**7.2.2 Sequencing-based allele mining**

This technique involves amplification of alleles in diverse genotypes through PCR followed by identification of nucleotide variation by DNA sequencing. Sequencing-based allele

Genetic Diversity and Allele Mining in Soybean Germplasm 15

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.

species. *Plant Mol. Biol. Rep.*, 9, 208-219.

Abe, J., Xu D. H., Suzuki, Y., Kanazawa, A. & Shimamoto, Y. (2003). Soybean germplasm pools in Asia revealed by nuclear SSRs. *Theor. Appl. Genet.,* 106, 445-453. An, W., Zhao, H., Dong, Y., Wang, Y., Li, Q., Zhuang, B., Gong, L. & Liu, B. (2009). Genetic

Arumuganathan, I., & Earle, E. D. (1991). Nuclear DNA content of some important plant

Baranek, M., Kadlec, M., Raddova, J., Vachun, M. & Pidra, M. (2002). Evaluation of genetic

collection of soybean genotypes. Czech J. Genet. Plant Breed, 38 , 69–74. Bennett, M. D., Heslop-Harrison, J. S., Smith, J. B. & Ward, J. P. (1983). DNA density in

diversity in annual wild soybean (*Glycine Soja* SIEB. ET ZUCC.) and cultivated soybean (*G. Max*. MERR.). from different latitudes in China. *Pak. J. Bot*., 41. 2229-

diversity in 19 *Glycine max* (L.) Merr. accessions included in the Czech national

mitotic and meiotic metaphase chromosomes of plants and animals. *J. Cell Sci.*, 63,

**9. References** 

2242.

173-179.

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