Genome-wide association study for traits related to seedling vigor in rice

Seedling vigor is a desirable trait in direct-seeded rice (Oryza sativa L.) to improve plant establishment and enhance weed competition. In this study, a genome-wide association study (GWAS) on seedling vigor traits was performed on a rice panel of 244 accessions consisting of the five major rice subpopulations (aromatic, aus, tropical japonica, temperate japonica, and indica) using the 7K SNP Cornell-IR LD Rice Array. A total of seven seedling vigor-related traits were evaluated under controlled conditions in a growth chamber. All traits had a normal distribution with a wide range of phenotypic variation with CV between 27.6 and 43.9%, except for seedling dry weight, which had a CV of 11.4%. We identified 43 GWAS-quantitative trait locus (QTL) regions associated with different seedling vigor traits, of which 19 QTL regions were near previously identified genes or QTL regions. These findings confirmed 19 previous QTL and identified 24 potential novel QTL targets for marker-assisted breeding programs. Additionally, superior donors with high seedling vigor were identified and can be used for rice crop improvement in direct-seeded systems.

Automated summary

Through a genome-wide association study, 43 QTL regions associated with different seedling vigor traits were identified, with 19 of them near previously identified genes or QTL regions, confirming 19 previous QTL and identifying 24 potential new targets for marker-assisted breeding programs. Additionally, superior donors with high seedling vigor were discovered and can be utilized in rice crop improvement in direct-seeded systems.