Journal Article

Structural variations and environmental specificities of flowering time-related genes in Brassica napus

Guo, Yuan, Wang, Ruisen, Lu, Yunhai, Chen, Mingxun, Cen, Haiyan, Wu, Dezhi, Dong, Jie, Jiang, Lixi, Xu, Ying, Zhu, Yang, Yao, Xiangtan, Chen, Xiaoyang, Yan, Tao, Kong, Xiangdong

2023

Overview

Key messageWe 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.

• Publisher: Springer Nature B.V
• Subject: Brassica napus / Ecotypes / Flowering / Gene polymorphism / Genome-wide association studies / Genomes / Life cycles / Oilseeds / Polymorphism / Population genetics / Rape plants / Single-nucleotide polymorphism / Winter