Title : Identification of genes to improve seed and nutrition quality traits in pigeonpea using Genome wide association study
Pigeonpea is an important legume crop with high protein content and nutritional attributes for more than a billion-people living in South Asia. Ever-increasing pigeonpea consumption as a major source of protein necessitates the improvement of varieties for more efficient production. The nutritional value enrichment of pigeopea is very much essential to reduce malnutrition of developing countries in the post green revolution era. To utilize its potential, a coordinated and comprehensive evaluation of germplasm is required. Identification of potential genes/alleles governing complex traits of seed quality and nutritional content such as seed weight, seed colour, total protein content (TPC), amino acid and resistance starch are essential in marker-assisted breeding for quality trait improvement of pigeonpea.
The current gain in knowledge on the seed quality and nutritional value related genes and QTLs will help into develop desired genotypes for the humankind. The availability of gene-based markers and advanced tool will assist breeders to accumulate specific alleles of genes known to play a role in nutritional grain quality traits in pigeonpea. Therefore, the present study on the profiling for the first-time to understand these complex genetic architectures of qualitative and quantitative traits in pigeonpea. For GWAS (genome-wide association study), high-throughput genotyping information of 62K SNP “CcSNPnks” genic chip genome-based SNPs discovered from 45 diverse varieties of pigeonpea utilized. The chip comprises total 62,053 SNPs from 9629 genes belonging to five different categories, including 4314 single-copy genes unique to pigeonpea, 4328 single-copy genes conserved between soybean and pigeonpea, 156 homologs of agronomically important cloned genes, 746 disease resistance and defense response genes and 85 multi-copy genes of pigeonpea. Our analysis revealed that the average protein content carrying genotypes are DG(RG)45, AKPR -324, MC-99, UP-73 and BRG-2 (16.8, 19.3, 21.5, 24.7, 30.3 gm). This led to identification of most effective genomic loci (genes) associated with seed quality and nutritional content in pigeonpea from diverse sets of wild and cultivated genetic backgrounds. The informative functionally relevant molecular tags scaled down essentially have potential to accelerate marker assisted genetic improvement by developing seed quality and nutritionally rich pigeonpea cultivars.
Keywords: genes, genotyping, GWAS, pigeonpea, nutritional quality, seed, SNP