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Int. J. Mol. Sci. 2018, 19(8), 2303; https://doi.org/10.3390/ijms19082303

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

1
Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
2
Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada
3
Department of Agronomy, Nanjing Agricultural University, Nanjing 210095, China
4
Crop Development Centre, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
5
Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB R7A 5Y3, Canada
6
Department of Plant Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
7
Agriaquaculture Nutritional Genomic Center, CGNA, Temuco 4871158, Chile
*
Authors to whom correspondence should be addressed.
Received: 20 July 2018 / Revised: 2 August 2018 / Accepted: 3 August 2018 / Published: 6 August 2018
(This article belongs to the Special Issue Plant Genomics)
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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. View Full-Text
Keywords: flax; genome-wide association study (GWAS); selective sweep; genotyping by sequencing (GBS); bi-parental population; single nucleotide polymorphism (SNP); seed yield; plant height; maturity; fatty acid composition flax; genome-wide association study (GWAS); selective sweep; genotyping by sequencing (GBS); bi-parental population; single nucleotide polymorphism (SNP); seed yield; plant height; maturity; fatty acid composition
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You, F.M.; Xiao, J.; Li, P.; Yao, Z.; Jia, G.; He, L.; Kumar, S.; Soto-Cerda, B.; Duguid, S.D.; Booker, H.M.; Rashid, K.Y.; Cloutier, S. Genome-Wide Association Study and Selection Signatures Detect Genomic Regions Associated with Seed Yield and Oil Quality in Flax. Int. J. Mol. Sci. 2018, 19, 2303.

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