Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China.
Theor Appl Genet. 2013 Jan;126(1):231-9. doi: 10.1007/s00122-012-1976-6. Epub 2012 Sep 13.
Genome-wide detection of short insertion/deletion length polymorphisms (InDels, <5 bp) in Brassica rapa (named the A genome) was performed by comparing whole-genome re-sequencing data from two B. rapa accessions, L144 and Z16, to the reference genome sequence of Chiifu-401-42. In total, we identified 108,558 InDel polymorphisms between Chiifu-401-42 and L144, 26,795 InDels between Z16 and Chiifu-401-42, and 26,693 InDels between L144 and Z16. From these, 639 InDel polymorphisms of 3-5 bp in length between L144 and Z16 were selected for experimental validation; 491 (77%) yielded single PCR fragments and showed polymorphisms, 7 (1%) did not amplify a product, and 141 (22%) showed no polymorphism. For further validation of these intra-specific InDel polymorphisms, 503 candidates, randomly selected from the 639 InDels, were screened across seven accessions representing different B. rapa cultivar groups. Of these assayed markers, 387 (77%) were polymorphic, 111 (22%) were not polymorphic and 5 (1%) did not amplify a PCR product. Furthermore, we randomly selected 518 InDel markers to validate their polymorphism in B. napus (the AC genome) and B. juncea (the AB genome), of which more than 90% amplified a PCR product; 132 (25%) showed polymorphism between the two B. napus accessions and 41 (8%) between the two B. juncea accessions. This set of novel PCR-based InDel markers will be a valuable resource for genetic studies and breeding programs in B. rapa.
通过比较两个甘蓝型油菜品种 L144 和 Z16 的全基因组重测序数据与 Chiifu-401-42 的参考基因组序列，在 Brassica rapa（命名为 A 基因组）中进行了短插入/缺失长度多态性（InDels，<5 bp）的全基因组检测。总共，我们在 Chiifu-401-42 与 L144 之间鉴定了 108558 个 InDel 多态性，在 Z16 与 Chiifu-401-42 之间鉴定了 26795 个 InDels，在 L144 与 Z16 之间鉴定了 26693 个 InDels。从这些中，选择了 L144 和 Z16 之间 3-5 bp 长度的 639 个 InDel 多态性进行实验验证；491（77%）产生了单 PCR 片段并显示出多态性，7（1%）未扩增产物，141（22%）没有多态性。为了进一步验证这些种内 InDel 多态性，从 639 个 InDels 中随机选择 503 个候选者，在代表不同甘蓝型油菜品种组的七个品种中进行筛选。在这些检测标记中，387（77%）是多态性的，111（22%）是非多态性的，5（1%）未扩增出 PCR 产物。此外，我们随机选择了 518 个 InDel 标记，以验证它们在油菜（AC 基因组）和芥菜（AB 基因组）中的多态性，其中超过 90%的标记可以扩增出 PCR 产物；在两个油菜品种之间有 132（25%）个显示多态性，在两个芥菜品种之间有 41（8%）个显示多态性。这组新的基于 PCR 的 InDel 标记将成为甘蓝型油菜遗传研究和育种计划的宝贵资源。
