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

Min Yao,Xin He,Rod J Snowdon,Mei Guan,Zhongsong Liu,Kai P Voss-Fels,Zhenqian Zhang,Wei Hua,Chunyun Guan,Yixin Cui,Hao Chen,Wei Liu,Habib U Jan,Lunwen Qian,Christian R Werner,Qiuping Zhang

doi:10.1186/s12864-020-6711-0

Abstract

BackgroundStrong 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.ResultsWe 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.ConclusionsOur 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.

Highlights

Strong artificial and natural selection causes the formation of highly conserved haplotypes that harbor agronomically important genes
BnaA02g12140D) in this haplotype region (Fig. 3). mtACP2 encodes a member of the mitochondrial acyl carrier protein (ACP) family that is involved in the fatty acid biosynthesis process, ABCI13 is an ATP-binding cassette (ABC) transporter that is involved in chloroplast lipid import, and ECI1 encodes a peroxisomal delta3, delta2-enoyl CoA isomerase that is involved in unsaturated fatty acid degradation (Additional file 2: Table S2)
In these three candidate gene subnetworks, 7 (27%), 3 (12%), 5 (11%) and 2 (8%) genes were lipid-related, fatty acid-related, glycerolrelated and carbohydrate-related, respectively. Another two clusters contained 12 (27%), 8 (18%) and 4 (9%) genes involved in lipid-related, fatty acid-related and photosynthesis processes, respectively (Fig. 5; Additional file 4: Table S4). These results showed that BnMTACP2A02, BnABCI13-A02 and BnECI1-A02 from the A02_ Hap region were interrelated with co-expression network genes that affected oleic acid content accumulation in rapeseed

Summary

Introduction

Strong artificial and natural selection causes the formation of highly conserved haplotypes that harbor agronomically important genes. Oilseed rape (Brassica napus L.) is an allotetraploid species with 2n = 38 chromosomes and two genomes (AA derived from B. rapa and CC from B. oleracea). It is the most important source of edible vegetable oil and protein-rich meal in China. Pinzi et al [3] suggested that high oleic acid oil was an ideal raw material for biodiesel production. High oleic acid oil can be heated to a higher temperature without smoking, which makes it more suitable as a cooking oil. Further improvement of the oleic acid oil content has become a primary goal of rapeseed breeding

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