Development of a new AgriSeq 4K mid-density SNP genotyping panel and its utility in pearl millet breeding

Semalaiyappan, J and Selvanayagam, S and Rathore, A and Gupta, S K and Chakraborty, A and Gujjula, K R and Haktan, S and Viswanath, A and Malipatil, R and Shah, P and Govindaraj, M and Ignacio, J C and Reddy, S and Singh, A K and Thirunavukkarasu, N (2023) Development of a new AgriSeq 4K mid-density SNP genotyping panel and its utility in pearl millet breeding. Frontiers in Plant Science, 13. 01-14. ISSN 1664-462X

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Pearl millet is a crucial nutrient-rich staple food in Asia and Africa and adapted to the climate of semi-arid topics. Since the genomic resources in pearl millet are very limited, we have developed a brand-new mid-density 4K SNP panel and demonstrated its utility in genetic studies. A set of 4K SNPs were mined from 925 whole-genome sequences through a comprehensive in-silico pipeline. Three hundred and seventy-three genetically diverse pearl millet inbreds were genotyped using the newly-developed 4K SNPs through the AgriSeq Targeted Genotyping by Sequencing technology. The 4K SNPs were uniformly distributed across the pearl millet genome and showed considerable polymorphism information content (0.23), genetic diversity (0.29), expected heterozygosity (0.29), and observed heterozygosity (0.03). The SNP panel successfully differentiated the accessions into two major groups, namely B and R lines, through genetic diversity, PCA, and structure models as per their pedigree. The linkage disequilibrium (LD) analysis showed Chr3 had higher LD regions while Chr1 and Chr2 had more low LD regions. The genetic divergence between the B- and R-line populations was 13%, and within the sub-population variability was 87%. In this experiment, we have mined 4K SNPs and optimized the genotyping protocol through AgriSeq technology for routine use, which is cost-effective, fast, and highly reproducible. The newly developed 4K middensity SNP panel will be useful in genomics and molecular breeding experiments such as assessing the genetic diversity, trait mapping, backcross breeding, and genomic selection in pearl millet.

Item Type: Article
Divisions: Global Research Program - Accelerated Crop Improvement
Uncontrolled Keywords: pearl millet, mid-density SNP, AgriSeq technology, high-throughput genotyping, genomics
Subjects: Mandate crops > Millets > Pearl Millet
Others > Genetics and Genomics
Depositing User: Mr Nagaraju T
Date Deposited: 12 May 2023 03:30
Last Modified: 12 May 2023 03:30
Official URL:
Projects: Bill and Melinda Gates Foundation project (INV-008187), ICAR-Indian Institute of Millets Research project (CI/2018-23/120)
Funders: Bill and Melinda Gates Foundation, ICAR-Indian Institute of Millets Research
Acknowledgement: The Supplementary Material for this article can be found online at: fpls.2022.1068883/full#supplementary-material
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