Genome-Wide Association Study and Selection Signatures Detect Genomic Regions Associated with Seed Yield and Oil Quality in Flax

• Published in: International journal of molecular sciences Vol. 19; no. 8; p. 2303
• Main Authors: You, Frank M, Xiao, Jin, Li, Pingchuan, Yao, Zhen, Jia, Gaofeng, He, Liqiang, Kumar, Santosh, Soto-Cerda, Braulio, Duguid, Scott D, Booker, Helen M, Rashid, Khalid Y, Cloutier, Sylvie
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 06-08-2018; MDPI
• Subjects: bi-parental population; fatty acid composition; Flax; Gene loci; Gene mapping; Genetic structure; Genome-wide association studies; genome-wide association study (GWAS); Genomes; Genotype & phenotype; genotyping by sequencing (GBS); Iodine; maturity; Oilseeds; Phenotypic variations; plant height; Quantitative trait loci; seed yield; selective sweep; single nucleotide polymorphism (SNP); Single-nucleotide polymorphism; flax; genotyping by sequencing (GBS); maturity; fatty acid composition; seed yield; single nucleotide polymorphism (SNP); selective sweep; genome-wide association study (GWAS); bi-parental population; plant height
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms19082303

A genome-wide association study (GWAS) was performed on a set of 260 lines which belong to three different bi-parental flax mapping populations. These lines were sequenced to an averaged genome coverage of 19× using the Illumina Hi-Seq platform. Phenotypic data for 11 seed yield and oil quality traits were collected in eight year/location environments. A total of 17,288 single nucleotide polymorphisms were identified, which explained more than 80% of the phenotypic variation for days to maturity (DTM), iodine value (IOD), palmitic (PAL), stearic, linoleic (LIO) and linolenic (LIN) acid contents. Twenty-three unique genomic regions associated with 33 quantitative trait loci (QTL) for the studied traits were detected, thereby validating four genomic regions previously identified. The 33 QTL explained 48⁻73% of the phenotypic variation for oil content, IOD, PAL, LIO and LIN but only 8⁻14% for plant height, DTM and seed yield. A genome-wide selective sweep scan for selection signatures detected 114 genomic regions that accounted for 7.82% of the flax pseudomolecule and overlapped with the 11 GWAS-detected genomic regions associated with 18 QTL for 11 traits. The results demonstrate the utility of GWAS combined with selection signatures for dissection of the genetic structure of traits and for pinpointing genomic regions for breeding improvement.