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

Frank You,Zhen Yao,Sylvie Cloutier,Gaofeng Jia,Pingchuan Li,Jin Xiao,Santosh Kumar,Braulio Soto-Cerda,Helen Booker,Scott Duguid,Khalid Rashid,Liqiang He

doi:10.3390/ijms19082303

Abstract

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.

Highlights

Flax (Linum usitatissimum L., 2n = 2x = 30) is a self-pollinating annual crop from the Linaceae family
71.1% of all single nucleotide polymorphism (SNP) were located in intergenic regions, 16.2% were in introns and 12.7% were in exons (Table S2)
Using the best linear unbiased prediction (BLUP) values of phenotyping data collected from six to eight year/location environments with both generalized linear model (GLM) and mixed linear model (MLM), we identified a total of 33 quantitative trait loci (QTL) for 11 traits, one for YLD, eight for oil content (OIL), five for plant height (PLH), four for PAL, three each for iodine value (IOD), LIO, and LIN, two each for days to maturity (DTM) and STE, and one each for protein content (PRO) and OLE (Table 3, Figure 1, Figures S1 and S2)

Summary

Introduction

Flax (Linum usitatissimum L., 2n = 2x = 30) is a self-pollinating annual crop from the Linaceae family. It is a dual-purpose crop grown for its seed oil or stem fiber, resulting in two morphotypes: linseed and fiber. Linseed breeding has focused on high seed yield (YLD), high oil content (OIL), and either high or low LIN content. Low LIN (2–4%) and high LIO (65–70%) lines have been developed through mutation breeding. Since 1910, a total of 82 flax cultivars have been released in Canada [5] These cultivars and elite breeding lines provide diverse genetic materials for dissecting the genetic architecture of oil biosynthesis and yield related traits in linseed

Methods

Results

Conclusion