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Background: Rapeseed(Brassica napus L.),a globally cultivated crop,provides one of the most important vegetable oil source for human consumption.Root system architecture(RSA)plays an important role in plant anchorage and acquisition of nutrients and water,which contributes significantly to plant productivity.To elucidate the genetic architecture of seedling root development in rapeseed,283 Brassica napus accessions with different origins were genotyped using the Brassica 60K SNP(single nucleotide polymorphism)array and 9 seedling root architecture related traits were phenotyped at 13d and 16d under hydroponic conditions.Results: With quality control and filtration,23,542 SNP markers were ultimately selected for further analyses.Using the mixed linear model(MLM)in TASSEL5.0,the GWAS study identified a total of 717 marker-trait associations(p ≤4.35×10-5)distributed on 18 chromosomes among four independent trials.Of these associations,147 significant SNP markers were detected in at least two independent trials,and they are located on chromosomes A2,A4,A9,C3 and C8.It is remarkable that several SNP markers located in 32.34 Mb on chromosomes C8 were associated with multiple root traits such as root fresh weight,total root length,and total root surface area etc.Several promising positional and functional candidate genes closing to these SNP markers(< 350 kb)were identified.These include orthologs of the Arabidopsis genes GRETCHEN HAGEN 3.3(GH3.3),NAC domain containing protein 38(NAC038)and SKU5 similar 15(SKS15),which have been shown previously to play a role in root growth in Arabidopsis.Conclusion: This study identifies putatively associated SNP markers associated with root traits at the seedling stage in B.napus.Otherwise,orthologs of AtGH3.3,AtNAC038 and AtSKS15 were identified as candidate genes responsible for phenotypic variation in cultivars.Our findings provide further insight into genetic improvement of root system architecture in rapeseed.