Han Xu, Tang Qingqing, Xu Liping, Guan Zhilin, Tu Jinxing, Yi Bin, Liu Kede, Yao Xuan, Lu Shaoping, Guo Liang
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
Hubei Hongshan Laboratory, Wuhan, China.
Front Plant Sci. 2022 Nov 21;13:1065766. doi: 10.3389/fpls.2022.1065766. eCollection 2022.
Flowering time is strongly related to the environment, while the genotype-by-environment interaction study for flowering time is lacking in . Here, a total of 11,700,689 single nucleotide polymorphisms in 490 accessions were used to associate with the flowering time and related climatic index in eight environments using a compressed variance-component mixed model, 3VmrMLM. As a result, 19 stable main-effect quantitative trait nucleotides (QTNs) and 32 QTN-by-environment interactions (QEIs) for flowering time were detected. Four windows of daily average temperature and precipitation were found to be climatic factors highly correlated with flowering time. Ten main-effect QTNs were found to be associated with these flowering-time-related climatic indexes. Using differentially expressed gene (DEG) analysis in semi-winter and spring oilseed rapes, 5,850 and 5,511 DEGs were found to be significantly expressed before and after vernalization. Twelve and 14 DEGs, including 7 and 9 known homologs in , were found to be candidate genes for stable QTNs and QEIs for flowering time, respectively. Five DEGs were found to be candidate genes for main-effect QTNs for flowering-time-related climatic index. These candidate genes, such as s, s, , and , were further validated by the haplotype, selective sweep, and co-expression networks analysis. The candidate genes identified in this study will be helpful to breed varieties adapted to particular environments with optimized flowering time.
开花时间与环境密切相关，然而目前缺乏对开花时间的基因型与环境互作研究。在此，利用压缩方差成分混合模型3VmrMLM，对490份材料中总共11700689个单核苷酸多态性与8种环境下的开花时间及相关气候指数进行关联分析。结果，检测到19个稳定的主效应数量性状核苷酸（QTN）和32个开花时间的QTN与环境互作（QEI）。发现日平均温度和降水量的四个窗口是与开花时间高度相关的气候因子。发现10个主效应QTN与这些开花时间相关的气候指数有关。通过对半冬性和春性油菜进行差异表达基因（DEG）分析，发现5850个和5511个DEG在春化前后有显著表达。分别发现12个和14个DEG，包括7个和9个已知同源基因，分别是开花时间稳定QTN和QEI的候选基因。发现5个DEG是开花时间相关气候指数主效应QTN的候选基因。这些候选基因，如s、s、和，通过单倍型、选择清除和共表达网络分析进一步验证。本研究中鉴定的候选基因将有助于培育具有优化开花时间、适应特定环境的品种。
