Integration of GWAS and transcriptome analyses to identify SNPs and candidate genes for aluminum tolerance in rapeseed (Brassica napus L.)

• Published in: BMC plant biology Vol. 22; no. 1; p. 130
• Main Authors: Zhou, Huiwen, Xiao, Xiaojun, Asjad, Ali, Han, Depeng, Zheng, Wei, Xiao, Guobin, Huang, Yingjin, Zhou, Qinghong
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 21.03.2022; BioMed Central; BMC
• Subjects: Abscisic acid; Acidic soils; Adaptation, Physiological - genetics; Aluminum; Aluminum - toxicity; Aluminum in the body; Analysis; Association analysis; Barley; Brassica; Brassica napus; Brassica napus - genetics; Brassica napus - physiology; Candidate gene; Cell walls; Chromosomes; Crop development; Crops; Crops, Agricultural - genetics; Crops, Agricultural - physiology; Elongation; Environmental stress; Gene Expression Profiling; Gene Expression Regulation, Plant; Gene loci; Gene mapping; Genes; Genes, Plant; Genetic aspects; Genetic diversity; Genetic Variation; Genome-Wide Association Study; Genomes; Genotype; Health aspects; Inbreeding; Integration; Metabolism; Molecular modelling; Oxidation; Phenotype; Physiological aspects; Plant toxins; Pollution tolerance; Polymorphism, Single Nucleotide; Proteins; Quantitative trait loci; Rape (Plant); Rape plants; Rapeseed; Ribonucleic acid; RNA; Seedlings; Signal transduction; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Toxicity; Transcriptomes; Transcriptomic analysis; Australia; China; Brassica napus; Candidate gene; Genome-wide association study; Transcriptomic analysis; Aluminum
• ISSN: 1471-2229; 1471-2229
• DOI: 10.1186/s12870-022-03508-w

The exchangeable aluminum (Al), released from the acid soils, is another addition to the environmental stress factors in the form of Al toxicity stress. Al stress affects the normal crop development and reduces the overall yield of rapeseed (Brassica napus L.). The response mechanism of plants to Al toxicity is complicated and difficult to understand with few QTL related studies in rapeseed under Al toxicity stress. Using 200,510 SNPs developed by SLAF-seq (specific-locus amplified fragment sequencing) technology, we carried out the genome-wide association analysis (GWAS) in a population of 254 inbred lines of B. napus with large genetic variation and Al-tolerance differences. There were 43 SNPs significantly associated with eight Al-tolerance traits in the seedling stage were detected on 14 chromosomes, and 777 candidate genes were screened at the flanking 100 kb region of these SNPs. Moreover, RNA-seq detected 8291 and 5341 DEGs (the differentially expressed gene) in the Al -tolerant line (ATL) and -sensitive line (ASL), respectively. Based on integration of GWAS and RNA-seq analysis, 64 candidate genes from GWAS analysis differentially expressed at least once in 6 h vs 0 h or 24 h vs 0 h conditions in ATL or ASL. Moreover, four out of sixty-four candidate genes (BnaA03g30320D, BnaA10g11500D, BnaC03g38360D and BnaC06g30030D) were differentially expressed in both 6 h and 24 h compared to 0 h (control) conditions in both lines. The proposed model based on the candidate genes excavated in this study highlighted that Al stress disturb the oxidation-redox balance, causing abnormal synthesis and repair of cell wall and ABA signal transduction, ultimately resulting in inhibition of root elongation. The integration of GWAS and transcriptome analysis provide an effective strategy to explore the SNPs and candidate genes, which has a potential to develop molecular markers for breeding Al tolerant rapeseed varieties along with theoretical basis of molecular mechanisms for Al toxicity response of Brassica napus plants.