Fine mapping and candidate gene analysis of qRN5a , a novel QTL promoting root number in rice under low potassium
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ORIGINAL ARTICLE
Fine mapping and candidate gene analysis of qRN5a, a novel QTL promoting root number in rice under low potassium Anowerul Islam1,2 · Yingxin Zhang1 · Galal Anis1,3 · Mohammad Hasanuzzaman Rani1,4 · Workie Anley1,5 · Qinqin Yang1 · Ling Liu1 · Xihong Shen1 · Liyong Cao1 · Shihua Cheng1 · Weixun Wu1 Received: 23 March 2020 / Accepted: 18 September 2020 © Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract 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. Abstract 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 F 2:3 (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.
Introduction
Communicated by Matthias Wissuwa. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00122-020-03692-z) contains supplementary material, which is available to authorized users. * Shihua Cheng [email protected] * Weixun Wu [email protected] 1
China National Center for Rice Improvement and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
Department of Agricultural Extension, Ministry of Agriculture, Dhaka 1215, Bangladesh
2
Rice (Oryza sativa L.) is one of the most important cereal grains globally, but especially in Asia, where it is a staple food and the main pillar of food securi
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