Genome-wide association studies and transcriptome analysis reveal novel genes associated with freezing tolerance in rapeseed (Brassica napus L.)

• Published in: PloS one Vol. 20; no. 5; p. e0322547
• Main Authors: Zheng, Guoqiang, Liu, Zigang, Jiang, Lixi, Yang, Qi, Wei, Jiaping, Wu, Zefeng, Cui, Junmei, Dong, Xiaoyun, Cao, Xiaodong, Yang, Xuezhen, Wang, Ying, Gong, Yongjie, Sa, Ermei, Wang, Xiaoxia
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 27.05.2025; Public Library of Science (PLoS)
• Subjects: Analysis; Antifreeze proteins; Biology and Life Sciences; Brassica; Brassica napus; Brassica napus - genetics; Brassica napus - physiology; Cold tolerance; Cultivars; Ecology and Environmental Sciences; Electrolyte leakage; Freezing; Gene Expression Profiling; Gene Expression Regulation, Plant; Genes; Genes, Plant; Genetic aspects; Genome-wide association studies; Genome-Wide Association Study; Genomes; Geographical distribution; Germplasm; Hardiness; Homeostasis; Lipid metabolism; Lipids; Metabolism; Peroxidase; Physical Sciences; Plant Proteins - genetics; Plants; Polymorphism, Single Nucleotide; Proteins; Rape (Plant); Rape plants; Rapeseed; Reactive oxygen species; Ribonucleic acid; RNA; RNA sequencing; Single-nucleotide polymorphism; Software; Transcriptome; Transcriptomes; China
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0322547

Freezing stress is the main obstacle affecting the geographical distribution, growth, development, quality, and productivity of rapeseed ( Brassica napus ) in northern China. However, there is a little knowledge of rapeseed freezing tolerance mechanism. Here, 289 core germplasms collected from 36 countries were used to identify SNPs associated with freezing tolerance. We used RNA-seq data to narrow down the candidate genes identified by genome-wide association studies. The frequency distributions of phenotypic values and best linear unbiased estimates (BLUE) values for each trait conform to normal or approximately normal distributions, with good repeatability across various locations. The results showed that 594, 513, 7, and 45 SNPs were significantly associated with malondialdehyde, peroxidase, soluble protein, and relative electrolyte leakage, respectively. Based on these significantly associated SNPs, we identified 4,998 associated genes. Crossover analysis indicated that 73 genes were overlapped between GWAS and RNA-seq datasets, and 13 candidate genes involved in transmission and perception of freeze stress signals, lipid metabolism, reactive oxygen species (ROS) homeostasis, antifreeze proteins synthesis, and other metabolic processes. These results reveal novel genes associated with freezing tolerance in rapeseed, and provide a basis for further research and improvement of freezing tolerance in rapeseed.