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Genome-wide association study revealed SNP alleles associated with seed size traits in African yam bean (Sphenostylis stenocarpa (Hochst ex. A. Rich.) harms)

dc.contributor.authorOlomitutu, O.E.
dc.contributor.authorPaliwal, R.
dc.contributor.authorAbe, A.
dc.contributor.authorOluwole, O.O.
dc.contributor.authorOyatomi, O.
dc.contributor.authorAbberton, M.
dc.date.accessioned2023-11-27T09:50:01Z
dc.date.available2023-11-27T09:50:01Z
dc.date.issued2023
dc.identifier.citationOlomitutu, O.E., Paliwal, R., Abe, A., Oluwole, O.O., Oyatomi, O. & Abberton, M. (2022). Genome-wide association study revealed SNP alleles associated with seed size traits in African yam bean (Sphenostylis stenocarpa (Hochst ex. A. Rich.) harms). Genes, 13(12): 2350, 1-19.
dc.identifier.issn2073-4425
dc.identifier.urihttps://hdl.handle.net/20.500.12478/8338
dc.description.abstractSeed size is an important yield and quality-determining trait in higher plants and is also crucial to their evolutionary fitness. In African yam bean (AYB), seed size varies widely among different accessions. However, the genetic basis of such variation has not been adequately documented. A genome-wide marker-trait association study was conducted to identify genomic regions associated with four seed size traits (seed length, seed width, seed thickness, and 100-seed weight) in a panel of 195 AYB accessions. A total of 5416 SNP markers were generated from the diversity array technology sequence (DArTseq) genotype-by-sequencing (GBS)- approach, in which 2491 SNPs were retained after SNP quality control and used for marker-trait association analysis. Significant phenotypic variation was observed for the traits. Broad-sense heritability ranged from 50.0% (seed width) to 66.4% (seed length). The relationships among the traits were positive and significant. Genome-wide association study (GWAS) using the general linear model (GLM) and the mixed linear model (MLM) approaches identified 12 SNP markers significantly associated with seed size traits across the six test environments. The 12 makers explained 6.5–10.8% of the phenotypic variation. Two markers (29420334|F|0-52:C>G-52:C>G and 29420736|F|0-57:G>T-57:G>T) with pleiotropic effects associated with seed width and seed thickness were found. A candidate gene search identified five significant markers (100026424|F|0-37:C>T-37:C>T, 100041049|F|0-42:G>C-42:G>C, 100034480|F|0-31:C>A-31:C>A, 29420365|F|0-55:C>G-55:C>G, and 29420736|F|0-57:G>T-57:G>T) located close to 43 putative genes whose encoding protein products are known to regulate seed size traits. This study revealed significant makers not previously reported for seed size in AYB and could provide useful information for genomic-assisted breeding in AYB.
dc.format.extent1-19
dc.language.isoen
dc.subjectAfrican Yam Beans
dc.subjectPhenotypic Variation
dc.subjectSeed Size
dc.subjectSingle Nucleotide Polymorphism
dc.titleGenome-wide association study revealed SNP alleles associated with seed size traits in African yam bean (Sphenostylis stenocarpa (Hochst ex. A. Rich.) harms)
dc.typeJournal Article
cg.contributor.crpGenebanks
cg.contributor.crpRoots, Tubers and Bananas
cg.contributor.affiliationUniversity of Ibadan
cg.contributor.affiliationInternational Institute of Tropical Agriculture
cg.coverage.regionAfrica
cg.coverage.regionWest Africa
cg.coverage.countryNigeria
cg.coverage.hubHeadquarters and Western Africa Hub
cg.researchthemeBiotech and Plant Breeding
cg.identifier.bibtexciteidOLOMITUTU:2023
cg.isijournalISI Journal
cg.authorship.typesCGIAR and developing country institute
cg.iitasubjectAgronomy
cg.iitasubjectFood Security
cg.iitasubjectGenetic Improvement
cg.iitasubjectGrain Legumes
cg.iitasubjectPlant Breeding
cg.iitasubjectPlant Production
cg.iitasubjectYam
cg.journalGenes
cg.notesOpen Access Journal
cg.accessibilitystatusOpen Access
cg.reviewstatusPeer Review
cg.usagerightslicenseCreative Commons Attribution 4.0 (CC BY 0.0)
cg.targetaudienceScientists
cg.identifier.doihttps://doi.org/10.3390/genes13122350
cg.iitaauthor.identifierOlaniyi Oyatomi: 0000-0003-3094-374X
cg.iitaauthor.identifierMichael Abberton: 0000-0003-2555-9591
cg.futureupdate.requiredNo
cg.identifier.issue12: 2350
cg.identifier.volume13
cg.contributor.acknowledgementsThe authors express gratitude to members of staff of the seed bank of the Genetic Resource Center, IITA, Ibadan, the cassava breeding unit, IITA, Ubiaja, the cowpea breeding unit, IITA, Kano, and the Bioscience Center, IITA, Ibadan, for their field and laboratory assistance.


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