**6.2 Arguments for preservation**

The experts collect the following economic, scientific, human cultural, socioeconomic, and environmental rationales for preservation beside the needs for development and sustainability mentioned formerly.

Genetic variation is the raw material for animal improvement. Prudent economy demands conservation. Lost flexibility will limit the ability of future generations to respond to changed markets and opportunities. Old breeds are of unique physiological or other traits. They can show specific adaptation ability, resistance to diseases. Biotechnology will need to reveal unique sequences of DNA. Based on microsatellites, Agaviezor et al. [97] concluded that these associated with unique ancestral alleles of certain functional genes may reflect a better adaptability in more agro-ecological zones. Firestone et al. [98] shown through simulations that with samples of at least 30–40 individuals found the correct ratio of private alleles in most cases can be. Due to the low frequencies of the private alleles in a study, the results should be interpreted cautiously and viewed more as a trend.

Animal husbandry is a special characteristic of human culture. It is comparable to other great reminders of man's past. Rare breeds are results of human creation (worth preserving and conserving as any other work of art, like monuments or buildings). They are kept for demonstration and showing of historical development of animal husbandry, and are of great advantage and value for physiological and genetic comparative studies. Some domestic animal breeds are historically closely linked to different farming cultures, environment and regions, traditional and regional. Livestock are part of life style in all the countries.

Impact of changed animal genetic diversity affects their whole life style. In integrated crossing programs with high yielding breeds it may be economical (crossed progenies for market and pure bred progenies for herd replacement!). Under unfavorable (harsh) conditions it can be bred with minimum input.

Our old, native breeds are multipurpose animals. However, we have become accustomed to using several benefits. Therefore, in addition to primary production (which is already known to be low), it is necessary to emphasize the use of animals in several ways during their lives (e.g. grazing/landscape care, traction, tourist attraction) and efficient processing of slaughtered animal parts through traditional handicrafts (e.g. fur and horned skull/trophy). What is very important, and what is realized exclusively in *in situ* gene conservation, is the regular use of animals. In the original, traditional environment, the genetic ability of the breed can be manifested. Raw materials of animal origin obtained directly or indirectly must be processed regularly and the product sold (although this is often seasonal).

Animal, plant, forest, fish, wildlife genetic resources are equal major components of global biological diversity and must be viewed together. The environmental implications of livestock are huge. Billions of livestock in human care moving over large areas of land where they affect the soil, water and vegetation, and interacting with other life. Therefore, the environment must be considered as a whole.

#### **6.3 Breed history for preservation**

In my opinion, maintaining a variety is more than finding and currently using a beneficial gene. The rationale for the preservation of old breeds is given by the history and former significance of the breed. Regarding the breed history, I would like to call the attention to the *in libro* concept of conservation worded by us formerly [99]. A longer version of the technical term is *in libro conservation in causa emoriendi*, namely the conscious preservation of an already extinct domestic animal breed or a lost characteristic entered. The meaning of the entered (in a book; booked) conservation in broader sense is the preservation of all the remaining knowledge, keepsake, documents and material heritage of a still living rare breed. As a reason for the *in libro* conservation the same arguments can be presented as for the *in vivo* and *in vitr*o approaches of conservation. The keeping in life of an extinct breed does not crop up but the "keeping alive" its one-time presence in the common knowledge is an important role. The cradle of the breed should not be forgotten.

In contrast to mtDNA, Peter et al. [100] among others, reports the disadvantage of microsatellites in search for breed history, especially in open flocks. Although microsatellites on nuclear chromosomes describe the current genetic nature and genetic relatedness of the herds, the genetic character depends heavily on the genetic makeup of the rams being actually used. The breeds can no longer be clearly assigned to one of the breed groups, but can be found in the mixed populations.

#### **6.4 Herd booking and pedigree analysis**

The official, mandatory individual animal numbering is essential for everyday breeding work. The parentage control is also essential for reliable pedigree registration. Of course, among the pedigree data we also store the regularly recorded (in many cases seemingly redundant) production data. Most multi-purpose indigenous breeds are utilized solely through their meat production today, however, in order to preserve the valuable traits, not only the fattening and slaughter values, but also, for example, the wool production traits must be recorded and selected for.

