Piao chicken breed to evaluate the genetic diversity. The results revealed that the genetic variation of this breed is high and has multiple origins for the Piao chicken breed. However, a study has been conducted to investigate the relationship of Dulong chicken breed with Chinese chicken breeds (Pengxian chickens, Jinyang chickens, Emei chickens, Jiuyuan chickens, Muchuan chickens, Miyi chickens, Shimian chickens, and Tianfu chickens) by using mtDNA analysis. The results have revealed the close relationship between Dulong chickens and studied chicken breeds and have suggested that Dulong chickens have a single matrilineal lineage [28].

Ouyang et al. [27] studied the genetic variation of 257 individuals from three chicken breeds (Labai high-leg chicken breed, Daweishan mini chicken breed, and Yunlong short-leg chicken breed) and using mtDNA) D-loop sequences. Based on genetic diversity results, they have suggested that there is a rich genetic diversity in these studied breeds and all of these breeds have a multiple maternal lineage, which supports the concept of various maternal ancestry of chicken. Wang et al. [38] used the mtDNA D-loop sequence to explore the origin and genetic variation of 30 individuals from the Labai high-leg chicken breed. Haplotype diversity and nucleotide diversity were 0.763 and 0.031, respectively. The findings showed that this breed kept a wealthy genetic variety and multiple origins for the Labai high-leg chicken breed.

### **4.2 Microsatellite's markers studies**

There are many of studies have been done by using microsatellites markers and most of these studies indicated to increase of genetic diversity within population of Yunnan chicken breed. Huo et al. [16] examined the genetic diversity and association between seven native breeds in Yunnan Province (Tengchong chicken, Banna chicken, Nixi chicken, Chahua chicken, Wuding chicken, Yanjin chicken, and Xichou chicken,) and Red Junglefowl chicken by utilizing 28 microsatellite markers. The numbers of alleles that were identified 342, 121 of them were specific, the heterozygosity among the population was high (0.663) and the FIS was low (−0.098–0.005) indicating the weakness of inbreeding between population, the FST, and the distance of genetic were high (0.1757–0.3015) and (0.4232–0.6950) respectively, indicating the high diversity among populations. Li et al. [39] also have used 30 microsatellite markers to study the genetic diversity of six Yunnan chicken breeds (Chahua, Xishuangbanna game, Wuding, Yunlong short-legged, Yanjin silky, and Tengchong chicken). The results have demonstrated the lowest value of heterozygosity was in Wuding chicken, and the highest value was in the Tengchong breed. In addition to the Yunlong chicken, Yanjin and Wuding chicken were grouped together, while Tengchong chicken and Xishuangbanna chicken were grouped together, however, Chahua chicken had grouped alone.

Ye et al. [40] used 33 microsatellites to evaluate the population structure and genetic diversity of 30 individuals from the Chahua chicken breed. The results showed an increased average value of heterozygosity (0.6129) and the polymorphism information content (0.5276) for all experimented microsatellites. LangThui et al. [41] used 33 microsatellites to assess the level of genetic diversity of 50 individuals from the Nixi chicken breed. The results have indicated to increase in the genetic diversity of this breed with average heterozygosity of 0.63 and 0.551 for polymorphic information content. Jia et al. [42] used 33 microsatellites to evaluate the population

### *Genetic Diversity and Evolution of Yunnan Chicken Breeds of China DOI: http://dx.doi.org/10.5772/intechopen.102915*

structure and genetic variability of 30 individuals from the Daweishan Mini chicken breed. The results have indicated to decrease in the heterozygosity (0.1737) and the polymorphism information content (0.3279) with increased homozygosity. Qian et al. [43] investigated the genetic diversity and genetic structure of 53 unrelated individuals from the Wuding chicken breed by using 25 microsatellite markers. The results indicated that the genetic diversity of this breed is high with average heterozygosity of 0.6957 and 0.6382 for the polymorphism information content of 25 microsatellites that have been studied. Chen et al. [44] examined the genetic diversity of 53 individuals from the Yanjin black-bone chicken breed, the findings revealed that the Yanjin black-bone chicken breed was rich in genetic variation with average heterozygosity of 0.6232 and 0.5712 for polymorphism information content.

### **4.3 Microsatellite's markers studies**

Wang et al. [45] have done an experiment on 10 chickens of Dulong Chicken breed to study the population structure and genes selection in the period of chicken domestication based on whole-genome resequencing using single nucleotide polymorphisms marker and the approach of fixation index. The results have identified 18,262,807 SNPs from the 10 genomes of Dulong Chickens and five genomes of Red Jungle Fowls that have been downloaded from the NCBI. The findings also have obtained 469 candidate genes, these genes may be related to small size, aggressiveness, and disease resistance in Dulong Chickens. Moreover, Guo et al. [46] used two methods (heterozygosity and fixation index) based on whole-genome resequencing to investigate selection signatures between eight individuals of Xishuangbanna chicken breed genome and six of Red Jungle Fowl genome that have been downloaded from the EMBL-EBI database. The results have identified more than 16 million SNPs from all individual's genomes and identified 413 candidate genes that are related to energy metabolism, disease resistance, aggressive behavior, immunity, and growth.

In addition, many studies have included some of Yunnan chicken breeds as a reference breed or experimented breed, particularly, chicken breeds that still preserve their morphological characteristics (Chahua chicken breed, Xishuangbanna game chicken breed, Dehong chicken breed, Mengzi chicken breed, Daweishan mini chicken breed, and Dulong chicken breed) which are similar to chicken species that wildly living in south Asia, including Yunnan Province to understand evolutionary of chicken, genetic variation and genetic relationship between them and other Chinese domesticated breeds, global domesticated chicken breeds, wild species chicken, commercial chicken breeds using SNPs marker [47–51], copy number variants [52], microsatellites marker [53], and mtDNA marker [54, 55].

### **5. Conclusions**

The ecological and topographical diversity of Yunnan Province in China has been reflected in the biological diversity, as this region is considered one of the centers of genetic resources for living organisms. Including chicken, as it is one of the centers of domestication of chickens in the world where it contains all types of chicken breeds fancy breeds, meat breeds, and eggs breeds. Research centers have begun to conduct many studies on the genetic variation and evolution of chickens using molecular methods. As many breeds are still discovered in succession to this day, it is necessary

to make more efforts to enumerate and describe all the chicken breeds that exist in Yunnan Province.

### **Conflict of interest**

The authors declare no conflict of interest.

### **Author details**

Mohammed Alsoufi1,2\* and Ge Changrong1

1 College of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan Province, People's Republic of China

2 Faculty of Agriculture, Department of Animal Production, Sana'a University, Sana'a, Yemen

\*Address all correspondence to: m-alsofy@hotmail.com

© 2022 The Author(s). Licensee IntechOpen. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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### Section 4
