Identification of QTLs and a candidate gene affecting rice grain volume via high-density genetic mapping

A total of eight QTLs for grain volume, explained 4.22-19.75% of the total phenotypic variation, were detected with LOD scores ranging from 3.33 to 13.25. Among these loci, five are known genes or loci related to grain size, and three loci, <i>qGV4-2</i>, <i>qGV7-1</i>, and <i>qGV7-2</i>, were newly identified. The major QTL, <i>qGV7-2</i>, explained the highest phenotypic variation, was validated using NIL pairs. By combining gene functional annotation, gene expression analysis and sequence comparison within the mapping interval of <i>qGV7-2</i>, a candidate gene (<i>LOC_Os07g15540</i>), encoding an ethylene receptor, OsETR4, was identified. Further haplotype-phenotype analysis revealed this gene to be significantly associated with grain length, width, and thousand-grain weight. Thus we identified <i>LOC_Os07g15540</i> as the most likely candidate gene. Taken together, our findings provide a basis for functional research on <i>qGV7-2</i>, and broaden our understanding of role of genetic factors in regulating grain volume, thus providing an important resource for yield improvement in rice.