Genome-wide association study and selection signatures detect genomic regions associated with seed yield and oil quality in flax

Citation

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. (2018). Genome-wide association study and selection signatures detect genomic regions associated with seed yield and oil quality in flax. International Journal of Molecular Sciences, [online] 19(8), http://dx.doi.org/10.3390/ijms19082303

Plain language summary

In times of food shortages as well as a rising global population, scientists are looking to aid help the growth and quality of food by marker-assisted breeding in plants. using Genetic markers that are present in every organism is a fragment of DNA presenting in every organism that can be transmitted from one generation to another. Thus, genetic markers are widely used as experimental tags to keep track of individual. . This study aims to demonstrate the utility application of a Genomegenome-wide association study (GWAS) combined with selection signatures when pinpointing regions in the genome to improve breeding. For this experiment, three bi-parental flax mapping populations of 260 flax individuals were re-sequenced and , of those populations, the phenotypic data for 11 seed yield and quality traits were collected in eight environments. From the samples that were gathered, 17,288 single-nucleotide polymorphisms (SNP’s) were identified and accounted for 53% of the physical variations for the studied traits and more than 80% of the physical variation for days to maturity (DTM), iodine value (IOD), palmitic (PAL), stearic, linoleic (LIO), and linolenic (LIN). Through a GWAS, 23 unique genomic regions were found to be associated with 33 qualitative trait loci (QTL). which, this validated four genomic regions which were previously associated with nine QTL . These QTL explained 56-73% of the phenotypic variation for oil content, IOD, PAL, LIO and LIN and 8-14% for plant height, DTM and seed yield. A genome-wide sweep scan detected 114 signatures, which accounted for 7.82% of flax pseudomolecules, the scan also overlapped with the 11 GWAS-detected genomic regions associated with 18 QTL for all 11 seed yield and oil quality 11 traits . The conclusion reached from these experiments was that GWAS combined with selection signatures help identify genomic regions locations in the genome toto improve crop breeding.

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.

Publication date

2018-08-06