Multi-locus genome-wide association studies reveal genomic regions and putative candidate genes associated with leaf spot diseases in African groundnut (Arachis hypogaea L.) germplasm

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dc.contributor.authorOteng-Frimpong, Richarden
dc.contributor.authorKarikari, Benjaminen
dc.contributor.authorSie, Emmanuel Kofien
dc.contributor.authorKassim, Yussif Babaen
dc.contributor.authorPuozaa, Doris Kanvenaaen
dc.contributor.authorRasheed, Masawudu Abdulen
dc.contributor.authorFonceka, Danielen
dc.contributor.authorOkello, David Kalluleen
dc.contributor.authorBalota, Mariaen
dc.contributor.authorBurow, Marken
dc.contributor.authorOzias-Akins, Peggyen
dc.date.accessioned2023-03-30T15:02:30Zen
dc.date.available2023-03-30T15:02:30Zen
dc.date.issued2023-01-05en
dc.description.abstractEarly leaf spot (ELS) and late leaf spot (LLS) diseases are the two most destructive groundnut diseases in Ghana resulting in <= 70% yield losses which is controlled largely by chemical method. To develop leaf spot resistant varieties, the present study was undertaken to identify single nucleotide polymorphism (SNP) markers and putative candidate genes underlying both ELS and LLS. In this study, six multi-locus models of genome-wide association study were conducted with the best linear unbiased predictor obtained from 294 African groundnut germplasm screened for ELS and LLS as well as image-based indices of leaf spot diseases severity in 2020 and 2021 and 8,772 high-quality SNPs from a 48 K SNP array Axiom platform. Ninety-seven SNPs associated with ELS, LLS and five image-based indices across the chromosomes in the 2 two sub-genomes. From these, twenty-nine unique SNPs were detected by at least two models for one or more traits across 16 chromosomes with explained phenotypic variation ranging from 0.01 - 62.76%, with exception of chromosome (Chr) 08 (Chr08), Chr10, Chr11, and Chr19. Seventeen potential candidate genes were predicted at +/- 300 kbp of the stable/prominent SNP positions (12 and 5, down- and upstream, respectively). The results from this study provide a basis for understanding the genetic architecture of ELS and LLS diseases in African groundnut germplasm, and the associated SNPs and predicted candidate genes would be valuable for breeding leaf spot diseases resistant varieties upon further validation.en
dc.description.notesThis study was made possible by the generous support of the BMGF funded Accelerated Varietal Improvement and Seed Systems for Legumes and Cereals in Africa (AVISA) Project Grant Number OPP1198373 and the American people through the United States Agency for International Development (USAID) Cooperative Agreement No. 7200AA 18CA00003 to the University of Georgia as management entity for U.S. Feed the Future Innovation Lab for Peanut (2018-2023). The funders had no role in experiments, data analyses and publication.en
dc.description.sponsorshipBMGF funded Accelerated Varietal Improvement and Seed Systems for Legumes and Cereals in Africa (AVISA) [OPP1198373]; American people through the United States Agency for International Development (USAID) [7200AA 18CA00003]en
dc.description.versionPublished versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.3389/fpls.2022.1076744en
dc.identifier.other1076744en
dc.identifier.pmid36684745en
dc.identifier.urihttp://hdl.handle.net/10919/114231en
dc.identifier.volume13en
dc.language.isoenen
dc.publisherFrontiersen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectcandidate genesen
dc.subjectenvironmentally friendlyen
dc.subjectgenomicsen
dc.subjectmarkerassisted selectionen
dc.subjectoilseeden
dc.subjectearly leaf spoten
dc.subjectlate leaf spoten
dc.titleMulti-locus genome-wide association studies reveal genomic regions and putative candidate genes associated with leaf spot diseases in African groundnut (Arachis hypogaea L.) germplasmen
dc.title.serialFrontiers in Plant Scienceen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

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