Pedigree data are fundamental to the assessment of the demographic structure and risk status of livestock breeds. Careful investigation of herd book data will

**193**

*Reality of Mitogenome Investigation in Preservation of Native Domestic Sheep Breeds*

preserving section that may not be perfectly implemented.

remount rate proportional to the Gaussian curve.

serve knowledge on pedigree completeness [101], effective population size [102], factual number and effective number of founders and ancestors, respectively (these two later explain the complete genetic diversity of a population [103]), and founder

The length of the generation interval (defined as the average age of parents at the birth of their progeny kept for reproduction) is one of the keys to demanding breed maintenance. The four pathways (sire-son, sire-daughter, dam-daughter, and dam-son) of generation interval should be as long and similar as possible. The higher this is, the lower the possibility of an annual gain even in the case of a

Based on pedigree data the average relatedness coefficient of each individual is evaluated together with the inbreeding coefficient. Inbreeding coefficient (autozygosity) is influenced by the length and completeness of pedigree, the longer and more complete the available pedigree is the more reliable the estimated inbreeding

When maintaining endangered animal breeds, care must be taken not to preserve the name of the breed in the new, upgraded population, or to ensure that the critical herd size is maintained for generations. The purpose of breed maintenance is to preserve the original level of phenotypic (and underlying genetic) characters of the breed. The constancy and possible, unexpected change of the production level can be verified in historical comparative study (e.g. [105–107]. That is, in order to maintain within-breed diversity, it is necessary to leave individuals from all phenotype groups (production levels, ideally based on their breeding value) for further breeding. This is the aim of preserving selection. The principle of diversitypreserving selection is very far from conventional truncation selection. The selection limit is not determined by the performing-ability, but by the measure of the

The genetic composition of a given sheep breed is also likely to be mixed in terms

From the current point of view, the essence of the pedigree study is the identification of female founder individuals and the families derived from them. In order to capture full diversity the DNA samples should be taken from the living descendants of the eldest families based on herd booking. In the study of mtDNA of two Hungarian native sheep breeds (Tsigai and Cikta), sample collection and analysis [55, 87] was preceded by the processing of pedigree data and the identification of

As previously described, reliable characterization of the breed for mtDNA should be performed on samples taken from representatives of maternal lineages. The genetic background and the current diversity thereby reliably discovering in

of mtDNA haplotypes. As a breed has a remarkable higher number of different mutant sites overall it can be assumed that more founder animals were present in this population have to. The long-known history of this breed (sheep herd of the area) and the current genetic mapping can provide certainty, confirming the colorful background, possibly the contribution of several breeds or sheep subspecies to

*DOI: http://dx.doi.org/10.5772/intechopen.95768*

genome equivalents [104].

**6.5 Preserving selection**

**6.6 Founder sampling**

ancient families [108, 109].

**6.7 Maternal lineages**

the gene pool.

coefficient.

*Reality of Mitogenome Investigation in Preservation of Native Domestic Sheep Breeds DOI: http://dx.doi.org/10.5772/intechopen.95768*

serve knowledge on pedigree completeness [101], effective population size [102], factual number and effective number of founders and ancestors, respectively (these two later explain the complete genetic diversity of a population [103]), and founder genome equivalents [104].

The length of the generation interval (defined as the average age of parents at the birth of their progeny kept for reproduction) is one of the keys to demanding breed maintenance. The four pathways (sire-son, sire-daughter, dam-daughter, and dam-son) of generation interval should be as long and similar as possible. The higher this is, the lower the possibility of an annual gain even in the case of a preserving section that may not be perfectly implemented.

Based on pedigree data the average relatedness coefficient of each individual is evaluated together with the inbreeding coefficient. Inbreeding coefficient (autozygosity) is influenced by the length and completeness of pedigree, the longer and more complete the available pedigree is the more reliable the estimated inbreeding coefficient.

#### **6.5 Preserving selection**

*Landraces - Traditional Variety and Natural Breed*

**6.3 Breed history for preservation**

**6.4 Herd booking and pedigree analysis**

Impact of changed animal genetic diversity affects their whole life style. In integrated crossing programs with high yielding breeds it may be economical (crossed progenies for market and pure bred progenies for herd replacement!). Under

Our old, native breeds are multipurpose animals. However, we have become accustomed to using several benefits. Therefore, in addition to primary production (which is already known to be low), it is necessary to emphasize the use of animals in several ways during their lives (e.g. grazing/landscape care, traction, tourist attraction) and efficient processing of slaughtered animal parts through traditional handicrafts (e.g. fur and horned skull/trophy). What is very important, and what is realized exclusively in *in situ* gene conservation, is the regular use of animals. In the original, traditional environment, the genetic ability of the breed can be manifested. Raw materials of animal origin obtained directly or indirectly must be

unfavorable (harsh) conditions it can be bred with minimum input.

processed regularly and the product sold (although this is often seasonal).

with other life. Therefore, the environment must be considered as a whole.

