biostudies-literatureUnknown3(3)Yan HUSDATransposable 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 foundPlant communications100270https://www.ebi.ac.uk/biostudies/studies/S-EPMC9251385biostudies-literatureExploring transposable element-based markers to identify allelic variations underlying agronomic traits in rice.PMC9251385Haak DCLi SHuang LBombarely AYan HfalseExploring transposable element-based markers to identify allelic variations underlying agronomic traits in rice.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 found2022-01-01T00:00:00Z2022 May2026-05-10T01:35:25.751Z2025-02-19T01:10:41.38ZS-EPMC92513853557615210.1016/j.xplc.2021.100270