title: Associative transcriptomics study dissects the genetic architecture of seed glucosinolate content in Brassica napus.
abstract: Breeding new varieties with low seed glucosinolate (GS) concentrations has long been a prime target in Brassica napus. In this study, a novel association mapping methodology termed 'associative transcriptomics' (AT) was applied to a panel of 101 B. napus lines to define genetic regions and also candidate genes controlling total seed GS contents. Over 100,000 informative single-nucleotide polymorphisms (SNPs) and gene expression markers (GEMs) were developed for AT analysis, which led to the identification of 10 SNP and 7 GEM association peaks. Within these peaks, 26 genes were inferred to be involved in GS biosynthesis. A weighted gene co-expression network analysis provided additional 40 candidate genes. The transcript abundance in leaves of two candidate genes, BnaA.GTR2a located on chromosome A2 and BnaC.HAG3b on C9, was correlated with seed GS content, explaining 18.8 and 16.8% of phenotypic variation, respectively. Resequencing of genomic regions revealed six new SNPs in BnaA.GTR2a and four insertions or deletions in BnaC.HAG3b. These deletion polymorphisms were then successfully converted into polymerase chain reaction-based diagnostic markers that can, due to high linkage disequilibrium observed in these regions of the genome, be used for marker-assisted breeding for low seed GS lines.
authors.affiliation: Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York YO10 5DD, UK Oil Crops Research Institute, CAAS, Wuhan 430062, Hubei, China.
authors.forename: Guangyuan
authors.initials: G
authors.lastname: Lu
authors.affiliation: Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York YO10 5DD, UK.
authors.forename: Andrea L
authors.initials: AL
authors.lastname: Harper
authors.affiliation: John Innes Centre, Norwich Research Park, Norwich, Norfolk NR4 7UH, UK.
authors.forename: Martin
authors.initials: M
authors.lastname: Trick
authors.affiliation: John Innes Centre, Norwich Research Park, Norwich, Norfolk NR4 7UH, UK.
authors.forename: Colin
authors.initials: C
authors.lastname: Morgan
authors.affiliation: John Innes Centre, Norwich Research Park, Norwich, Norfolk NR4 7UH, UK.
authors.forename: Fiona
authors.initials: F
authors.lastname: Fraser
authors.affiliation: John Innes Centre, Norwich Research Park, Norwich, Norfolk NR4 7UH, UK.
authors.forename: Carmel
authors.initials: C
authors.lastname: O'Neill
authors.affiliation: Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York YO10 5DD, UK ian.bancroft@york.ac.uk.
authors.forename: Ian
authors.initials: I
authors.lastname: Bancroft
mesh_terms: D029688:Brassica napus / Q000235:genetics / Q000378:metabolism; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000502:physiology*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000502:physiology*; D005961:Glucosinolates / Q000096:biosynthesis / Q000235:genetics; D015810:Linkage Disequilibrium / Q000502:physiology; D009004:Monosaccharide Transport Proteins / Q000096:biosynthesis / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D012639:Seeds / Q000235:genetics / Q000378:metabolism
chemical_list: D005961:Glucosinolates; D009004:Monosaccharide Transport Proteins
keywords: GEM; SNP; associative transcriptomics; glucosinolate