Genome-wide association study reveals early seedling vigour-associated quantitative trait loci in indica rice

Direct seeding is becoming a popular method of rice production in many rice-growing areas. Therefore, rice early seedling vigour (ESV) has also become an important agricultural research topic. To explore more genetic loci related to ESV, we used a germplasm resource containing 200 indica varieties genotyped by sequencing (GBS), and 161,657 high-quality SNPs were obtained. Nine phenotypes associated with ESV were evaluated. A genome-wide association study (GWAS) based on a mixed linear model (MLM) revealed 224 genetic loci for all traits, among which 70 genetic loci were repeatedly detected across two seasons and were reliable. In total, 1609 genes were predicted in the 200-kb genomic region harbouring these 70 loci. Furthermore, 16,184 differentially expressed genes (DEGs) were identified using RNA sequencing (RNA-seq). With the combination of RNA sequencing and GWAS, 666 candidate DEGs were obtained. Based on gene annotation and quantitative real-time PCR (qRT-PCR), we predicted the 5 most promising candidate genes (Os09g0278000, Os09g0279100, Os09g0279400, Os09g0279500 and Os09g0280300) at locus 167, which had a strong association signal. These findings provide valuable information for understanding the genetic control of ESV and for molecular marker-assisted breeding of indica rice.