National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
BMC Genet. 2012 Dec 6;13:105. doi: 10.1186/1471-2156-13-105.
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 B. napus have been identified, but information on candidate genes for identified QTLs of this important trait is still rare.
In this study, a whole genome genetic linkage map for B. napus 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 B. napus with its two progenitor diploid species B. rapa and B. oleracea through extensive bioinformatics analysis. With the aid of B. rapa and B. oleracea genome sequences, the 421 homologous colinear loci deduced from the SSR loci of B. napus were shown to correspond to 398 homologous loci in Arabidopsis thaliana. Through comparative mapping of Arabidopsis and the three Brassica species, 227 homologous genes for seed size/weight were mapped on the B. napus 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 BnAP2 was developed through molecular cloning using the seed weight/size gene distribution map in B. napus.
Our study showed that it is feasible to identify candidate genes of QTLs using a SSR-based B. napus genetic map through comparative mapping among Arabidopsis and B. napus and its two progenitor species B. rapa and B. oleracea. Identification of candidate genes for seed weight in amphidiploid B. napus 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.
在多倍体作物物种中，基于图谱的数量性状基因座（QTL）克隆仍然是一个挑战，因为它们的基因组结构复杂。已经鉴定了油菜籽种子重量的 QTL，但对于鉴定出的这个重要性状的候选基因信息仍然很少。
本研究利用简单序列重复（SSR）标记构建了油菜的全基因组遗传连锁图谱，该图谱覆盖了 2126.4 cM 的遗传距离，标记之间的平均距离为 5.36 cM。通过广泛的生物信息学分析，开发了一种将油菜 SSR 位点与两个二倍体祖先物种甘蓝型油菜和白菜型油菜进行共线性定位的方法。借助甘蓝型油菜和白菜型油菜基因组序列，从油菜 SSR 位点推断出的 421 个同源共线性位点与拟南芥的 398 个同源位点相对应。通过拟南芥和三种芸薹属物种的比较作图，将 227 个与种子大小/重量相关的同源基因映射到油菜遗传图谱上，为该双二倍体物种的重要农艺性状建立了遗传基础。此外，鉴定了 8 个种子重量 QTL 的 12 个候选基因，并通过利用油菜种子重量/大小基因分布图谱进行分子克隆，开发了一个针对 BnAP2 的基因特异性标记。
本研究表明，通过比较拟南芥和油菜及其两个祖先种甘蓝型油菜和白菜型油菜之间的基于 SSR 的油菜遗传图谱，利用该图谱识别 QTL 的候选基因是可行的。鉴定双二倍体油菜中种子重量的候选基因将加速该重要性状的映射 QTL 的分离过程，这种方法可能对其他具有重要农艺意义的性状的 QTL 鉴定有用。
