A Systems Genetics Approach Identifies Gene Regulatory Networks Associated with Fatty Acid Composition in Brassica rapa Seed. Issue 1 (30th October 2015)

• Record Type: Journal Article
• Authors: Basnet, Ram Kumar; Del Carpio, Dunia Pino; Xiao, Dong; Bucher, Johan; Jin, Mina; Boyle, Kerry; Fobert, Pierre; Visser, Richard G.F.; Maliepaard, Chris; Bonnema, Guusje
• Is Part Of: Plant physiology. Volume 170:Issue 1(2016)
• Page Start: 568
• Page End: 585
• Publication Date: 2015-10-30
• Subjects: Plant physiology -- Periodicals; Botany -- Periodicals; Periodicals; Electronic journals; 571.2
• DOI: 10.1104/pp.15.00853
• Languages: English
• ISSNs: 0032-0889

Abstract

Abstract : A systems genetics approach identifies gene regulatory networks associated with fatty acid composition in Brassica rapa seed. Abstract: Fatty acids in seeds affect seed germination and seedling vigor, and fatty acid composition determines the quality of seed oil. In this study, quantitative trait locus (QTL ) mapping of fatty acid and transcript abundance was integrated with gene network analysis to unravel the genetic regulation of seed fatty acid composition in a Brassica rapa doubled haploid population from a cross between a yellow sarson oil type and a black-seeded pak choi. The distribution of major QTL s for fatty acids showed a relationship with the fatty acid types: linkage group A03 for monounsaturated fatty acids, A04 for saturated fatty acids, and A05 for polyunsaturated fatty acids. Using a genetical genomics approach, expression quantitative trait locus (eQTL ) hotspots were found at major fatty acid QTL s on linkage groups A03, A04, A05, and A09. An eQTL -guided gene coexpression network of lipid metabolism-related genes showed major hubs at the genes BrPLA2 -ALPHA, BrWD-40, a number of seed storage protein genes, and the transcription factor BrMD-2, suggesting essential roles for these genes in lipid metabolism. Three subnetworks were extracted for the economically important and most abundant fatty acids erucic, oleic, linoleic, and linolenic acids. Network analysis, combined with comparison of the genome positions of cis- or trans-eQTL s with fatty acid QTL s, allowed the identification of candidate genes for genetic regulation of these fatty acids. The generated insights in the genetic architecture of fatty acid composition and the underlying complex gene regulatory networks in B. rapa seeds are discussed.