深入解析复杂动植物的个体基因组，使个体间染色体结构差异尤其是一些大的结构变异能够被检出并正确地组装到基因组中，是基因组学领域“泛基因组时代”所面临的重要挑战。本研究提出改进双亲本遗传作图，以遗传差异较大的常规甘蓝型油菜和“新型”甘蓝型油菜，及其衍生的四亲本交叉作图群体为材料，构建彼此高度关联的若干高密度遗传图；通过图谱间的比较分析，检出不同亲本基因组间隐含的倒位、易位及大片段的重复、缺失等结构变异，并在后续的基因组测序过程中筛查出含有这些结构变异的Scaffold并正确地组装到基因组中；鉴定新型甘蓝型油菜在基因有无、基因序列、拷贝数、转座子插入、染色体重构等多种类型的基因组变异，并通过对控制产量、品质等性状的QTL的定位分析，将QTL与这些基因组变异相联系并探索其生物学意义，揭示经过大规模种间杂交和高强度的人工选择后，异源四倍体油菜基因组所产生的深刻和广泛的个体基因组变异及其对性状的影响。

Comprehensively dissecting the individual genomes of animals and plants with relatively complex genome, and enabling the chromosome structural variation between individuals, especially large structural variations detected and correctly assembled into the genome, is an important challenge in the "pan-genome era" of genomics. In this study, we propose to improve the genetic mapping based on two.parents, and to construct high-density genetic maps correlated with each other using four-parent related mapping populations, which derived from the crosses among conventional Brassica napus and “new-type” B. napus with significant genetic difference. Through the comparative analysis between the maps, the structural variation among the parents including inversions, translocations, and large fragments of duplication and deletions would be detected, and be further screened in the subsequent genome sequencing analysis of the mapping parents, and allow those Scaffold with structural variations to be correctly assembled into the genome. The genome of the new-type B. napus will be investigated on various types of genomic variation in terms of present and absent variation, gene sequence, copy number variation, transposon insertion, chromosome structural variation, and so on. The linkage atlas and their biological significance will be further analyzed between these variations and the QTL identified by QTL mapping on seed yield and seed quality related traits of the four-parent populations. These results would reveal the profound and extensive individual genomic variations of the allotetraploid rapeseed genomes and their impacts on traits after large-scale interspecific hybridization and high-intensity artificial selection.