Abstract
BackgroundSeveral major crop species are current or ancient polyploids. To better describe the genetic factors controlling traits of agronomic interest (QTL), it is necessary to understand the structural and functional organisation of these QTL regions in relation to genome duplication. We investigated quantitative resistance to the fungal disease stem canker in Brassica napus, a highly duplicated amphidiploid species, to assess the proportion of resistance QTL located at duplicated positions.ResultsGenome-wide association analysis on a panel of 116 oilseed rape varieties genotyped with 3228 SNP indicated that 321 markers, corresponding to 64 genomic regions, are associated with resistance to stem canker. These genomic regions are relatively equally distributed on the A (53%) and C (47%) genomes of B. napus. Overall, 44% of these regions (28/64) are duplicated homoeologous regions. They are located in duplications of six (E, J, R, T, U and W) of the 24 ancestral blocks that constitute the B. napus genome. Overall, these six ancestral blocks have 34 duplicated copies in the B.napus genome. Almost all of the duplicated copies (82% of the 34 regions) harboured resistance associated markers for stem canker resistance, which suggests structural and functional conservation of genetic factors involved in this trait in B. napus.ConclusionsOur study provides information on the involvement of duplicated loci in the control of stem canker resistance in B. napus. Further investigation of the similarity/divergence in sequence and gene content of these duplicated regions will provide insight into the conservation and allelic diversity of the underlying genes.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-498) contains supplementary material, which is available to authorized users.
Highlights
Several major crop species are current or ancient polyploids
As the B. rapa and B. oleracea genomes contain three subgenomes resulting from a meso-triplication [14], paralogous regions within the B. napus A and C genomes could correspond to ancient homoeologous regions in the B. rapa and B. oleracea genomes
We focused on the quantitative resistance to stem canker, caused by the fungal pathogen Leptosphaeria maculans, which is one of the major diseases of B. napus crops worldwide [28,29]
Summary
Several major crop species are current or ancient polyploids. To better describe the genetic factors controlling traits of agronomic interest (QTL), it is necessary to understand the structural and functional organisation of these QTL regions in relation to genome duplication. Brassica ancestors have undergone two duplication events (α and β) [12,13] and two triplication events, one ancient event shared by a large majority of Angiosperms (γ) and a more recent event specific to the Brassica clade [14] These WGD events, along with the merger of the two parental genomes, have resulted in a large number of duplicated regions in the B. napus genome. Twenty four conserved blocks of colinearity were identified between the Arabidopsis and Brassica genomes [17,18] in comparative mapping studies which showed that these blocks were highly duplicated in the B. napus genome [17,19] These duplications are regions that are either orthologous between (located on homoeologous linkage groups) or paralogous within the A and C genomes. In the present study all these duplicated regions will be referred to as homoeologous/duplicated regions
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