| Summary: | <p>Abstract</p> <p>Background</p> <p>Map-based cloning of quantitative trait loci (QTLs) in polyploidy crop species remains a challenge due to the complexity of their genome structures. QTLs for seed weight in <it>B. napus</it> have been identified, but information on candidate genes for identified QTLs of this important trait is still rare.</p> <p>Results</p> <p>In this study, a whole genome genetic linkage map for <it>B. napus</it> was constructed using simple sequence repeat (SSR) markers that covered a genetic distance of 2,126.4 cM with an average distance of 5.36 cM between markers. A procedure was developed to establish colinearity of SSR loci on <it>B. napus</it> with its two progenitor diploid species <it>B. rapa</it> and <it>B. oleracea</it> through extensive bioinformatics analysis. With the aid of <it>B. rapa</it> and <it>B. oleracea</it> genome sequences, the 421 homologous colinear loci deduced from the SSR loci of <it>B. napus</it> were shown to correspond to 398 homologous loci in <it>Arabidopsis thaliana</it>. Through comparative mapping of <it>Arabidopsis</it> and the three <it>Brassica</it> species, 227 homologous genes for seed size/weight were mapped on the <it>B. napus</it> genetic map, establishing the genetic bases for the important agronomic trait in this amphidiploid species. Furthermore, 12 candidate genes underlying 8 QTLs for seed weight were identified, and a gene-specific marker for <it>BnAP2</it> was developed through molecular cloning using the seed weight/size gene distribution map in <it>B. napus</it>.</p> <p>Conclusions</p> <p>Our study showed that it is feasible to identify candidate genes of QTLs using a SSR-based <it>B. napus</it> genetic map through comparative mapping among <it>Arabidopsis</it> and <it>B. napus</it> and its two progenitor species <it>B. rapa</it> and <it>B. oleracea</it>. Identification of candidate genes for seed weight in amphidiploid <it>B. napus</it> will accelerate the process of isolating the mapped QTLs for this important trait, and this approach may be useful for QTL identification of other traits of agronomic significance.</p>
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