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

Zhiguang Sun ¹ Hongzhou An ² Zeyu Qiu ^3* Jingfang Li ¹ Jian Li ¹ Bo Yang ¹ Jinbo Liu ¹ Tingmu Chen ¹ Yuqin Zhang ¹ Baiguan Lu ¹ Yan Liu ^1* Baoxiang Wang ^1* Da Yong Xu ¹

• ¹ Lianyungang Academy of Agricultural Sciences (JAAS), Lianyungang, China
• ² Hebei Academy of Agriculture and Forestry Sciences (HAAFS), Shijiazhuang, Hebei Province, China
• ³ Jiangsu Academy of Agricultural Sciences (JAAS), Nanjing, Jiangsu Province, China

Grain volume is a key agronomic trait that affects yield and quality of rice, yet the molecular mechanism is still not fully understood. In this study, a mapping population of Ludao (weedy rice) and Guangbaixiangzhan (GBXZ) was developed in Lianyungang, Jiangsu province, China, and was employed to construct a high-density genetic map by use of the RICE 1 K mGPS chip in 2021. As a result, 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, qGV4-2, qGV7-1, and qGV7-2, were newly identified. The major QTL, qGV7-2, 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 qGV7-2, a candidate gene (LOC_Os07g15540), 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 LOC_Os07g15540 as the most likely candidate gene. Our findings provide a basis for functional research on qGV7-2.