**8. Conclusion**

Soybean oil is used in many foods, industrial and fuel products. Whereas soybean meal is incorporated into animal feed. The variation in the quality and quantity of these products is basically dependent on the genetic diversity of soybean germplasm. The genetic diversity in

mining would help to analyze individuals for haplotype structure and diversity to infer genetic association studies in plants. Unlike EcoTilling, sequencing-based allele mining does not require much sophisticated equipment or involve tedious steps, but involves huge costs

Allele mining can be effectively and efficiently used for (1) discovery of superior alleles, through 'mining' the gene of interest from diverse genetic resources, (2) providing insight into molecular basis of novel trait variations and identifying the nucleotide sequence changes associated with superior alleles, (3) studying the rate of evolution of alleles; allelic similarity/dissimilarity at a candidate gene and allelic synteny with other members of the family, (4) paving way for molecular discrimination among related species through development of allele-specific molecular markers, and (5) facilitating introgression of novel alleles through Marker Assisted Selection (MAS) or deployment through Genetic Engineering (GE). Allele mining can also be potentially employed in the identification of nucleotide variation at a candidate gene associated with phenotypic variation for a trait. Through this, the frequency, type and the extent of occurrence of new haplotypes and the

The genetic resources collections, which are held collectively in various gene banks, harbour a wealth of undisclosed allelic variants. Now the challenge is how to efficiently identify and exploit the useful variation of these collections to exploit in crop improvement. The challenges stand as stampling block to make use of these collections are (1) selection of genotypes, (2) handling genomic resources, (3) demarcation of promoter region, (4) characterization of regulatory region, and (5) higher sequencing costs. The selection of germplasm to be 'mined' is one of the utmost challenges face the scholars because of the huge genetic resources collections. To overcome the aforementioned challenges, we must (1) narrow down the core collection to a manageable size while maintaining the variability, (2) refine phenotyping protocols to increase the efficiency of allele mining, (3) exploit the developments in allele mining, association genetics and comparative genomics by combining expertise from several disciplines, including molecular genetics, statistics and bioinformatics, (4) develop cheaper and faster sequencing platforms for high through put detection of allelic variations (5) develop flexible computational tools to manage genetic resources, select desirable alleles, analyze the functional nucleotide diversity to predict specific nucleotide changes responsible for altered function, accurately predict the core promoter region based on the representation/over-representation of consensus regulatory motifs, and get the snapshot of the regulatory elements which can be further examined

Soybean oil is used in many foods, industrial and fuel products. Whereas soybean meal is incorporated into animal feed. The variation in the quality and quantity of these products is basically dependent on the genetic diversity of soybean germplasm. The genetic diversity in

of sequencing. (Kumar *et al*., 2010)

resulting phenotypic changes can be evaluated.

**7.3 Applications** 

**7.4 Challenges** 

through suitable experiments.

**8. Conclusion** 

soybean germplasm was evolved from the dispersion of the cultivated soybean domesticated by the Chinese farmers. Many factors are affecting the dispersion of soybean including regional adaptation and selection. Morphological, cellular, biochemical (proteins and isozymes) and molecular markers have been used on the wide scale for the study of the genetic diversity of the cultivated and wild relative of soybean. These analyses were carried out to meet wide rang of objectives from simply testing the usefulness of a particular marker system to identifying exotic germplasm accessions to expand the genetic diversity of the elite germplasm pool in order to permit genetic improvement for increased soybean yield. Exploitation of soybean germplasm for efficient utilization depends on the knowledge of genetic diversity, in general, and allelic diversity at candidate gene(s) of interest, in particular. The beneficial alleles from vast soybean genetic resources existing worldwide were derived from cultivated germplasm. However, a significant portion of these beneficial alleles were still resided in the wild soybean germplasm. Nowadays, considerable attention has focused on allele mining (gene polymorphisms) and their potential use to alter protein function in ways that might prove biologically important. But increasing numbers of polymorphisms are also being identified in the regulatory and non coden regions of genes. Therefore, allele mining is a promising approach to dissect naturally occurring allelic variation at candidate genes controlling key agronomic traits which has potential applications in crop improvement programs. Allele mining can be effectively used for discovery of superior alleles, through 'mining' the gene of interest from soybean germplasm. It can also provide insight into molecular basis of novel trait variations and identify the nucleotide sequence changes associated with superior alleles. In addition, the rate of evolution of alleles; allelic similarity/dissimilarity at a candidate gene and allelic synteny with other members of the family can also be studied. Allele mining may also pave way for molecular discrimination among related species within the genus *Glycine*, development of allele-specific molecular markers, facilitating introgression of novel alleles through Marker Assisted Selection or deployment through genetic engineering. The alleles mining approaches and the challenges associated with it are also discussed.
