Identification of SNP loci and candidate genes related to four important fatty acid composition in Brassica napus using genome wide association study

Qianglong Zhu; Graham J King; Xingyue Liu; Nan Shan; Priyakshee Borpatragohain; Abdul Baten; Putao Wang; Sha Luo; Qinghong Zhou

doi:10.1371/journal.pone.0221578

Identification of SNP loci and candidate genes related to four important fatty acid composition in Brassica napus using genome wide association study

PLoS One. 2019 Aug 23;14(8):e0221578. doi: 10.1371/journal.pone.0221578. eCollection 2019.

Authors

Qianglong Zhu¹, Graham J King², Xingyue Liu¹, Nan Shan¹, Priyakshee Borpatragohain², Abdul Baten², Putao Wang¹, Sha Luo¹, Qinghong Zhou¹

Affiliations

¹ Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, China.
² Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia.

Abstract

Rapeseed oil (canola, Brassica napus L.) is an important healthy vegetable oil throughout the world, the nutritional and economical value of which largely depends on its seed fatty acid composition. In this study, based on 201,187 SNP markers developed from the SLAF-seq (specific locus amplified fragment sequencing), a genome wide association study of four important fatty acid content traits (erucic acid, oleic acid, linoleic acid and linolenic acid) in a panel of 300 inbred lines of rapeseed in two environments (JXAU and JXRIS) was carried out. A total of 148 SNP loci significantly associated with these traits were detected by MLM model analysis respectively, and 30 SNP loci on A08 and C03 chromosomes were detected in three traits of erucic acid, oleic acid and linoleic acid contents simultaneously. Furthermore, 108 highly favorable alleles for increasing oleic acid and linoleic acid content, also for decreasing erucic acid content simultaneously were observed. By a basic local alignment search tool (BLAST) search with in a distance of 100 Kb around these significantly SNP-trait associations, we identified 20 orthologs of the functional candidate genes related to fatty acid biosynthesis, including the known vital fatty acid biosynthesis genes of BnaA.FAE1 and BnaC. FAE1 on the A08 and C03 chromosomes, and other potential candidate genes involving in the fatty acid biosynthesis pathway, such as the orthologs genes of FAD2, LACS09, KCS17, CER4, TT16 and ACBP5. This study lays a basis for uncovering the genetic variations and the improvement of fatty acid composition in B. napus.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Brassica napus / genetics*
Ecotype
Fatty Acids / metabolism*
Gene Expression Regulation, Plant
Genes, Plant*
Genetic Loci*
Genome-Wide Association Study*
Phenotype
Polymorphism, Single Nucleotide / genetics*
Quantitative Trait, Heritable

Substances

Fatty Acids

Grants and funding

This work was supported by the National Science Foundation of China project “Exploration of SNP loci and vital candidate genes related to Aluminum tolerance of Brassica napus by combining genome-wide association study and RNA-sequencing analysis”, project number 31860392. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.