State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
Novel Bioinformatics Company, Shanghai, 200240, China.
J Integr Plant Biol. 2015 Nov;57(11):980-91. doi: 10.1111/jipb.12354. Epub 2015 Sep 1.
DNA markers play important roles in plant breeding and genetics. The Insertion/Deletion (InDel) marker is one kind of co-dominant DNA markers widely used due to its low cost and high precision. However, the canonical way of searching for InDel markers is time-consuming and labor-intensive. We developed an end-to-end computational solution (InDel Markers Development Platform, IMDP) to identify genome-wide InDel markers under a graphic pipeline environment. IMDP constitutes assembled genome sequences alignment pipeline (AGA-pipe) and next-generation re-sequencing data mapping pipeline (NGS-pipe). With AGA-pipe we are able to identify 12,944 markers between the genome of rice cultivars Nipponbare and 93-11. Using NGS-pipe, we reported 34,794 InDels from re-sequencing data of rice cultivars Wu-Yun-Geng7 and Guang-Lu-Ai4. Combining AGA-pipe and NGS-pipe, we developed 205,659 InDels in eight japonica and nine indica cultivars and 2,681 InDels showed a subgroup-specific pattern. Polymerase chain reaction (PCR) analysis of subgroup-specific markers indicated that the precision reached 90% (86 of 95). Finally, to make them available to the public, we have integrated the InDels/markers information into a website (Rice InDel Marker Database, RIMD, http://202.120.45.71/). The application of IMDP in rice will facilitate efficiency for development of genome-wide InDel markers, in addition it can be used in other species with reference genome sequences and NGS data.
DNA 标记在植物育种和遗传学中起着重要作用。插入/缺失 (InDel) 标记是一种共显性 DNA 标记，由于其成本低、精度高而被广泛应用。然而，寻找 InDel 标记的传统方法既耗时又费力。我们开发了一种端到端的计算解决方案 (InDel Markers Development Platform，IMDP)，以便在图形管道环境下识别全基因组范围内的 InDel 标记。IMDP 由组装基因组序列比对管道 (AGA-pipe) 和下一代重测序数据映射管道 (NGS-pipe) 组成。通过 AGA-pipe，我们能够在水稻品种 Nipponbare 和 93-11 的基因组之间识别出 12944 个标记。使用 NGS-pipe，我们报告了水稻品种 Wu-Yun-Geng7 和 Guang-Lu-Ai4 的重测序数据中的 34794 个 InDels。通过 AGA-pipe 和 NGS-pipe 的组合，我们在 8 个粳稻和 9 个籼稻品种中开发了 205659 个 InDels，其中 2681 个 InDels 显示出亚组特异性模式。亚组特异性标记的聚合酶链反应 (PCR) 分析表明，精度达到 90%（86 个中的 95 个）。最后，为了使它们可供公众使用，我们将 InDels/标记信息集成到一个网站中（水稻 InDel 标记数据库，RIMD，http://202.120.45.71/）。IMDP 在水稻中的应用将提高全基因组 InDel 标记开发的效率，此外，它还可以在具有参考基因组序列和 NGS 数据的其他物种中使用。
