Genome-wide association analyses reveal complex genetic architecture underlying natural variation for flowering time in canola

Harsh Raman, Rosy Raman, Neil Coombes, Roslyn Prangnell, Champa Bandaranayake, R. Tahira, Vignesh Sundaramoorthi, Jinling Meng, Elizabeth Dennis, Sureshkumar Balasubramanian

Research output: Contribution to journalArticle

36 Citations (Scopus)

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 20Kb 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 14Kb 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.
Original languageEnglish
Pages (from-to)1228-1239
Number of pages12
JournalPlant, Cell and Environment
Volume39
Issue number6
DOIs
Publication statusPublished - 2016
Externally publishedYes

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Genome-Wide Association Study
canola
flowering
Single Nucleotide Polymorphism
genome
Phytochrome B
loci
Plant Oils
Biofuels
Quantitative Trait Loci
varespladib methyl
canola meal
Meals
biodiesel
phytochrome
Genotype
vegetable oil
marker-assisted selection
Genome
single nucleotide polymorphism

Cite this

Raman, H., Raman, R., Coombes, N., Prangnell, R., Bandaranayake, C., Tahira, R., ... Balasubramanian, S. (2016). Genome-wide association analyses reveal complex genetic architecture underlying natural variation for flowering time in canola. Plant, Cell and Environment, 39(6), 1228-1239. https://doi.org/10.1111/pce.12644
Raman, Harsh ; Raman, Rosy ; Coombes, Neil ; Prangnell, Roslyn ; Bandaranayake, Champa ; Tahira, R. ; Sundaramoorthi, Vignesh ; Meng, Jinling ; Dennis, Elizabeth ; Balasubramanian, Sureshkumar. / Genome-wide association analyses reveal complex genetic architecture underlying natural variation for flowering time in canola. In: Plant, Cell and Environment. 2016 ; Vol. 39, No. 6. pp. 1228-1239.
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Raman, H, Raman, R, Coombes, N, Prangnell, R, Bandaranayake, C, Tahira, R, Sundaramoorthi, V, Meng, J, Dennis, E & Balasubramanian, S 2016, 'Genome-wide association analyses reveal complex genetic architecture underlying natural variation for flowering time in canola', Plant, Cell and Environment, vol. 39, no. 6, pp. 1228-1239. https://doi.org/10.1111/pce.12644

Genome-wide association analyses reveal complex genetic architecture underlying natural variation for flowering time in canola. / Raman, Harsh; Raman, Rosy; Coombes, Neil; Prangnell, Roslyn; Bandaranayake, Champa; Tahira, R.; Sundaramoorthi, Vignesh; Meng, Jinling; Dennis, Elizabeth; Balasubramanian, Sureshkumar.

In: Plant, Cell and Environment, Vol. 39, No. 6, 2016, p. 1228-1239.

Research output: Contribution to journalArticle

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T1 - Genome-wide association analyses reveal complex genetic architecture underlying natural variation for flowering time in canola

AU - Raman, Harsh

AU - Raman, Rosy

AU - Coombes, Neil

AU - Prangnell, Roslyn

AU - Bandaranayake, Champa

AU - Tahira, R.

AU - Sundaramoorthi, Vignesh

AU - Meng, Jinling

AU - Dennis, Elizabeth

AU - Balasubramanian, Sureshkumar

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N2 - 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 20Kb 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 14Kb 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.

AB - 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 20Kb 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 14Kb 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.

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M3 - Article

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SP - 1228

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JO - Plant, Cell and Environment

JF - Plant, Cell and Environment

SN - 0140-7791

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ER -