National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China.
Mol Plant. 2021 Mar 1;14(3):470-487. doi: 10.1016/j.molp.2020.12.003. Epub 2020 Dec 10.
Seed oil content (SOC) is a highly important and complex trait in oil crops. Here, we decipher the genetic basis of natural variation in SOC of Brassica napus by genome- and transcriptome-wide association studies using 505 inbred lines. We mapped reliable quantitative trait loci (QTLs) that control SOC in eight environments, evaluated the effect of each QTL on SOC, and analyzed selection in QTL regions during breeding. Six-hundred and ninety-two genes and four gene modules significantly associated with SOC were identified by analyzing population transcriptomes from seeds. A gene prioritization framework, POCKET (prioritizing the candidate genes by incorporating information on knowledge-based gene sets, effects of variants, genome-wide association studies, and transcriptome-wide association studies), was implemented to determine the causal genes in the QTL regions based on multi-omic datasets. A pair of homologous genes, BnPMT6s, in two QTLs were identified and experimentally demonstrated to negatively regulate SOC. This study provides rich genetic resources for improving SOC and valuable insights toward understanding the complex machinery that directs oil accumulation in the seeds of B. napus and other oil crops.
种子含油量（SOC）是油料作物的一个重要且复杂的特性。在这里，我们通过使用 505 个自交系进行全基因组和转录组关联研究，解析了甘蓝型油菜 SOC 自然变异的遗传基础。我们在八个环境中定位了可靠的控制 SOC 的数量性状位点（QTL），评估了每个 QTL 对 SOC 的影响，并分析了在育种过程中 QTL 区域的选择。通过分析来自种子的群体转录组，鉴定了 692 个与 SOC 显著相关的基因和四个基因模块。基于多组学数据集，通过实施一个名为 POCKET（通过整合基于知识的基因集信息、变体效应、全基因组关联研究和转录组关联研究来优先考虑候选基因）的基因优先级框架，确定了 QTL 区域中的因果基因。在两个 QTL 中鉴定了一对同源基因 BnPMT6s，它们被实验证明可负调控 SOC。这项研究为提高 SOC 提供了丰富的遗传资源，并为理解指导油菜和其他油料作物种子中油脂积累的复杂机制提供了有价值的见解。
