Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

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

Frank You
* ORCID logo ,
Jin Xiao
,
Pingchuan Li
,
Zhen Yao
,
Gaofeng Jia
,
Liqiang He
,
Santosh Kumar
,
Braulio Soto-Cerda
ORCID logo ,
Scott Duguid
,
Helen Booker
ORCID logo ,
Khalid Rashid
,
Sylvie Cloutier
Version 1 : Received: 20 July 2018 / Approved: 21 July 2018 / Online: 21 July 2018 (14:49:39 CEST)
Version 2 : Received: 2 August 2018 / Approved: 3 August 2018 / Online: 3 August 2018 (15:34:24 CEST)

A peer-reviewed article of this Preprint also exists.

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. 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.

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 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.

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

Subject

Biology and Life Sciences, Agricultural Science and Agronomy

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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