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

Autor:	Semalaiyappan J; Genomics and Molecular Breeding Lab, ICAR-Indian Institute of Millets Research, Rajendranagar, India., Selvanayagam S; Accelerated Crop Improvement, International Crop Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India., Rathore A; Excellence in Breeding (EiB) Platform, The International Maize and Wheat Improvement Center (CIMMYT), El Batán, Mexico., Gupta SK; Accelerated Crop Improvement, International Crop Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India., Chakraborty A; Genomics and Molecular Breeding Lab, ICAR-Indian Institute of Millets Research, Rajendranagar, India., Gujjula KR; Bioinformatics, Thermo Fisher Scientific, Austin, TX, United States., Haktan S; Bioinformatics, Thermo Fisher Scientific, Austin, TX, United States., Viswanath A; Genomics and Molecular Breeding Lab, ICAR-Indian Institute of Millets Research, Rajendranagar, India., Malipatil R; Genomics and Molecular Breeding Lab, ICAR-Indian Institute of Millets Research, Rajendranagar, India., Shah P; Genomics and Molecular Breeding Lab, ICAR-Indian Institute of Millets Research, Rajendranagar, India., Govindaraj M; HarvestPlus, International Center for Tropical Agriculture, Cali, Colombia., Ignacio JC; Department of Horticulture and Crop Science, The Ohio State University, Wooster, OH, United States., Reddy S; Genomics and Molecular Breeding Lab, ICAR-Indian Institute of Millets Research, Rajendranagar, India., Singh AK; ICAR-Indian Agricultural Research Institute, New Delhi, India., Thirunavukkarasu N; Genomics and Molecular Breeding Lab, ICAR-Indian Institute of Millets Research, Rajendranagar, India.
Jazyk:	angličtina
Zdroj:	Frontiers in plant science [Front Plant Sci] 2023 Jan 10; Vol. 13, pp. 1068883. Date of Electronic Publication: 2023 Jan 10 (Print Publication: 2022).
DOI:	10.3389/fpls.2022.1068883
Abstrakt:	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 mid-density 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. Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. (Copyright © 2023 Semalaiyappan, Selvanayagam, Rathore, Gupta, Chakraborty, Gujjula, Haktan, Viswanath, Malipatil, Shah, Govindaraj, Ignacio, Reddy, Singh and Thirunavukkarasu.)
Databáze:	MEDLINE
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