**Abstract**

For centuries, crop improvement has served as the basis of food security of ever increasing human population. Though vast germplasm collections are available; their exploitation for crop improvement still depends upon efficient assessment of genetic diversity. Genetic variability is the key element in adaptation of plants to varying climates. While crops with narrow genetic diversity are vulnerable to stresses. The estimation of extent and pattern of genetic variability is a prerequisite for generating superior varieties. Genetic diversity analysis generates key information to dissect genetic variations in crop germplasm with the help of morphometrical, biochemical and molecular tools. Among these, DNA markers provide a reliable and detailed insight into the similarities and differences among crops. In this chapter, we discuss the applications of phenotypic and molecular markers to probe genetic divergence in crops and present case studies that describe the significance of these tools to characterize sorghum germplasm. Furthermore, we spotlight sorghum biodiversity exploration efforts worldwide and propose future directions.

**Keywords:** molecular markers, *Sorghum bicolor*, PCR, RAPDs, SSRs, SNPs, GWAS, association mapping, UPGMA, dendrogram

#### **1. Introduction**

The term "variability" refers to variation in one or more than one characters of living organisms. The cumulative influence of environment and the genetic factors brings about variations in a specific trait. Genetic variation refers to variation in sequences of genes between individuals in a population. Allelic variation is the building block of hereditary variation that is expressed in the form of different phenotypes. Processes like mutation, random mating and fertilization and gene duplication may introduce new genes and alleles thereby increasing genetic variation. Random mutations are the source of genetic variations. Mutations are either heritable or non-heritable; the beneficial heritable mutations exert a great influence on the genetic variations of living organisms. Likewise, gene flow is also a means of introducing new alleles to a population and thereby broadening the genetic diversity of living organisms. Genetic variability provides baseline for genetic diversity;

a broader term that reflects the degree/amount of variation existing within a population. Without genetic variability, populations fail to adapt to varying climatic conditions and are prone to extinction. Genetic variability is a source of natural selection, that is the key driver of evolution of living organisms.

species. Initially, morphometric, cytological and biochemical markers were frequently used to evaluate the extent of similarities and differences among crop germplasm. Genetic and molecular markers were developed in the genomics and post genomics era and now are the widely used method for crop genetic divergence

*Exploring Plant Genetic Variations with Morphometric and Molecular Markers*

Evaluation of phenotypic traits in glasshouse or field- grown plants has long been used for selection of diverse crop plants. Effective morphometric characterization involves field plantation of large number of plants following specific lay out design. The morphological traits are recorded at vegetative growth (germination percentage, number of leaves, nodes, leaf area index, leaf color, stem thickness etc.), reproductive growth (Days to flowering, days to maturity, flower color, morphology, brix value etc.) and maturity stage (Plant height, yield, dry biomass and grain weight etc.). Plants express physiological and morphological changes under biotic and a biotics stresses. Hence, phenotypic characterization is vital in the

This approach is easy, simple, inexpensive and directly measurable. However, experienced staff is required for effective selection of promising plants. Such fieldbased evaluation is directly influenced by environmental factors. Moreover, labor and field requirements pose extra work. Morphological evaluations must be detailed

morphological characterization provides a base line for breeders to develop diverse genotypes having stress tolerant attributes. Furthermore, good quality phenotypic data is the foundation of new genomics and molecular approaches to successfully dissect the molecular basis of complex quantitative traits such as yield, disease resistance etc. Morphological markers have limitation of delayed expression till the specific developmental stage of the plant. Moreover, genotype x environmental interactions render the morphological markers less reliable than other marker types.