Animal, plant, forest, fish, wildlife genetic resources are equal major components of global biological diversity and must be viewed together. The environmental implications of livestock are huge. Billions of livestock in human care moving over large areas of land where they affect the soil, water and vegetation, and interacting

In my opinion, maintaining a variety is more than finding and currently using a beneficial gene. The rationale for the preservation of old breeds is given by the history and former significance of the breed. Regarding the breed history, I would like to call the attention to the *in libro* concept of conservation worded by us formerly [99]. A longer version of the technical term is *in libro conservation in causa emoriendi*, namely the conscious preservation of an already extinct domestic animal breed or a lost characteristic entered. The meaning of the entered (in a book; booked) conservation in broader sense is the preservation of all the remaining knowledge, keepsake, documents and material heritage of a still living rare breed. As a reason for the *in libro* conservation the same arguments can be presented as for the *in vivo* and *in vitr*o approaches of conservation. The keeping in life of an extinct breed does not crop up but the "keeping alive" its one-time presence in the common knowledge is an important role. The cradle of the breed should not be forgotten. In contrast to mtDNA, Peter et al. [100] among others, reports the disadvantage of microsatellites in search for breed history, especially in open flocks. Although microsatellites on nuclear chromosomes describe the current genetic nature and genetic relatedness of the herds, the genetic character depends heavily on the genetic makeup of the rams being actually used. The breeds can no longer be clearly assigned to one of the breed groups, but can be found in the mixed populations.

The official, mandatory individual animal numbering is essential for everyday breeding work. The parentage control is also essential for reliable pedigree registration. Of course, among the pedigree data we also store the regularly recorded (in many cases seemingly redundant) production data. Most multi-purpose indigenous breeds are utilized solely through their meat production today, however, in order to preserve the valuable traits, not only the fattening and slaughter values, but also, for

Pedigree data are fundamental to the assessment of the demographic structure and risk status of livestock breeds. Careful investigation of herd book data will

example, the wool production traits must be recorded and selected for.

**192**

When maintaining endangered animal breeds, care must be taken not to preserve the name of the breed in the new, upgraded population, or to ensure that the critical herd size is maintained for generations. The purpose of breed maintenance is to preserve the original level of phenotypic (and underlying genetic) characters of the breed. The constancy and possible, unexpected change of the production level can be verified in historical comparative study (e.g. [105–107]. That is, in order to maintain within-breed diversity, it is necessary to leave individuals from all phenotype groups (production levels, ideally based on their breeding value) for further breeding. This is the aim of preserving selection. The principle of diversitypreserving selection is very far from conventional truncation selection. The selection limit is not determined by the performing-ability, but by the measure of the remount rate proportional to the Gaussian curve.

#### **6.6 Founder sampling**

The genetic composition of a given sheep breed is also likely to be mixed in terms of mtDNA haplotypes. As a breed has a remarkable higher number of different mutant sites overall it can be assumed that more founder animals were present in this population have to. The long-known history of this breed (sheep herd of the area) and the current genetic mapping can provide certainty, confirming the colorful background, possibly the contribution of several breeds or sheep subspecies to the gene pool.

From the current point of view, the essence of the pedigree study is the identification of female founder individuals and the families derived from them. In order to capture full diversity the DNA samples should be taken from the living descendants of the eldest families based on herd booking. In the study of mtDNA of two Hungarian native sheep breeds (Tsigai and Cikta), sample collection and analysis [55, 87] was preceded by the processing of pedigree data and the identification of ancient families [108, 109].

#### **6.7 Maternal lineages**

As previously described, reliable characterization of the breed for mtDNA should be performed on samples taken from representatives of maternal lineages. The genetic background and the current diversity thereby reliably discovering in

any breeds. The number of haplotypes representing individuals in the sampled families or providing the sample is likely to be less than the number of samples. Unfortunately, it can also be predicted that the number of surviving founder families will decrease from generation to generation. Thus, it is recommended to leave breeding offspring from all families, from all haplotypes, to replenish the female herd. Since the number of individuals is higher than the number of haplotypes a rigid selection focussing on haplotype maintenance can lead to loss of many other genetic information (like in selection against scrapy genotypes).

Of course, it is a big question whether, in the case of outlier haplotypes, we choose to save or discard it in the endangered population of small size. Each cell contains many copies of mtDNA which, except in very rare cases of heteroplasmy, are identical and shared by all members of the maternal lineage. Another problem may then be the treatment of the heteroplasmy.

To my mind, the searching for ancient families is very crucial aspect of breed conservation. I consider it important to inform farmers about the family and haplotype of their sheep. In this respect, close long-term cooperation is needed between breeders and breeders' associations, and even with the breeding authority in obtaining state subsidies. In other words, the individual sheep genetic knowledge gained from the researches should be communicated to the animal owners.

