Genome-wide delineation of natural variation for pod shatter resistance in Brassica napus

Harsh Raman, Rosy Raman, Neil Coombes, Simon Diffey, Gururaj Kadkol, David Edwards, Margaret McCully, Pradeep Ruperao, Isobel Parkin, Jacqueline Batley, David Luckett, Neil Wratten

Research output: Contribution to journalArticle

86 Citations (Scopus)

Abstract

Resistance to pod shattering (shatter resistance) is a target trait for global rapeseed (canola, Brassica napus L.), improvement programs to minimise grain loss in the mature standing crop, and during windrowing and mechanical harvest. We describe the genetic basis of natural variation for shatter resistance in B. napus and show that several quantitative trait loci (QTL) control this trait. To identify loci underlying shatter resistance, we used a novel genotyping-by-sequencing approach DArT-Seq. QTL analysis detected a total of 12 significant QTL on chromosomes A03, A07, A09, C03, C04, C06, and C08; which jointly account for approximately 57% of the genotypic variation in shatter resistance. Through Genome-Wide Association Studies, we show that a large number of loci, including those that are involved in shattering in Arabidopsis, account for variation in shatter resistance in diverse B. napus germplasm. Our results indicate that genetic diversity for shatter resistance genes in B. napus is limited; many of the genes that might control this trait were not included during the natural creation of this species, or were not retained during the domestication and selection process. We speculate that valuable diversity for this trait was lost during the natural creation of B. napus. To improve shatter resistance, breeders will need to target the introduction of useful alleles especially from genotypes of other related species of Brassica, such as those that we have identified. © 2014 Raman et al.
Original languageEnglish
Article numbere101673
Pages (from-to)1-13
Number of pages13
JournalPLoS One
Volume9
Issue number7
DOIs
Publication statusPublished - 2014
Externally publishedYes

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Brassica napus
pods
Genes
Genome
Quantitative Trait Loci
genome
quantitative trait loci
Chromosomes
Crops
Brassica rapa
loci
Internal-External Control
Genome-Wide Association Study
Brassica
rapeseed
canola
domestication
Arabidopsis
genotyping
germplasm

Cite this

Raman, H., Raman, R., Coombes, N., Diffey, S., Kadkol, G., Edwards, D., ... Wratten, N. (2014). Genome-wide delineation of natural variation for pod shatter resistance in Brassica napus. PLoS One, 9(7), 1-13. [e101673]. https://doi.org/10.1371/journal.pone.0101673
Raman, Harsh ; Raman, Rosy ; Coombes, Neil ; Diffey, Simon ; Kadkol, Gururaj ; Edwards, David ; McCully, Margaret ; Ruperao, Pradeep ; Parkin, Isobel ; Batley, Jacqueline ; Luckett, David ; Wratten, Neil. / Genome-wide delineation of natural variation for pod shatter resistance in Brassica napus. In: PLoS One. 2014 ; Vol. 9, No. 7. pp. 1-13.
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Raman, H, Raman, R, Coombes, N, Diffey, S, Kadkol, G, Edwards, D, McCully, M, Ruperao, P, Parkin, I, Batley, J, Luckett, D & Wratten, N 2014, 'Genome-wide delineation of natural variation for pod shatter resistance in Brassica napus', PLoS One, vol. 9, no. 7, e101673, pp. 1-13. https://doi.org/10.1371/journal.pone.0101673

Genome-wide delineation of natural variation for pod shatter resistance in Brassica napus. / Raman, Harsh; Raman, Rosy; Coombes, Neil; Diffey, Simon; Kadkol, Gururaj; Edwards, David; McCully, Margaret; Ruperao, Pradeep; Parkin, Isobel; Batley, Jacqueline; Luckett, David; Wratten, Neil.

In: PLoS One, Vol. 9, No. 7, e101673, 2014, p. 1-13.

Research output: Contribution to journalArticle

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T1 - Genome-wide delineation of natural variation for pod shatter resistance in Brassica napus

AU - Raman, Harsh

AU - Raman, Rosy

AU - Coombes, Neil

AU - Diffey, Simon

AU - Kadkol, Gururaj

AU - Edwards, David

AU - McCully, Margaret

AU - Ruperao, Pradeep

AU - Parkin, Isobel

AU - Batley, Jacqueline

AU - Luckett, David

AU - Wratten, Neil

PY - 2014

Y1 - 2014

N2 - Resistance to pod shattering (shatter resistance) is a target trait for global rapeseed (canola, Brassica napus L.), improvement programs to minimise grain loss in the mature standing crop, and during windrowing and mechanical harvest. We describe the genetic basis of natural variation for shatter resistance in B. napus and show that several quantitative trait loci (QTL) control this trait. To identify loci underlying shatter resistance, we used a novel genotyping-by-sequencing approach DArT-Seq. QTL analysis detected a total of 12 significant QTL on chromosomes A03, A07, A09, C03, C04, C06, and C08; which jointly account for approximately 57% of the genotypic variation in shatter resistance. Through Genome-Wide Association Studies, we show that a large number of loci, including those that are involved in shattering in Arabidopsis, account for variation in shatter resistance in diverse B. napus germplasm. Our results indicate that genetic diversity for shatter resistance genes in B. napus is limited; many of the genes that might control this trait were not included during the natural creation of this species, or were not retained during the domestication and selection process. We speculate that valuable diversity for this trait was lost during the natural creation of B. napus. To improve shatter resistance, breeders will need to target the introduction of useful alleles especially from genotypes of other related species of Brassica, such as those that we have identified. © 2014 Raman et al.

AB - Resistance to pod shattering (shatter resistance) is a target trait for global rapeseed (canola, Brassica napus L.), improvement programs to minimise grain loss in the mature standing crop, and during windrowing and mechanical harvest. We describe the genetic basis of natural variation for shatter resistance in B. napus and show that several quantitative trait loci (QTL) control this trait. To identify loci underlying shatter resistance, we used a novel genotyping-by-sequencing approach DArT-Seq. QTL analysis detected a total of 12 significant QTL on chromosomes A03, A07, A09, C03, C04, C06, and C08; which jointly account for approximately 57% of the genotypic variation in shatter resistance. Through Genome-Wide Association Studies, we show that a large number of loci, including those that are involved in shattering in Arabidopsis, account for variation in shatter resistance in diverse B. napus germplasm. Our results indicate that genetic diversity for shatter resistance genes in B. napus is limited; many of the genes that might control this trait were not included during the natural creation of this species, or were not retained during the domestication and selection process. We speculate that valuable diversity for this trait was lost during the natural creation of B. napus. To improve shatter resistance, breeders will need to target the introduction of useful alleles especially from genotypes of other related species of Brassica, such as those that we have identified. © 2014 Raman et al.

KW - Brassica napus/anatomy & histology

KW - Chromosome Mapping

KW - Genes, Plant

KW - Genetic Association Studies

KW - Genetic Markers

KW - Polymorphism, Single Nucleotide

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KW - Seeds/anatomy & histology

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Raman H, Raman R, Coombes N, Diffey S, Kadkol G, Edwards D et al. Genome-wide delineation of natural variation for pod shatter resistance in Brassica napus. PLoS One. 2014;9(7):1-13. e101673. https://doi.org/10.1371/journal.pone.0101673