These markers are related to morphological variations in chromosome size, shape, number, length, arm ratio, volume, behavior in cell divisions and DNA content etc. These chromosomal features can be identified through microscopy and expressed by chromosome karyotype and bands. The G, Q, R and C banding patterns of chromosomes indicate regions of chromatin that are stained with the help of different fluorescent dyes, viz.; Quinacrine hydrochloride (Q bands) and Giemsa stain (G bands) [1]. The presence or absence of a chromosome band is associated with the specific traits. A thinnest chromosome band hosts over hundreds of genes. These are used to detect cytological mutations and track evolutionary chromosomal rearrangements. The fusion of chromosomal and molecular biology protocols in 1990 introduced fluorescence *in situ* hybridization (FISH) method. It is capable of physical mapping of nuclear content directly on the chromosomes and identifying protein content of a cell. A more advanced variant of *in situ* hybridization, "genomic *in situ* hybridization (GISH)" technique utilizes total genomic DNA of plant as a probe. Both GISH and FISH are powerful tools to characterize alien introgressions in crop species and dissect genetic makeup of natural and artificial hybrids [2]. However, cytological markers have limited use in genetic diversity estimation due to their small number and discrete detection.

involving all growth stages of plants. Presently high throughput phenomics approaches have refined the morphological data recording of large number of entries in the field with precision. The growth-stage dependent physio-

estimation.

**2.1 Morphological markers**

*DOI: http://dx.doi.org/10.5772/intechopen.95026*

**2.2 Cytological markers**

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selection of tolerant plants under stress environment.

Agriculture is directly influenced by environmental degradation and biodiversity loss leading to compromised quantity and quality of diverse and nutritious foods. Globally, people are relying on three major cereal crops wheat, maize and rice to fulfill their dietary needs and in turn are adopting similar dietary plans. Due to selective exploitation of few crops and large scale cultivation of genetically homogeneous cultivars, other wild and more nutritious crops are wiped out of global atlas. Not only we have compromised our health due to poor nutrition, the resilience of our food system is also at stake due to loss of crop diversity. Such lack of biodiversity was the root cause of Irish potato famine in the nineteenth-century. Presence of genetic diversity is the vital element of all variety development programs. Existence of genetic diversity in crop germplasm aides in the efficient selection of high yielding, better adapted crop plants with possible uses of direct introduction as a variety or one of the parents in crossing scheme of breeders for variety development programs. Since genetically diverse germplasm offers wider tolerance to biotic and abiotic stresses; such programs extensively involve exploring and exploiting diverse crop germplasm.

There is a continuous shift in the focus of agriculture from time to time. Agriculture in ancient times was focused on meeting subsistence food requirement. While, present day agriculture is focused to maximize yields for growing populations. That's why breeders are utilizing crop genetic resources for targeted and sustainable development of new high yielding and nutritious crop varieties in order to address malnutrition and balanced diet of human population. Under prevailing conditions of scarce water resources and escalating temperatures, development of climate resilient crop varieties is gaining momentum. Climate smart agriculture relies on cultivars with novel biotic/abiotic stress tolerance traits. However, depletion of natural variability persists in existing crop germplasm. Targeted breeding to improve specific traits and repeated use of few breeding parents has narrowed the genetic base of existing major crop varieties, raising serious concerns about genetic vulnerability of modern crops and making breeder's task even harder. In this context, new sources of desirable alleles are exploited from wild as well as closely related crop species and mutants. Hence, for ever changing breeding goals, it is imperative to conserve genetic diversity as germplasm resource. Crop genetic diversity is the core element of climate smart agro ecosystem to promise sustainable food availability and thereby to alleviate hunger and poverty.

A dire need exists to brought back underutilized and forgotten crops of every region to the canvas of agriculture for enhancing sustainable food production under anticipated harsh climates of the planet. A huge resource of alternative crops like sorghum, can replace the monoculture of three dominating cereal crops. Sorghum is a grass of multiple uses including food, feed, fiber, sugar, ethanol etc. Exploiting this and other nutritious and hardy crops is the best way to diversify present cropping system and enhance its resilience towards climate change. We need concerted collective efforts to increase awareness of farmers, policy makers and consumers towards benefits of diversification in agricultural systems.

#### **2. Crop genetic diversity assessment methods**

The assessment, extent and distribution of genetic divergence is the base line of preservation and exploitation of genetic variability within and between crop

#### *Exploring Plant Genetic Variations with Morphometric and Molecular Markers DOI: http://dx.doi.org/10.5772/intechopen.95026*

species. Initially, morphometric, cytological and biochemical markers were frequently used to evaluate the extent of similarities and differences among crop germplasm. Genetic and molecular markers were developed in the genomics and post genomics era and now are the widely used method for crop genetic divergence estimation.
