title: 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 QTLs 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 QTLs 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-eQTLs with fatty acid QTLs, 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.
authors.affiliation: Wageningen UR Plant Breeding, Wageningen University and Research, 6708PB Wageningen, The Netherlands (R.K.B., D.P.D.C., D.X., J.B., R.G.F.V., C.M., G.B.);Centre for BioSystems Genomics, 6708PB Wageningen, The Netherlands (R.K.B., R.G.F.V., C.M.);Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Korea (M.J.); andNational Research Council of Canada, Saskatoon, Saskatchewan, Canada SK S7N 0W9 (K.B., P.F.).
authors.forename: Ram Kumar
authors.identifier: http://orcid.org/0000-0002-8028-1345
authors.initials: RK
authors.lastname: Basnet
authors.affiliation: Wageningen UR Plant Breeding, Wageningen University and Research, 6708PB Wageningen, The Netherlands (R.K.B., D.P.D.C., D.X., J.B., R.G.F.V., C.M., G.B.);Centre for BioSystems Genomics, 6708PB Wageningen, The Netherlands (R.K.B., R.G.F.V., C.M.);Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Korea (M.J.); andNational Research Council of Canada, Saskatoon, Saskatchewan, Canada SK S7N 0W9 (K.B., P.F.).
authors.forename: Dunia Pino
authors.identifier: http://orcid.org/0000-0002-8519-2245
authors.initials: DP
authors.lastname: Del Carpio
authors.affiliation: Wageningen UR Plant Breeding, Wageningen University and Research, 6708PB Wageningen, The Netherlands (R.K.B., D.P.D.C., D.X., J.B., R.G.F.V., C.M., G.B.);Centre for BioSystems Genomics, 6708PB Wageningen, The Netherlands (R.K.B., R.G.F.V., C.M.);Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Korea (M.J.); andNational Research Council of Canada, Saskatoon, Saskatchewan, Canada SK S7N 0W9 (K.B., P.F.).
authors.forename: Dong
authors.initials: D
authors.lastname: Xiao
authors.affiliation: Wageningen UR Plant Breeding, Wageningen University and Research, 6708PB Wageningen, The Netherlands (R.K.B., D.P.D.C., D.X., J.B., R.G.F.V., C.M., G.B.);Centre for BioSystems Genomics, 6708PB Wageningen, The Netherlands (R.K.B., R.G.F.V., C.M.);Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Korea (M.J.); andNational Research Council of Canada, Saskatoon, Saskatchewan, Canada SK S7N 0W9 (K.B., P.F.).
authors.forename: Johan
authors.initials: J
authors.lastname: Bucher
authors.affiliation: Wageningen UR Plant Breeding, Wageningen University and Research, 6708PB Wageningen, The Netherlands (R.K.B., D.P.D.C., D.X., J.B., R.G.F.V., C.M., G.B.);Centre for BioSystems Genomics, 6708PB Wageningen, The Netherlands (R.K.B., R.G.F.V., C.M.);Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Korea (M.J.); andNational Research Council of Canada, Saskatoon, Saskatchewan, Canada SK S7N 0W9 (K.B., P.F.).
authors.forename: Mina
authors.initials: M
authors.lastname: Jin
authors.affiliation: Wageningen UR Plant Breeding, Wageningen University and Research, 6708PB Wageningen, The Netherlands (R.K.B., D.P.D.C., D.X., J.B., R.G.F.V., C.M., G.B.);Centre for BioSystems Genomics, 6708PB Wageningen, The Netherlands (R.K.B., R.G.F.V., C.M.);Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Korea (M.J.); andNational Research Council of Canada, Saskatoon, Saskatchewan, Canada SK S7N 0W9 (K.B., P.F.).
authors.forename: Kerry
authors.initials: K
authors.lastname: Boyle
authors.affiliation: Wageningen UR Plant Breeding, Wageningen University and Research, 6708PB Wageningen, The Netherlands (R.K.B., D.P.D.C., D.X., J.B., R.G.F.V., C.M., G.B.);Centre for BioSystems Genomics, 6708PB Wageningen, The Netherlands (R.K.B., R.G.F.V., C.M.);Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Korea (M.J.); andNational Research Council of Canada, Saskatoon, Saskatchewan, Canada SK S7N 0W9 (K.B., P.F.).
authors.forename: Pierre
authors.initials: P
authors.lastname: Fobert
authors.affiliation: Wageningen UR Plant Breeding, Wageningen University and Research, 6708PB Wageningen, The Netherlands (R.K.B., D.P.D.C., D.X., J.B., R.G.F.V., C.M., G.B.);Centre for BioSystems Genomics, 6708PB Wageningen, The Netherlands (R.K.B., R.G.F.V., C.M.);Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Korea (M.J.); andNational Research Council of Canada, Saskatoon, Saskatchewan, Canada SK S7N 0W9 (K.B., P.F.).
authors.forename: Richard G F
authors.identifier: http://orcid.org/0000-0002-0213-4016
authors.initials: RG
authors.lastname: Visser
authors.affiliation: Wageningen UR Plant Breeding, Wageningen University and Research, 6708PB Wageningen, The Netherlands (R.K.B., D.P.D.C., D.X., J.B., R.G.F.V., C.M., G.B.);Centre for BioSystems Genomics, 6708PB Wageningen, The Netherlands (R.K.B., R.G.F.V., C.M.);Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Korea (M.J.); andNational Research Council of Canada, Saskatoon, Saskatchewan, Canada SK S7N 0W9 (K.B., P.F.).
authors.forename: Chris
authors.initials: C
authors.lastname: Maliepaard
authors.affiliation: Wageningen UR Plant Breeding, Wageningen University and Research, 6708PB Wageningen, The Netherlands (R.K.B., D.P.D.C., D.X., J.B., R.G.F.V., C.M., G.B.);Centre for BioSystems Genomics, 6708PB Wageningen, The Netherlands (R.K.B., R.G.F.V., C.M.);Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Korea (M.J.); andNational Research Council of Canada, Saskatoon, Saskatchewan, Canada SK S7N 0W9 (K.B., P.F.) guusje.bonnema@wur.nl.
authors.forename: Guusje
authors.identifier: http://orcid.org/0000-0002-2298-6849
authors.initials: G
authors.lastname: Bonnema
mesh_terms: D029741:Brassica rapa / Q000737:chemistry / Q000235:genetics*; D005227:Fatty Acids / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D008040:Genetic Linkage; D006238:Haploidy; D010858:Pigmentation / Q000235:genetics; D040641:Quantitative Trait Loci; D012639:Seeds / Q000737:chemistry / Q000235:genetics*
chemical_list: D005227:Fatty Acids