{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"volume":["3(3)"],"submitter":["Yan H"],"funding":["USDA"],"pubmed_abstract":["Transposable 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"],"journal":["Plant communications"],"pagination":["100270"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC9251385"],"repository":["biostudies-literature"],"pubmed_title":["Exploring transposable element-based markers to identify allelic variations underlying agronomic traits in rice."],"pmcid":["PMC9251385"],"pubmed_authors":["Haak DC","Li S","Huang L","Bombarely A","Yan H"],"additional_accession":[]},"is_claimable":false,"name":"Exploring transposable element-based markers to identify allelic variations underlying agronomic traits in rice.","description":"Transposable 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","dates":{"release":"2022-01-01T00:00:00Z","publication":"2022 May","modification":"2026-05-10T01:35:25.751Z","creation":"2025-02-19T01:10:41.38Z"},"accession":"S-EPMC9251385","cross_references":{"pubmed":["35576152"],"doi":["10.1016/j.xplc.2021.100270"]}}