Abstract
All crop species are current or ancient polyploids. Following whole genome duplication, structural and functional modifications result in differential gene content or regulation in the duplicated regions, which can play a fundamental role in the diversification of genes underlying complex traits. We have investigated this issue in Brassica napus, a species with a highly duplicated genome, with the aim of studying the structural and functional organization of duplicated regions involved in quantitative resistance to stem canker, a disease caused by the fungal pathogen Leptosphaeria maculans. Genome-wide association analysis on two oilseed rape panels confirmed that duplicated regions of ancestral blocks E, J, R, U, and W were involved in resistance to stem canker. The structural analysis of the duplicated genomic regions showed a higher gene density on the A genome than on the C genome and a better collinearity between homoeologous regions than paralogous regions, as overall in the whole B. napus genome. The three ancestral sub-genomes were involved in the resistance to stem canker and the fractionation profile of the duplicated regions corresponded to what was expected from results on the B. napus progenitors. About 60% of the genes identified in these duplicated regions were single-copy genes while less than 5% were retained in all the duplicated copies of a given ancestral block. Genes retained in several copies were mainly involved in response to stress, signaling, or transcription regulation. Genes with resistance-associated markers were mainly retained in more than two copies. These results suggested that some genes underlying quantitative resistance to stem canker might be duplicated genes. Genes with a hydrolase activity that were retained in one copy or R-like genes might also account for resistance in some regions. Further analyses need to be conducted to indicate to what extent duplicated genes contribute to the expression of the resistance phenotype.
Highlights
Polyploidization is a common mode of evolution in flowering plants which occurs through genome merging or genome doubling and results in an increased gene set (Doyle et al, 2008; Wang et al, 2012)
When two different translated B. napus genes showed the best matches to the same A. thaliana protein we considered that the two B. napus genes were likely to be homoeologous or paralogous
We identified a set of genes that were retained in duplicated regions and associated with quantitative resistance to stem canker and many were involved in stress responses, signaling and transcriptional regulation
Summary
Polyploidization is a common mode of evolution in flowering plants which occurs through genome merging (allopolyploidy) or genome doubling (autopolyploidy) and results in an increased gene set (Doyle et al, 2008; Wang et al, 2012). The loss/retention of duplicated genes might depend on their parental origin In this case, one of the parental genomes is more likely to retain genes and has a higher gene density than the other(s) genome(s). One of the parental genomes is more likely to retain genes and has a higher gene density than the other(s) genome(s) This phenomenon, referred to as biased fractionation, has been demonstrated in several species including Zea mays (Schnable et al, 2011), Triticum aestivum (Pont et al, 2013), Arabidopsis thaliana (Thomas et al, 2006), and Brassica rapa (Cheng et al, 2012; Tang et al, 2012). Expression bias, as described by Wang et al (2011), has been reported in allopolyploid species: when considering homoeologous gene pairs in allopolyploids, mRNA transcripts from the sub-genome that retains more genes tend to be more highly expressed and contribute more to the total transcriptome (Bardil et al, 2011; Schnable et al, 2011; Yoo et al, 2013; Woodhouse et al, 2014)
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