Evaluation of linkage disequilibrium, population structure, and genetic diversity in the U.S. peanut mini core collection

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cg.authorship.typesCGIAR single centreen
cg.contributor.affiliationUniversity of Georgiaen
cg.contributor.affiliationUniversity of Floridaen
cg.contributor.affiliationInternational Potato Centeren
cg.contributor.affiliationIowa State Universityen
cg.creator.identifierPaul I. Otyama: 0000-0002-9962-7190
cg.creator.identifierAndrew Wilkey: 0000-0002-5731-0048
cg.creator.identifierRoshan Kulkarni: 0000-0001-9578-866X
cg.creator.identifierYe Chu: 0000-0002-9204-9498
cg.creator.identifierJosh Clevenger: 0000-0002-9830-9481
cg.creator.identifierGraeme Wright: 0000-0002-7113-6429
cg.creator.identifierPeggy Ozias-Akins: 0000-0002-8864-2766
cg.creator.identifierSteven Cannon: 0000-0003-2777-8034
cg.creator.identifierNoelle L. Anglin: 0000-0002-3454-1142
cg.howPublishedFormally Publisheden
cg.identifier.doihttps://doi.org/10.1186/s12864-019-5824-9en
cg.isijournalISI Journalen
cg.issn1471-2164en
cg.issue1en
cg.journalBMC Genomicsen
cg.reviewStatusPeer Reviewen
cg.subject.cipBIODIVERSITY FOR THE FUTUREen
cg.subject.cipGENETICS, GENOMICS AND CROP IMPROVEMENT SCIENCES GGCIen
cg.subject.cipGENEBANKen
cg.volume20en
dc.contributor.authorOtyama, P.I.en
dc.contributor.authorWilkey, A.en
dc.contributor.authorKulkarni, R.en
dc.contributor.authorAssefa, T.en
dc.contributor.authorChu, Y.en
dc.contributor.authorClevenger, J.en
dc.contributor.authorO’Connor, D.J.en
dc.contributor.authorWright, G.C.en
dc.contributor.authorDezern, S.W.en
dc.contributor.authorMacDonald, G.E.en
dc.contributor.authorAnglin, Noelle L.en
dc.contributor.authorCannon, Ethalinda K.S.en
dc.contributor.authorOzias-Akins, P.en
dc.contributor.authorCannon, Steven B.en
dc.date.accessioned2019-07-08T21:17:01Zen
dc.date.available2019-07-08T21:17:01Zen
dc.identifier.urihttps://hdl.handle.net/10568/102104
dc.titleEvaluation of linkage disequilibrium, population structure, and genetic diversity in the U.S. peanut mini core collectionen
dcterms.abstractBackground Due to the recent domestication of peanut from a single tetraploidization event, relatively little genetic diversity underlies the extensive morphological and agronomic diversity in peanut cultivars today. To broaden the genetic variation in future breeding programs, it is necessary to characterize germplasm accessions for new sources of variation and to leverage the power of genome-wide association studies (GWAS) to discover markers associated with traits of interest. We report an analysis of linkage disequilibrium (LD), population structure, and genetic diversity, and examine the ability of GWA to infer marker-trait associations in the U.S. peanut mini core collection genotyped with a 58 K SNP array. Results LD persists over long distances in the collection, decaying to r2 = half decay distance at 3.78 Mb. Structure within the collection is best explained when separated into four or five groups (K = 4 and K = 5). At K = 4 and 5, accessions loosely clustered according to market type and subspecies, though with numerous exceptions. Out of 107 accessions, 43 clustered in correspondence to the main market type subgroup whereas 34 did not. The remaining 30 accessions had either missing taxonomic classification or were classified as mixed. Phylogenetic network analysis also clustered accessions into approximately five groups based on their genotypes, with loose correspondence to subspecies and market type. Genome wide association analysis was performed on these lines for 12 seed composition and quality traits. Significant marker associations were identified for arachidic and behenic fatty acid compositions, which despite having low bioavailability in peanut, have been reported to raise cholesterol levels in humans. Other traits such as blanchability showed consistent associations in multiple tests, with plausible candidate genes. Conclusions Based on GWA, population structure as well as additional simulation results, we find that the primary limitations of this collection for GWAS are a small collection size, significant remaining structure/genetic similarity and long LD blocks that limit the resolution of association mapping. These results can be used to improve GWAS in peanut in future studies – for example, by increasing the size and reducing structure in the collections used for GWAS.en
dcterms.accessRightsOpen Access
dcterms.audienceScientistsen
dcterms.audienceAcademicsen
dcterms.audienceCGIARen
dcterms.audienceDevelopment Practitionersen
dcterms.audienceDonorsen
dcterms.audienceExtensionen
dcterms.available2019-06-11
dcterms.bibliographicCitationOtyama, P.I.; Wilkey, A.; Kulkarni, R.; Assefa, T.; Chu, Y.; Clevenger, J.; O’Connor, D.J.; Wright, G.C.; Dezern, S.W.; Macdonald, G.E.; Anglin, N.L.; Cannon, E.K.S.; Ozias-Akins, P.; Cannon, S.B. 2019. Evaluation of linkage disequilibrium, population structure, and genetic diversity in the U.S. peanut mini core collection. BMC Genomics. ISSN: 1471-2164. 17 p.en
dcterms.extent1-17 p.en
dcterms.issued2019-12
dcterms.languageen
dcterms.licenseCC-BY-4.0
dcterms.publisherSpringeren
dcterms.subjectpopulation structureen
dcterms.subjectgenetic diversityen
dcterms.subjectgeneticsen
dcterms.subjectbiotechnologyen
dcterms.typeJournal Article

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