Exploring 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 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.

Automated summary

Transposable elements (TEs) are a major force in the production of new alleles during domestication, but their complexity has limited their use in association studies. A TE genotyping pipeline (TEmarker) was developed and applied to a whole-genome GWAS study on Oryza sativa subsp. japonica to identify genetic elements associated with agronomic traits. TE markers were able to recover a large proportion of SNP-based GWAS peaks and reduce false positives associated with SNP marker linkage disequilibrium. The study also revealed positive selection on TEs associated with agronomic traits and identified insertion and deletion variants potentially resulting from the direct action of TEs.