Genome-wide association study identified QTLs and genes underlying early seedling vigour in aus rice (Oryza sativa L.).

Early seedling vigour (ESV) is a key trait that enhances early establishment, stress tolerance, and grain yield in rice, especially in direct-seeded rice (DSR) systems. The aus varietal groups is known for its high seedling vigour. The screening of aus diversity panel for ESV traits and subsequent genome-wide association study (GWAS) can lead to the identification of genetic components of ESV. Here, we report the genetic variation in seven ESV traits along with days to 50% flowering and grain yield in a panel of 181 aus accessions evaluated under field conditions. We observed significant variations in the studied traits. The vegetative vigour, scored visually, was significantly correlated with most of the traits, suggesting its impact on overall plant performance. Comparative analysis of aus genetic groups revealed significant variations, and the subpopulation that includes early maturing drought tolerant genotypes was the most vigorous, and thus ideal for donor selection. GWAS using 918, 863 single nucleotide polymorphism (SNP) markers identified 14 significant QTLs, including seven novel ones, linked to vegetative vigour, average growth rate and seedling biomass. Candidate genes like OsPDR1, NCKAP1, and OsSAUR10, involved in jasmonic acid biosynthesis, ABA signaling, and brassinosteroid pathways, were identified to be associated with ESV regulation. This study provides insights into the genetic basis of ESV in aus rice, identifying promising germplasm and genes that could improve seedling vigour and yield in DSR systems. Future research should validate these findings and integrate them into breeding programs for enhanced rice performance in various environments.