LAUSR

Grain size and shape are important for grain yield and quality in rice (Oryza sativa L.). Grain thickness (GT) is one of the constituent characteristics of grain shape and has a strong influence on grain weight in rice. In this study, a japonica cultivar (02428) with a thick grain phenotype was crossed with an indica cultivar (YZX) with a thin grain phenotype to construct a set of 192 recombinant inbred lines (RILs). Quantitative trait locus (QTL) analysis was performed with a high-density genetic map harbouring 2711 bin markers. We identified 6 QTLs for GT in three environments and two stable QTLs with high heritability residing on the known grain width (GW) genes GW5 and GL7/GW7, verifying the effectiveness and reliability of our study. We detected a novel QTL on chromosome 9 with strong association signals for both GW and GT. Using transcript profiles and quantitative RT-PCR, we identified a candidate gene, Os09g0535500, which encodes a zinc finger C3HC4-type domain, that showed the highest expression level and significant differential expression between parents in the development of young panicle and grain. Further haplotype-phenotype association analysis revealed that Os09g0535500 was strongly correlated with GW and GT. Thus, our results indicated that Os09g0535500 was the most promising candidate gene in WTG9 and is likely important for rice grain development, which lays a foundation for further functional validation and breeding utilization.