Exploring transposable element-based markers to identify allelic variations underlying agronomic traits in rice

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dc.contributor.authorYan, Haidongen
dc.contributor.authorHaak, David C.en
dc.contributor.authorLi, Songen
dc.contributor.authorHuang, Linkaien
dc.contributor.authorBombarely, Aurelianoen
dc.date.accessioned2022-06-15T14:08:33Zen
dc.date.available2022-06-15T14:08:33Zen
dc.date.issued2022-05-09en
dc.description.abstractTransposable elements (TEs) are a major force in the production of new alleles during domestication; nevertheless, their use in association studies has been limited because of their complexity. We have developed a TE genotyping pipeline (TEmarker) and applied it to whole-genome genome-wide association study (GWAS) data from 176 Oryza sativa subsp. japonica accessions to identify genetic elements associated with specific agronomic traits. TE markers recovered a large proportion (69%) of single-nucleotide polymorphism (SNP)-based GWAS peaks, and these TE peaks retained ca. 25% of the SNPs. The use of TEs in GWASs may reduce false positives associated with linkage disequilibrium (LD) among SNP markers. A genome scan revealed positive selection on TEs associated with agronomic traits. We found several cases of insertion and deletion variants that potentially resulted from the direct action of TEs, including an allele of LOC_Os11g08410 associated with plant height and panicle length traits. Together, these findings reveal the utility of TE markers for connecting genotype to phenotype and suggest a potential role for TEs in influencing phenotypic variations in rice that impact agronomic traits.en
dc.description.notesThe authors want to acknowledge the School of Plant and Environmental Sciences at Virginia Tech for the support of H.Y. They also want to acknowledge the Advanced Research Computing unit (www.arc.vt.edu) for the use of computational resources. Finally, the authors would like to acknowledge the reviewers for their useful suggestions that helped to improve the article.en
dc.description.sponsorshipSchool of Plant and Environmental Sciences at Virginia Techen
dc.description.versionPublished versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1016/j.xplc.2021.100270en
dc.identifier.issn2590-3462en
dc.identifier.issue3en
dc.identifier.other100270en
dc.identifier.pmid35576152en
dc.identifier.urihttp://hdl.handle.net/10919/110783en
dc.identifier.volume3en
dc.language.isoenen
dc.publisherElsevieren
dc.rightsCreative Commons Attribution-NonCommercial-NoDerivatives 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/en
dc.subjecttransposable elementen
dc.subjectmarkeren
dc.subjectagronomic traiten
dc.subjectriceen
dc.subjectGWASen
dc.titleExploring transposable element-based markers to identify allelic variations underlying agronomic traits in riceen
dc.title.serialPlant Communicationsen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

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