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

dc.creatorSemalaiyappan, J.
dc.creatorSelvanayagam, S.
dc.creatorRathore, A.
dc.creatorGupta, S.K.
dc.creatorChakraborty, A.
dc.creatorGujjula, K.R.
dc.creatorHaktan, S.
dc.creatorViswanath, A.
dc.creatorMalipatil, R.
dc.creatorShah, P.
dc.creatorGovindaraj, M.
dc.creatorIgnacio, J.C.
dc.creatorReddy, S.
dc.creatorAshok Kumar Singh
dc.creatorThirunavukkarasu, N.
dc.date2023-02-10T19:07:40Z
dc.date2023-02-10T19:07:40Z
dc.date2023
dc.date.accessioned2023-07-17T20:10:21Z
dc.date.available2023-07-17T20:10:21Z
dc.identifierhttps://hdl.handle.net/10883/22509
dc.identifier10.3389/fpls.2022.1068883
dc.identifier.urihttps://repositorioslatinoamericanos.uchile.cl/handle/2250/7514252
dc.descriptionPearl 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.
dc.languageEnglish
dc.publisherFrontiers Media
dc.relationhttps://figshare.com/collections/Development_of_a_new_AgriSeq_4K_mid-density_SNP_genotyping_panel_and_its_utility_in_pearl_millet_breeding/6378273
dc.rightsCIMMYT manages Intellectual Assets as International Public Goods. The user is free to download, print, store and share this work. In case you want to translate or create any other derivative work and share or distribute such translation/derivative work, please contact CIMMYT-Knowledge-Center@cgiar.org indicating the work you want to use and the kind of use you intend; CIMMYT will contact you with the suitable license for that purpose
dc.rightsOpen Access
dc.source13
dc.source1664-462X
dc.sourceFrontiers in Plant Science
dc.source1068883
dc.subjectAGRICULTURAL SCIENCES AND BIOTECHNOLOGY
dc.subjectMid-Density SNP
dc.subjectAgriSeq Technology
dc.subjectHigh Throughput Genotyping
dc.subjectGENOMICS
dc.subjectSINGLE NUCLEOTIDE POLYMORPHISM
dc.subjectPEARL MILLET
dc.subjectTECHNOLOGY
dc.subjectInstitutional
dc.titleDevelopment of a new AgriSeq 4K mid-density SNP genotyping panel and its utility in pearl millet breeding
dc.typeArticle
dc.typePublished Version
dc.coverageSwitzerland


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