Deng Xiaoshu, Gan Lu, Liu Yan, Luo Ancai, Jin Liang, Chen Jiao, Tang Ruyu, Lei Lixia, Tang Jianghong, Zhang Jiani, Zhao Zhengwu
Chongqing Normal University/Chongqing Engineering Research Center of Specialty Crop Resources, Chongqing, 401331, China.
Chongqing University, Chongqing, 401331, China.
Genes Genomics. 2018 Dec;40(12):1351-1361. doi: 10.1007/s13258-018-0731-z. Epub 2018 Aug 31.
A new cold tolerant germplasm resource named glutinous rice 89-1 (Gr89-1, Oryza sativa L.) can overwinter using axillary buds, with these buds being ratooned the following year. The overwintering seedling rate (OSR) is an important factor for evaluating cold tolerance. Many quantitative trait loci (QTLs) controlling cold tolerance at different growth stages in rice have been identified, with some of these QTLs being successfully cloned. However, no QTLs conferring to the OSR trait have been located in the perennial O. sativa L. To identify QTLs associated with OSR and to evaluate cold tolerance. 286 F recombinant inbred lines (RILs) derived from a cross between the cold tolerant variety Gr89-1 and cold sensitive variety Shuhui527 (SH527) were used. A total of 198 polymorphic simple sequence repeat (SSR) markers that were distributed uniformly on 12 chromosomes were used to construct the linkage map. The gene ontology (GO) annotation of the major QTL was performed through the rice genome annotation project system. Three main-effect QTLs (qOSR2, qOSR3, and qOSR8) were detected and mapped on chromosomes 2, 3, and 8, respectively. These QTLs were located in the interval of RM14208 (35,160,202 base pairs (bp))-RM208 (35,520,147 bp), RM218 (8,375,236 bp)-RM232 (9,755,778 bp), and RM5891 (24,626,930 bp)-RM23608 (25,355,519 bp), and explained 19.6%, 9.3%, and 11.8% of the phenotypic variations, respectively. The qOSR2 QTL displayed the largest effect, with a logarithm of odds score (LOD) of 5.5. A total of 47 candidate genes on the qOSR2 locus were associated with 219 GO terms. Among these candidate genes, 11 were related to cell membrane, 7 were associated with cold stress, and 3 were involved in response to stress and biotic stimulus. OsPIP1;3 was the only one candidate gene related to stress, biotic stimulus, cold stress, and encoding a cell membrane protein. After QTL mapping, a total of three main-effect QTLs-qOSR2, qOSR3, and qOSR8-were detected on chromosomes 2, 3, and 8, respectively. Among these, qOSR2 explained the highest phenotypic variance. All the QTLs elite traits come from the cold resistance parent Gr89-1. OsPIP1;3 might be a candidate gene of qOSR2.
一种名为糯米89 - 1（Gr89 - 1，水稻）的新型耐冷种质资源能够利用腋芽越冬，这些腋芽次年可进行再生。越冬成苗率（OSR）是评估耐冷性的一个重要因素。已鉴定出许多控制水稻不同生长阶段耐冷性的数量性状基因座（QTL），其中一些QTL已成功克隆。然而，在多年生水稻中尚未定位到与OSR性状相关的QTL。为了鉴定与OSR相关的QTL并评估耐冷性，使用了由耐冷品种Gr89 - 1和冷敏感品种蜀恢527（SH527）杂交产生的286个F重组自交系（RIL）。总共198个均匀分布在12条染色体上的多态性简单序列重复（SSR）标记用于构建连锁图谱。通过水稻基因组注释项目系统对主要QTL进行基因本体（GO）注释。检测到三个主效QTL（qOSR2、qOSR3和qOSR8），分别定位在第2、3和8号染色体上。这些QTL位于RM14208（35,160,202碱基对（bp）） - RM208（35,520,147 bp）、RM218（8,375,236 bp） - RM232（9,755,778 bp）和RM5891（24,626,930 bp） - RM23608（25,355,519 bp）区间内，分别解释了19.6%、9.3%和11.8%的表型变异。qOSR2 QTL表现出最大效应，其对数似然比分数（LOD）为5.5。qOSR2基因座上共有47个候选基因与219个GO术语相关。在这些候选基因中，11个与细胞膜相关，7个与冷胁迫相关，3个参与对胁迫和生物刺激的响应。OsPIP1;3是唯一与胁迫、生物刺激、冷胁迫相关且编码细胞膜蛋白的候选基因。经过QTL定位，分别在第2、3和8号染色体上检测到三个主效QTL——qOSR2、qOSR3和qOSR8。其中，qOSR2解释的表型变异最高。所有QTL的优良性状均来自抗寒亲本Gr89 - 1。OsPIP1;3可能是qOSR2的一个候选基因。
