Crop Cultivation and Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin 150086, China.
Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
Int J Mol Sci. 2020 Feb 14;21(4):1284. doi: 10.3390/ijms21041284.
Among all cereals, rice is highly sensitive to cold stress, especially at the germination stage, which adversely impacts its germination ability, seed vigor, crop stand establishment, and, ultimately, grain yield. The dissection of novel quantitative trait loci (QTLs) or genes conferring a low-temperature germination (LTG) ability can significantly accelerate cold-tolerant rice breeding to ensure the wide application of rice cultivation through the direct seeding method. In this study, we identified 11 QTLs for LTG using 144 recombinant inbred lines (RILs) derived from a cross between a cold-tolerant variety, Lijiangxintuanheigu (LTH), and a cold-sensitive variety, Shennong265 (SN265). By resequencing two parents and RIL lines, a high-density bin map, including 2,828 bin markers, was constructed using 123,859 single-nucleotide polymorphisms (SNPs) between two parents. The total genetic distance corresponding to all 12 chromosome linkage maps was 2,840.12 cm. Adjacent markers were marked by an average genetic distance of 1.01 cm, corresponding to a 128.80 kb physical distance. Eight and three QTL alleles had positive effects inherited from LTH and SN265, respectively. Moreover, a pleiotropic QTL was identified for a higher number of erected panicles and a higher grain number on Chr-9 near the previously cloned gene. Among the LTG QTLs, and were also located at relatively small genetic intervals that define two known LTG genes, and . Sequencing comparisons between the two parents demonstrated that LTH possesses and genes, and SN-265 owns the gene. These comparison results strengthen the accuracy and mapping resolution power of the bin map and population. Later, fine mapping was done for at 45.80 kb through four key homozygous recombinant lines derived from a population with 1569 segregating plants. Finally, was identified as the most possible candidate gene for , which contains a missense mutation and a 32-bp deletion/insertion at the promoter between the two parents. LTH was observed to have lower expression levels in comparison with SN265 and was commonly detected at low temperatures. In conclusion, these results strengthen our understanding of the impacts of cold temperature stress on seed vigor and germination abilities and help improve the mechanisms of rice breeding programs to breed cold-tolerant varieties.
在所有谷物中，水稻对冷胁迫高度敏感，尤其是在发芽阶段，这会对其发芽能力、种子活力、作物群体建立产生不利影响，最终影响谷物产量。解析赋予低温发芽（LTG）能力的新数量性状位点（QTL）或基因可以显著加速耐冷水稻的培育，确保通过直播方法广泛应用水稻种植。在这项研究中，我们使用 144 个重组自交系（RIL），这些 RIL 是由一个耐冷品种丽江新团黑谷（LTH）和一个对冷敏感的品种神农 265（SN265）杂交产生的，鉴定出了 11 个 LTG 的 QTL。通过对两个亲本和 RIL 系进行重测序，使用两个亲本之间的 123859 个单核苷酸多态性（SNP）构建了一个高密度 bin 图谱，该图谱包含 2828 个 bin 标记。所有 12 条染色体连锁图谱的总遗传距离为 2840.12cm。相邻标记的平均遗传距离为 1.01cm，对应于 128.80kb 的物理距离。来自 LTH 和 SN265 的分别有 8 个和 3 个 QTL 等位基因具有正向效应。此外，在 9 号染色体上靠近先前克隆的 基因附近，鉴定出一个具有更多直立穗和更高粒数的多效性 QTL。在 LTG QTL 中，和 也位于相对较小的遗传区间内，这些区间定义了两个已知的 LTG 基因 和 。两个亲本之间的测序比较表明，LTH 具有 和 基因，而 SN-265 则拥有 基因。这些比较结果增强了 bin 图谱和群体的准确性和映射分辨率能力。后来，通过来自包含 1569 个分离植物的群体的四个关键纯合重组系，在 45.80kb 处对 进行了精细作图。最终，在两个亲本之间的启动子中发现了一个错义突变和一个 32-bp 的缺失/插入，将 鉴定为 最有可能的候选基因，其包含一个错义突变和一个 32-bp 的缺失/插入。与 SN265 相比，LTH 的表达水平较低，并且在低温下普遍检测到。总之，这些结果加强了我们对低温胁迫对种子活力和发芽能力的影响的理解，并有助于提高水稻育种计划的机制，以培育耐冷品种。
