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

Area of Science:

• Genomics
• Plant Genetics
• Molecular Biology

Background:

• Transposable elements (TEs) drive genetic diversity during crop domestication.
• Their complexity has limited their application in genome-wide association studies (GWAS).

Purpose of the Study:

• To develop a TE genotyping pipeline (TEmarker) for GWAS.
• To identify genetic elements associated with agronomic traits in rice (Oryza sativa subsp. japonica).

Main Methods:

• Applied the TEmarker pipeline to whole-genome GWAS data from 176 japonica rice accessions.
• Analyzed TE marker association with agronomic traits and linkage disequilibrium (LD).
• Performed a genome scan to detect positive selection on TEs.

Main Results:

• TE markers captured 69% of SNP-based GWAS peaks, retaining 25% of SNPs.
• TEs in GWAS potentially reduce false positives caused by SNP marker LD.
• Identified TEs associated with positive selection and agronomic traits, including variants affecting plant height and panicle length.

Conclusions:

• TE markers are valuable for genotype-phenotype association studies in rice.
• TEs play a significant role in shaping phenotypic variation relevant to agronomic traits.