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.
Highlights
Canola is the world’s second largest oil producing crop after soybean
For the synthesis of unsaturated fatty acids, which are affected by the fatty acid desaturase activity in plant, the fatty acid desaturase genes have been proved as the major genes for the control of oleic acid content as same as the ratio of polyunsaturated fatty acid, we found the important candidate genes of BnaC03g03500D orthologous to Fatty acid desaturase 2 (FAD2) in the distance of 45.18 from Bn-C03-1664875, which is the major enzyme responsible for the synthesis of 18:2 fatty acids in plant endoplasmic reticulum [3], and Fatty acid desaturase-2 (FAD2) gene had been mapped in B. napus on chromosomes A1, A5, C1, and C5 in previous studies [4, 52]
Recent efforts have been made in detecting the genetic loci responsible for fatty acid composition in B. napus based on the Illumina Infinium Brassica 60K SNP array, some genome wide analysis were carried out to identified genomic region and candidate genes associated with fatty acid content in the past few years [26, 27, 31]
Summary
Canola (rapeseed; Brassica napus, AACC genome, 2n = 38) is the world’s second largest oil producing crop after soybean Merrill), cultivated in temperate regions of many countries worldwide, and accounts for 14% of all edible vegetable oil production [1]. The nutritional and healthy oil qualities of canola seed are mostly determined by the fatty acid compositions [2]. Genome wide association study of four important fatty acid composition in Brassica napus 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
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