Dataset Information

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

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.

SUBMITTER: You FM

PROVIDER: S-EPMC6121305 | biostudies-literature | 2018 Aug

REPOSITORIES: biostudies-literature

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

You Frank M FM Xiao Jin J Li Pingchuan P Yao Zhen Z Jia Gaofeng G He Liqiang L Kumar Santosh S Soto-Cerda Braulio B Duguid Scott D SD Booker Helen M HM Rashid Khalid Y KY Cloutier Sylvie S

International journal of molecular sciences 20180806 8

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 ...[more]

PMID: 30082613

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Project description:IntroductionCultivated peanut (Arachis hypogaea L.) is an important oil crop for human nutrition and is cultivated in >100 countries. However, the present knowledge of its genomic diversity, evolution, and loci related to the seed traits is limited.ObjectivesOur study intended to (1) uncover the population structure and the demographic history of peanuts, (2) identify signatures of selection that occurred during peanut improvement breeding, and (3) detect and verify the functions of candidate genes associated with seed traits.MethodsWe explored the population relationship and the evolution of peanuts using a largescale single nucleotide polymorphism dataset generated from the genome-wide resequencing of 203 cultivated peanuts. Genetic diversity and genomic scan analyses were applied to identify selective loci for genomic-selection breeding. Genome-wide association studies, transgenic experiments, and RNA-seq were employed to identify the candidate genes associated with seed traits.ResultsOur study revealed that the 203 resequenced accessions were divided into four genetic groups, consistent with their botanical classification. Moreover, the var. peruviana and var. fastigiata subpopulations have diverged to a greater extent than the others, and var. peruviana may be the earliest variant in the evolution from tetraploid ancestors. A recent dramatic expansion in the effective population size of the cultivated peanuts ca. 300-500 years ago was also noted. Selective sweeps underlying quantitative trait loci and genes of seed size, plant architecture, and disease resistance coincide with the major goals of improved peanut breeding compared with the landrace and cultivar populations. Genome-wide association testing with functional analysis led to the identification of two genes involved in seed weight and seed length regulation.ConclusionOur study provides valuable information for understanding the genomic diversity and the evolution of peanuts and serves as a genomic basis for improving peanut cultivars.

Dataset Information

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

Publications

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

Similar Datasets

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