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

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Relation http://oar.icrisat.org/12084/
https://www.frontiersin.org/articles/10.3389/fpls.2022.1068883/full
https://doi.org/10.3389/fpls.2022.1068883
 
Title Development of a new AgriSeq 4K mid-density SNP genotyping
panel and its utility in pearl millet breeding
 
Creator Semalaiyappan, J
Selvanayagam, S
Rathore, A
Gupta, S K
Chakraborty, A
Gujjula, K R
Haktan, S
Viswanath, A
Malipatil, R
Shah, P
Govindaraj, M
Ignacio, J C
Reddy, S
Singh, A K
Thirunavukkarasu, N
 
Subject Pearl Millet
Genetics and Genomics
 
Description 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.
 
Publisher Frontiers Media
 
Date 2023-01-10
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
Rights cc_attribution
 
Identifier http://oar.icrisat.org/12084/1/Frontiers%20in%20Plant%20Science_13_SS.pdf
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