Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Xinjiang Academy of Agricultural and Reclamation Science, Shihezi 832000, China.
Plant Sci. 2021 Mar;304:110797. doi: 10.1016/j.plantsci.2020.110797. Epub 2020 Dec 14.
Maize is one of the most broadly cultivated crops throughout the world, and flowering time is a major adaptive trait for its diffusion. The biggest challenge in understanding maize flowering genetic architecture is that the trait is confounded with population structure. To eliminate the effect, we revisited the flower time genetic network by using a tropical maize population Pop32, which was under mass selection for adaptation to early flowering time in China for six generations from tropical to temperate regions. The days to anthesis (DTA) of the initial (Pop32C0), intermedia (Pop32C3), and final population (Pop32C5) was 90.77, 84.63, and 79.72 days on average, respectively. To examine the genetic mechanism and identify the genetic loci underlying this rapid change in flowering time of Pop32, we bulked 30 individuals from C0, C3, and C5 to conduct the whole genome sequencing. And we finally identified 4,973,810 high-quality single nucleotide polymorphisms (SNPs) and 6,517 genes with allele frequency significantly changed during the artificial improvement process. We speculate that these genes might participate in the adaptive improvement process and control flowering time. To identify the candidate genes for flowering time from the gene set with allele frequency changed, we carried out weighted gene co-expression network analysis (WGCNA), and identified four co-expression modules that highly associated with the flowering time development, as well as constructed the co-expression network of key flowering time genes. Gene Ontology (GO) enrichment analysis revealed that the GO terms photosynthesis/light reaction, carbohydrate binding, auxin mediated signaling pathway, response to temperature stimulus that are closely connected with flowering time. Furthermore, targeted GWAS revealed the genes are significantly connected with the flowering time. qRT-PCR of four candidate genes GRMZM2G019879, GRMZM2G055905, GRMZM2G058158, and GRMZM2G171365 showed that their expression level is similar to the flowering time genes, which playing a key role in maize flowering time transition. This study revealed that the changes of flowering time in mass selection process may be strongly associated with the variations of allele frequency changes, and we identified some important candidate genes for flowering time, which will provide a new insight for the rapid improvement of maize important agronomic traits and promote the gene cloning of maize flowering time.
玉米是世界上种植最广泛的作物之一，开花时间是其扩散的主要适应性特征。理解玉米开花遗传结构的最大挑战是该特征与群体结构混淆。为了消除这种影响，我们重新研究了通过使用热带玉米群体 Pop32 的花时间遗传网络，该群体在从热带到温带的六个世代中经历了大规模选择，以适应早期开花时间。初始群体（Pop32C0）、中间群体（Pop32C3）和最终群体（Pop32C5）的开花期（DTA）平均值分别为 90.77、84.63 和 79.72 天。为了研究遗传机制并鉴定 Pop32 开花时间快速变化背后的遗传位点，我们将 30 个个体从 C0、C3 和 C5 中进行了批量测序。最终鉴定出 4973810 个高质量的单核苷酸多态性（SNP）和 6517 个等位基因频率在人工改良过程中发生显著变化的基因。我们推测这些基因可能参与适应性改良过程并控制开花时间。为了从等位基因频率发生变化的基因集中鉴定出开花时间的候选基因，我们进行了加权基因共表达网络分析（WGCNA），并鉴定出与开花时间发育高度相关的四个共表达模块，以及构建了关键开花时间基因的共表达网络。GO 富集分析表明，GO 术语光合作用/光反应、碳水化合物结合、生长素介导的信号通路、对温度刺激的反应与开花时间密切相关。此外，靶向 GWAS 显示这些基因与开花时间显著相关。四个候选基因 GRMZM2G019879、GRMZM2G055905、GRMZM2G058158 和 GRMZM2G171365 的 qRT-PCR 结果表明，它们的表达水平与开花时间基因相似，在玉米开花时间的转变中起着关键作用。本研究表明，大规模选择过程中开花时间的变化可能与等位基因频率变化的变化密切相关，我们鉴定出一些开花时间的重要候选基因，这将为玉米重要农艺性状的快速改良提供新的见解，并促进玉米开花时间基因的克隆。
