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.

在许多水稻种植区，直播正成为一种流行的水稻生产方法。因此，水稻早苗活力（ESV）也成为重要的农业研究课题。为了探索更多与 ESV 相关的遗传位点，我们使用了一个包含 200 个籼稻的种质资源通过测序（GBS）基因分型的品种，获得了161,657个高质量的SNP。评估了与 ESV 相关的九种表型。基于混合线性模型 (MLM) 的全基因组关联研究 (GWAS) 揭示了所有性状的 224 个遗传位点，其中 70 个遗传位点在两个季节重复检测到并且是可靠的。在包含这 70 个基因座的 200 kb 基因组区域中，总共预测了 1609 个基因。此外，使用 RNA 测序 (RNA-seq) 鉴定了 16,184 个差异表达基因 (DEG)。结合RNA测序和GWAS，获得了666个候选DEG。基于基因注释和实时定量 PCR（qRT-PCR），我们预测了 5 个最有希望的候选基因（Os09g0278000、Os09g0279100、Os09g0279400、Os09g0279500和Os09g0280300 ) 在基因座 167 处，具有很强的关联信号。这些发现为了解 ESV 的遗传控制和籼稻的分子标记辅助育种提供了有价值的信息。