title: Genome-wide association analyses reveal complex genetic architecture underlying natural variation for flowering time in canola.
abstract: Optimum flowering time is the key to maximize canola production in order to meet global demand of vegetable oil, biodiesel and canola-meal. We reveal extensive variation in flowering time across diverse genotypes of canola under field, glasshouse and controlled environmental conditions. We conduct a genome-wide association study and identify 69 single nucleotide polymorphism (SNP) markers associated with flowering time, which are repeatedly detected across experiments. Several associated SNPs occur in clusters across the canola genome; seven of them were detected within 20 Kb regions of a priori candidate genes; FLOWERING LOCUS T, FRUITFUL, FLOWERING LOCUS C, CONSTANS, FRIGIDA, PHYTOCHROME B and an additional five SNPs were localized within 14 Kb of a previously identified quantitative trait loci for flowering time. Expression analyses showed that among FLC paralogs, BnFLC.A2 accounts for ~23% of natural variation in diverse accessions. Genome-wide association analysis for FLC expression levels mapped not only BnFLC.C2 but also other loci that contribute to variation in FLC expression. In addition to revealing the complex genetic architecture of flowering time variation, we demonstrate that the identified SNPs can be modelled to predict flowering time in diverse canola germplasm accurately and hence are suitable for genomic selection of adaptative traits in canola improvement programmes.
authors.affiliation: Graham Centre for Agricultural Innovation (an alliance between NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia.
authors.forename: H
authors.initials: H
authors.lastname: Raman
authors.affiliation: Graham Centre for Agricultural Innovation (an alliance between NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia.
authors.forename: R
authors.initials: R
authors.lastname: Raman
authors.affiliation: Graham Centre for Agricultural Innovation (an alliance between NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia.
authors.forename: N
authors.initials: N
authors.lastname: Coombes
authors.affiliation: Diversity Arrays Technology P/L, University of Canberra, Canberra, ACT, 2601, Australia.
authors.forename: J
authors.initials: J
authors.lastname: Song
authors.affiliation: Graham Centre for Agricultural Innovation (an alliance between NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia.
authors.forename: R
authors.initials: R
authors.lastname: Prangnell
authors.affiliation: School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia.
authors.forename: C
authors.initials: C
authors.lastname: Bandaranayake
authors.affiliation: School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia.
authors.forename: R
authors.initials: R
authors.lastname: Tahira
authors.affiliation: School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia.
authors.forename: V
authors.initials: V
authors.lastname: Sundaramoorthi
authors.affiliation: Diversity Arrays Technology P/L, University of Canberra, Canberra, ACT, 2601, Australia.
authors.forename: A
authors.initials: A
authors.lastname: Killian
authors.affiliation: National Key Laboratory of Crop Improvement, Huazhong Agricultural University, Wuhan, China.
authors.forename: J
authors.initials: J
authors.lastname: Meng
authors.affiliation: CSIRO Division of Plant Industry, Canberra, ACT, 2601, Australia.
authors.forename: E S
authors.initials: ES
authors.lastname: Dennis
authors.affiliation: School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia.
authors.forename: S
authors.identifier: 0000-0002-1057-2606
authors.initials: S
authors.lastname: Balasubramanian
mesh_terms: D000483:Alleles; D029741:Brassica rapa / Q000235:genetics* / Q000502:physiology; D035264:Flowers / Q000235:genetics / Q000502:physiology*; D018506:Gene Expression Regulation, Plant / Q000502:physiology; D017343:Genes, Plant / Q000235:genetics / Q000502:physiology*; D014644:Genetic Variation / Q000235:genetics / Q000502:physiology; D055106:Genome-Wide Association Study; D060005:Genotyping Techniques; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide / Q000235:genetics / Q000502:physiology; D059467:Transcriptome
keywords: gene expression; genomic selection; linkage analysis