Genome-wide association analysis and molecular marker development for effective tiller number in rice natural population

Effective tiller number (ETN) has a pivotal role in determination of rice (Oryza sativa L.) grain yield. ETN is a complex quantitative trait regulated by both genetic and environmental factors. Multiple tillering-related genes have been cloned previously, few of them have been utilized in practical breeding programs. In this study, a genome-wide association study (GWAS) for ETN was conducted on 270 rice accessions with 1,019,883 SNPs. Total of 214 SNPs were detected on eight rice chromosomes for ETN at a significance level of -log10(P) > 6.0. 12 QTLs associated with ETN were identified, including three known functional genes (e.g., D10, D27, Stvb-i) and one novel gene OsIAA3. Compared to wild-type plants, OsIAA3-overexpressing plants could significantly increase ETN in rice. In the natural population, haplotype analysis was conducted for D10, D27, Stvb-i, and OsIAA3, and their favorable alleles were identified. Molecular markers were also developed and validated within the natural population and bi-parent population, and the validation results demonstrated that the developed molecular markers can be utilized for marker-assisted selection breeding. This study not only enhances our understanding of the genetic regulatory basis of rice ETN but also provides excellent germplasm and favorable haplotypes that serve as valuable breeding resources and genetic material for improving ETN and yield in rice.