State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China.
BMC Genet. 2020 Nov 26;21(1):133. doi: 10.1186/s12863-020-00952-1.
Due to the diversity of rice varieties and cropping systems in China, the limitation of seeding density and seedling quality makes it hard to improve machine-transplanted efficiency. Previous studies have shown that indica and japonica varieties varied in machine transplanting efficiency and optimal seeding density. In this study, a RIL population derived from '9311' and 'Nipponbare' were performed to explore the seedling traits variations and the genetic mechanism under three seeding densities.
The parents and RIL population exhibited similar trends as the seeding density increased, including seedling height and first leaf sheath length increases, shoot dry weight and root dry weight decreases. Among the 37 QTLs for six traits detected under the three seeding densities, 12 QTLs were detected in both three seeding densities. Five QTL hotspots identified clustered within genomic regions on chromosomes 1, 2, 4, 6 and 11. Specific QTLs such as qRDW and qFLSL were detected under low and high seeding densities, respectively. Detailed analysis the QTL regions identified under specific seeding densities revealed several candidate genes involved in phytohormones signals and abiotic stress responses. Whole-genome additive effects showed that '9311' contributed more loci enhancing trait performances than 'Nipponbare', indicating '9311' was more sensitive to the seeding density than 'Nipponbare'. The prevalence of negative epistasis effects indicated that the complementary two-locus homozygotes may not have marginal advantages over the means of the two parental genotypes.
Our results revealed the differences between indica rice and japonica rice seedling traits in response to seeding density. Several QTL hotspots involved in different traits and specific QTLs (such as qRDW and qFLSL) in diverse seeding densities had been detected. Genome-wide additive and two-locus epistasis suggested a dynamic of the genetic control underlying different seeding densities. It was concluded that novel QTLs, additive and epistasis effects under specific seeding density would provide adequate information for rice seedling improvement during machine transplanting.
由于中国水稻品种和种植制度的多样性，播种密度和秧苗质量的限制使得提高机械移栽效率变得困难。以前的研究表明，籼稻和粳稻品种在机械移栽效率和最佳播种密度上存在差异。本研究利用‘9311’和‘日本晴’构建的 RIL 群体，在三个播种密度下研究了秧苗性状的变化及其遗传机制。
亲本和 RIL 群体表现出相似的趋势，随着播种密度的增加，秧苗高度和第一叶鞘长度增加，地上部干重和根干重降低。在三个播种密度下检测到的 6 个性状的 37 个 QTL 中，有 12 个 QTL 在三个播种密度下都被检测到。在第 1、2、4、6 和 11 号染色体上鉴定到的 5 个 QTL 热点聚集在基因组区域内。在低和高播种密度下分别检测到特定的 QTL，如 qRDW 和 qFLSL。对特定播种密度下鉴定的 QTL 区域进行详细分析，发现了几个参与植物激素信号和非生物胁迫反应的候选基因。全基因组加性效应表明，‘9311’比‘日本晴’贡献了更多增强性状表现的位点，表明‘9311’对播种密度比‘日本晴’更敏感。负上位性效应的普遍存在表明，两个位点的纯合子互补可能没有比两个亲本基因型的平均值有更大的优势。
本研究结果揭示了籼稻和粳稻秧苗对播种密度的响应差异。在不同的播种密度下，检测到涉及不同性状的多个 QTL 热点和特定 QTL（如 qRDW 和 qFLSL）。全基因组加性和两位点上位性表明了不同播种密度下遗传控制的动态变化。研究结果认为，特定播种密度下的新 QTL、加性和上位性效应为机械移栽过程中水稻秧苗的改良提供了充分的信息。
