Fine mapping and candidate gene analysis of qRN5a, a novel QTL promoting root number in rice under low potassium.

KEY MESSAGE: qRN5a, a novel QTL for increasing root number under low K in rice, was fine mapped to a 48.8-kb region on chromosome 5, and LOC_Os05g27980 is the most likely candidate gene. Potassium (K) is a mineral nutrient essential for plant growth and development, but the molecular mechanism for low-K (LK) tolerance in rice remains poorly understood. In our previous study, the quantitative trait locus (QTL) qRN5a for root number (RN) under LK was identified in the chromosome segment substitution line CSSL35 carrying segments from XieqingzaoB in the genetic background of Zhonghui9308 (ZH9308). CSSL35 developed more roots than ZH9308 under LK at the seedling stage, and qRN5a was initially located within a 1,023-kb genomic region. In this study, to understand the molecular basis of qRN5a, a large F2:3 (BC5F2:3) population obtained from crossing CSSL35 and ZH9308 was constructed for fine mapping. High-resolution linkage analysis narrowed down qRN5a to a 48.8-kb interval flanked by markers A99 and A139. Seven putative candidate genes were annotated in the delimited region, and three genes (Os05g0346700, LOC_Os05g27980, and LOC_Os05g28000) had nonsynonymous single-nucleotide polymorphisms in the coding sequence between the two parents. Expression analysis suggests that LOC_Os05g27980, which encodes a LATERAL ORGAN BOUNDARIES domain-containing protein, is a positive regulator of RN under LK and is the most likely candidate gene for qRN5a. Moreover, we found that qRN5a promotes expression of OsIAA23 and represses OsHAK5 expression in root tissues to promote root initiation in CSSL35 under LK conditions. Additional investigations on OsHAK5 in rice are needed to elucidate the basis of changing root architecture under different K+ concentrations. qRN5a is useful for marker-assisted selection to develop an ideotype with improved root architecture in rice under K deficiency.