Xu Ying, Kong Xiangdong, Guo Yuan, Wang Ruisen, Yao Xiangtan, Chen Xiaoyang, Yan Tao, Wu Dezhi, Lu Yunhai, Dong Jie, Zhu Yang, Chen Mingxun, Cen Haiyan, Jiang Lixi
Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China.
Jiguang Gene Biotechnology Co., Ltd., Nanjing, 210000, China.
Theor Appl Genet. 2023 Mar 10;136(3):42. doi: 10.1007/s00122-023-04326-w.
We found that the flowering time order of accessions in a genetic population considerably varied across environments, and homolog copies of essential flowering time genes played different roles in different locations. Flowering time plays a critical role in determining the life cycle length, yield, and quality of a crop. However, the allelic polymorphism of flowering time-related genes (FTRGs) in Brassica napus, an important oil crop, remains unclear. Here, we provide high-resolution graphics of FTRGs in B. napus on a pangenome-wide scale based on single nucleotide polymorphism (SNP) and structural variation (SV) analyses. A total of 1337 FTRGs in B. napus were identified by aligning their coding sequences with Arabidopsis orthologs. Overall, 46.07% of FTRGs were core genes and 53.93% were variable genes. Moreover, 1.94%, 0.74%, and 4.49% FTRGs had significant presence-frequency differences (PFDs) between the spring and semi-winter, spring and winter, and winter and semi-winter ecotypes, respectively. SNPs and SVs across 1626 accessions of 39 FTRGs underlying numerous published qualitative trait loci were analyzed. Additionally, to identify FTRGs specific to an eco-condition, genome-wide association studies (GWASs) based on SNP, presence/absence variation (PAV), and SV were performed after growing and observing the flowering time order (FTO) of plants in a collection of 292 accessions at three locations in two successive years. It was discovered that the FTO of plants in a genetic population changed a lot across various environments, and homolog copies of some key FTRGs played different roles in different locations. This study revealed the molecular basis of the genotype-by-environment (G × E) effect on flowering and recommended a pool of candidate genes specific to locations for breeding selection.
我们发现，遗传群体中不同材料的开花时间顺序在不同环境下有很大差异，且开花时间关键基因的同源拷贝在不同地点发挥着不同作用。开花时间对决定作物的生命周期长度、产量和品质起着关键作用。然而，重要油料作物甘蓝型油菜中开花时间相关基因（FTRGs）的等位基因多态性仍不清楚。在此，我们基于单核苷酸多态性（SNP）和结构变异（SV）分析，在全基因组范围内提供了甘蓝型油菜FTRGs的高分辨率图谱。通过将其编码序列与拟南芥直系同源基因比对，共鉴定出甘蓝型油菜中的1337个FTRGs。总体而言，46.07%的FTRGs为核心基因，53.93%为可变基因。此外，分别有1.94%、0.74%和4.49%的FTRGs在春性与半冬性、春性与冬性、冬性与半冬性生态型之间存在显著的存在频率差异（PFDs）。分析了39个FTRGs在1626份材料中的SNP和SV，这些FTRGs位于众多已发表的质量性状位点之下。此外，为了鉴定特定生态条件下的FTRGs，在连续两年于三个地点对292份材料的植株进行开花时间顺序（FTO）的生长观察后，基于SNP、存在/缺失变异（PAV）和SV进行了全基因组关联研究（GWAS）。研究发现，遗传群体中植株的FTO在不同环境下变化很大，一些关键FTRGs的同源拷贝在不同地点发挥着不同作用。本研究揭示了开花的基因型×环境（G×E）效应的分子基础，并推荐了一批特定地点的候选基因用于育种选择。