#### **6.8 Within-family selection**

If differentiated families with their specific haplotype are already available, it is reasonable to select offspring for further breeding within these. Using a withinfamily selection, potential offspring are identified by sophisticated breeding software, while the breeder remains free to choose which one to actually stay for breeding.

At this point, I would like to draw attention to the differences between the professional work of the association and the ideas of the private breeder, and the necessary cooperation, or the antagonism in many places that the breeder is the owner of the animal but the breed must be preserved by the state.

### **7. Conclusions**

During the phylogenetic investigation of sheep species, and characterization for improvement and conservation of sheep breeds, mtDNA diversity plays an important role. This is indeed noticeable as it is being applied more and more widely. However, opinions differ on the degree of success of the study in terms of its purpose. Here, too, it is true that any doubt encourages further appropriate work.

For comparison between domestic and wild sheep the less mutagen gene (Cyt b) sequences are advisable. But, for the exploration of haplogroup relationships among domestic sheep processing of a Cyt b gene dataset combined with CR is recommended. Then, for a precise differentiation of haplotypes a hypervariable sequence set of CR seems to be the most reliable. High levels of mutations observed in the control region (emphatically hypervariable sequence) may skew dating estimates for many mammalian species. Before drawing phylogenetic conclusions the removal or reduction of repetitive sequence elements located within the CR is to advice because of its known heteroplasmic behavior.

Coding regions are conservative, for function with sameness making them less useful for isolating species, breeds, and individuals. Investigation of these is important in screening for deleterious alleles.

**195**

**Author details**

**Acknowledgements**

**Conflict of interest**

VEKOP-2.3.2.-16-2016-00012).

András Gáspárdy

University of Veterinary Medicine, Budapest, Hungary

provided the original work is properly cited.

The Author declares no conflict of interest.

\*Address all correspondence to: gaspardy.andras@univet.hu

© 2021 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,

*Reality of Mitogenome Investigation in Preservation of Native Domestic Sheep Breeds*

furthermore transfer historical and cultural values continuously.

the depositaries of realization and maintenance of genetic diversity.

This project is supported by the European Union and co-financed by the European Regional Development Fund (ERDF) (Grant Contract No:

At the same time, there is a need to consider more segments of the mitogenome which are used to outline the phylogeography of the species (since a single segregating locus does not adequately represent the origin of the entire genome), and the more of these, the more reliable they are. However, consideration of one or a few sequences in the context of species domestication may be advantageous in itself. In addition to the number of sequences investigated, their length (number of mutant sites) and the number of individuals sampled should not be overlooked in terms of

The fluent determination genetic diversity and its maintenance at a high level is indispensable on the course of preservation of our old, rare landraces. Indigenous breeds are national treasures and an aim of the saving of such breeds is not only to be prepared to compensate for the genetic erosion of another breed, but manufacture local products, preserve ancient knowledge and conserve natural landscape,

In order to map the broad genetic background biological samples should be taken from the descendants of the founders. During the future preservation work special attention should be paid to maternal families and representatives of ancient families should be preserved. A more intense focusing on the maternal side is motivated also by the fact that the females exceed in number the males, respectively they remain in breeding for a longer period of time, so they can at larger extent be

*DOI: http://dx.doi.org/10.5772/intechopen.95768*

processing reliability and comparability.

#### *Reality of Mitogenome Investigation in Preservation of Native Domestic Sheep Breeds DOI: http://dx.doi.org/10.5772/intechopen.95768*

At the same time, there is a need to consider more segments of the mitogenome which are used to outline the phylogeography of the species (since a single segregating locus does not adequately represent the origin of the entire genome), and the more of these, the more reliable they are. However, consideration of one or a few sequences in the context of species domestication may be advantageous in itself. In addition to the number of sequences investigated, their length (number of mutant sites) and the number of individuals sampled should not be overlooked in terms of processing reliability and comparability.

The fluent determination genetic diversity and its maintenance at a high level is indispensable on the course of preservation of our old, rare landraces. Indigenous breeds are national treasures and an aim of the saving of such breeds is not only to be prepared to compensate for the genetic erosion of another breed, but manufacture local products, preserve ancient knowledge and conserve natural landscape, furthermore transfer historical and cultural values continuously.

In order to map the broad genetic background biological samples should be taken from the descendants of the founders. During the future preservation work special attention should be paid to maternal families and representatives of ancient families should be preserved. A more intense focusing on the maternal side is motivated also by the fact that the females exceed in number the males, respectively they remain in breeding for a longer period of time, so they can at larger extent be the depositaries of realization and maintenance of genetic diversity.
