GWAS and co-expression network combination uncovers multigenes with close linkage effects on the oleic acid content accumulation in Brassica napus.

Brassica napus / classification Chromosome Mapping Chromosomes, Plant / genetics Gene Expression Profiling / methods Gene Expression Regulation, Plant Gene Ontology Gene Regulatory Networks Genes, Plant / genetics Genetic Linkage Genome-Wide Association Study / methods Haplotypes Oleic Acid / metabolism Polymorphism, Single Nucleotide Whole Genome Sequencing / methods
Brassica napus Co-expression network GWAS Haplotype Oleic acid

Journal

BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258

Informations de publication

Date de publication:
23 Apr 2020
Historique:
received: 12 06 2019
accepted: 31 03 2020
entrez: 25 4 2020
pubmed: 25 4 2020
medline: 12 1 2021
Statut: epublish

Résumé

Strong artificial and natural selection causes the formation of highly conserved haplotypes that harbor agronomically important genes. GWAS combination with haplotype analysis has evolved as an effective method to dissect the genetic architecture of complex traits in crop species. We used the 60 K Brassica Infinium SNP array to perform a genome-wide analysis of haplotype blocks associated with oleic acid (C18:1) in rapeseed. Six haplotype regions were identified as significantly associated with oleic acid (C18:1) that mapped to chromosomes A02, A07, A08, C01, C02, and C03. Additionally, whole-genome sequencing of 50 rapeseed accessions revealed three genes (BnmtACP2-A02, BnABCI13-A02 and BnECI1-A02) in the A02 chromosome haplotype region and two genes (BnFAD8-C02 and BnSDP1-C02) in the C02 chromosome haplotype region that were closely linked to oleic acid content phenotypic variation. Moreover, the co-expression network analysis uncovered candidate genes from these two different haplotype regions with potential regulatory interrelationships with oleic acid content accumulation. Our results suggest that several candidate genes are closely linked, which provides us with an opportunity to develop functional haplotype markers for the improvement of the oleic acid content in rapeseed.

Sections du résumé

BACKGROUND BACKGROUND
Strong artificial and natural selection causes the formation of highly conserved haplotypes that harbor agronomically important genes. GWAS combination with haplotype analysis has evolved as an effective method to dissect the genetic architecture of complex traits in crop species.
RESULTS RESULTS
We used the 60 K Brassica Infinium SNP array to perform a genome-wide analysis of haplotype blocks associated with oleic acid (C18:1) in rapeseed. Six haplotype regions were identified as significantly associated with oleic acid (C18:1) that mapped to chromosomes A02, A07, A08, C01, C02, and C03. Additionally, whole-genome sequencing of 50 rapeseed accessions revealed three genes (BnmtACP2-A02, BnABCI13-A02 and BnECI1-A02) in the A02 chromosome haplotype region and two genes (BnFAD8-C02 and BnSDP1-C02) in the C02 chromosome haplotype region that were closely linked to oleic acid content phenotypic variation. Moreover, the co-expression network analysis uncovered candidate genes from these two different haplotype regions with potential regulatory interrelationships with oleic acid content accumulation.
CONCLUSIONS CONCLUSIONS
Our results suggest that several candidate genes are closely linked, which provides us with an opportunity to develop functional haplotype markers for the improvement of the oleic acid content in rapeseed.

Identifiants

DOI: 10.1186/s12864-020-6711-0 PMID: 32326904 PMC: PMC7181522
pubmed: 32326904
doi: 10.1186/s12864-020-6711-0
pii: 10.1186/s12864-020-6711-0
pmc: PMC7181522
doi:

Substances chimiques

Oleic Acid 2UMI9U37CP

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

320

Subventions

Organisme : Hunan Province Science and Technology Plan
ID : 2014FJ1000
Organisme : Hunan Provincial Key Research and Development Program
ID : 2016JC2024

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Auteurs

Min Yao (M)

Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128, China.

Mei Guan (M)

Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128, China.

Zhenqian Zhang (Z)

Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128, China.

Qiuping Zhang (Q)

Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128, China.

Yixin Cui (Y)

College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China.

Hao Chen (H)

Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128, China.

Wei Liu (W)

Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128, China.

Habib U Jan (HU)

Precision Medicine Lab, Rehman Medical Institute (RMI), Phase 5, Hayatabad, Peshawar, 25000, Pakistan.

Kai P Voss-Fels (KP)

Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia.

Christian R Werner (CR)

The Roslin Institute University of Edinburgh Easter Bush Research Centre Midlothian, Edinburgh, EH25 9RG, UK.

Xin He (X)

Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128, China.

Zhongsong Liu (Z)

Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128, China.

Chunyun Guan (C)

Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128, China.

Rod J Snowdon (RJ)

Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.

Wei Hua (W)

Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128, China. huawei@oilcrops.cn.
Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062, China. huawei@oilcrops.cn.

Lunwen Qian (L)

Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128, China. qianlunwen@163.com.

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Classifications MeSH

questionsmedicales.fr › Eucaryotes › Viridiplantae › Streptophyta › Embryophyta › Tracheobionta › Magnoliopsida › Brassicaceae › Brassica › Brassica napus › GWAS and co-expression network combination...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Cartographie chromosomique › GWAS and co-expression network combination...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Chromosomes › Chromosomes de plante › GWAS and co-expression network combination...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de profil d'expression de gènes › GWAS and co-expression network combination...
questionsmedicales.fr › Phénomènes génétiques › Régulation de l'expression des gènes › Régulation de l'expression des gènes végétaux › GWAS and co-expression network combination...
questionsmedicales.fr › Sciences de l'information › Sources d'information › Services d'information › Documentation › Vocabulaire contrôlé › Ontologies biologiques › Gene Ontology › GWAS and co-expression network combination...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Séquences d'acides nucléiques régulatrices › Réseaux de régulation génique › GWAS and co-expression network combination...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome végétal › Gènes de plante › GWAS and co-expression network combination...
questionsmedicales.fr › Phénomènes génétiques › Liaison génétique › GWAS and co-expression network combination...
questionsmedicales.fr › Environnement et santé publique › Santé publique › Méthodes épidémiologiques › Épidémiologie moléculaire › Étude d'association pangénomique › GWAS and co-expression network combination...
questionsmedicales.fr › Phénomènes génétiques › Génotype › Haplotypes › GWAS and co-expression network combination...
questionsmedicales.fr › Lipides › Acides gras › Acides gras insaturés › Acides gras monoinsaturés › Acides oléiques › Acide oléique › GWAS and co-expression network combination...
questionsmedicales.fr › Phénomènes génétiques › Variation génétique › Polymorphisme génétique › Polymorphisme de nucléotide simple › GWAS and co-expression network combination...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ADN › Séquençage du génome entier › GWAS and co-expression network combination...