Abstract
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Pigeonpea stands as the second most vital leguminous crop in South Asia, playing a crucial role in ensuring food and nutritional security. To expedite breeding efforts, we have harnessed advanced genomic tools, specifically a high-throughput 62 K SNP chip array named 'CcSNPnks' designed for the Affymetrix GeneTitan® platform. This array is a product of meticulous filtration of 645,662 genic-SNPs identified through the re-sequencing of 45 diverse genotypes.
Comprising 62,053 SNPs from 9629 genes across five distinct categories, 'CcSNPnks' includes single-copy genes unique to pigeonpea, those conserved between soybean and pigeonpea, homologs of crucial agronomic genes, disease resistance and defense response genes, and multi-copy genes of pigeonpea. This comprehensive genic chip boasts a distribution of 28.94% exonic, 33.04% intronic, 27.56% 5′UTR, and 10.46% 3′UTR SNPs, featuring multiple SNPs per gene for effective gene haplotype network analysis.
The utility of 'CcSNPnks' extends to various applications, as evidenced by its successful deployment in analyzing the genetic diversity and population structure of 95 pigeonpea varieties. Furthermore, it facilitated high-resolution mapping of 11 QTLs related to yield traits in a biparental RIL population, specifically targeting the number of branches, pod-bearing length, and number of seeds per pod.
Functioning as a precise and high-density genotyping tool, the 'CcSNPnks' chip array emerges as a valuable resource for activities such as high-resolution fingerprinting, QTL mapping, and conducting genome-wide, as well as gene-based association studies in the context of pigeonpea research.
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