title: Development of genome-wide insertion/deletion markers in rice based on graphic pipeline platform.
abstract: 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.
authors: State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
authors: Yang
authors: Y
authors: Lü
authors: State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
authors: Xiao
authors: X
authors: Cui
authors: State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
authors: Rui
authors: R
authors: Li
authors: State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
authors: Piaopiao
authors: P
authors: Huang
authors: Novel Bioinformatics Company, Shanghai, 200240, China.
authors: Jie
authors: J
authors: Zong
authors: Shanghai Agricultural Technology Extension and Service Center, Shanghai, 201103, China.
authors: Danqing
authors: D
authors: Yao
authors: Shanghai Agricultural Technology Extension and Service Center, Shanghai, 201103, China.
authors: Gang
authors: G
authors: Li
authors: State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
authors: Dabing
authors: D
authors: Zhang
authors: State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
authors: Zheng
authors: Z
authors: Yuan
mesh_terms: D005819:Genetic Markers; D023281:Genomics / Q000379:methods*; D054643:INDEL Mutation; D012275:Oryza / Q000235:genetics*
chemical_list: D005819:Genetic Markers
keywords: Genetic polymorphism; InDel marker; genome alignment; molecular breeding; next-generation sequencing