J Integr Plant Biol. ›› 2015, Vol. 57 ›› Issue (11): 980-991.DOI: 10.1111/jipb.12354

• New Technology • Previous Articles    

Development of genome-wide insertion/deletion markers in rice based on graphic pipeline platform

Yang Lü1, Xiao Cui1†, Rui Li1, Piaopiao Huang1, Jie Zong2, Danqing Yao3, Gang Li3, Dabing Zhang1 and Zheng Yuan1*   

  1. 1State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
    2Novel Bioinformatics Company, Shanghai, China
    3Shanghai Agricultural Technology Extension and Service Center, Shanghai, China
  • Received:2014-12-18 Accepted:2015-03-19 Published:2015-11-01
  • About author:These authors contribute equally to this work.
    *Correspondence: E-mail: zyuan@sjtu.edu.cn


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, 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.


Lu Y, Cui X, Li R, Huang P, Zong J, Yao D, Li G, Zhang D, Yuan Z (2015) Development of genome-wide insertion/deletion markers in rice based on graphic pipeline platform. J Integr Plant Biol 57: 980–991 doi: 10.1111/jipb.12354

Key words: Genetic polymorphism, genome alignment, InDel marker, molecular breeding, next-generation sequencing

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