Development of genome-wide insertion/deletion markers in rice based on graphic pipeline platform |
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Authors: | Yang Lü Xiao Cui Rui Li Piaopiao Huang Jie Zong Danqing Yao Gang Li Dabing Zhang Zheng Yuan |
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Affiliation: | 1.State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China;2.Novel Bioinformatics Company, Shanghai, China;3.Shanghai Agricultural Technology Extension and Service Center, Shanghai, China |
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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 laborintensive.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 resequencing 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 AGApipe 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. |
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Keywords: | Genetic polymorphism genome alignment InDel marker molecular breeding next-generation sequencing |
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