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Genome-scale identification of resistance gene analogs and the development of their intron length polymorphism markers in maize

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Abstract

As introns are vulnerable to changes such as insertions and deletions when exposed to various evolutionary forces, they constitute a repository for developing genetic markers based on intron length polymorphisms (ILP). This study developed a set of genetic markers that use the potential intron length polymorphism in resistance gene analogs (RGAs) in Zea mays. By searching the genome of Zea mays B73 for the homologs of 73 R genes which have already been identified in plants, we found 861 RGAs, 632 of which have at least one intron that can serve as putative markers targeting the intron length polymorphism in RGAs (RGA-ILP). We developed 1972 candidate markers via electronic PCR (e-PCR) with primer pairs designed in each pair of exonic regions that flank an intron. Furthermore, the performance of RGA-ILP among four maize inbred lines (Huangzao4, B73, Mo17, and Dan340) was evaluated with 69 pairs of randomly selected primers. Of them, 46.4% showed bands that had discriminating length polymorphism, and between any two of the inbred lines the proportion of polymorphism ranged from 23.2 to 31.9%. To make it convenient to use these markers for those interested in molecular breeding of disease-resistant maize, we provide all related information in a web-based database named MaizeRGA, which is available at http://www.sicau.edu.cn/web/yms/rga/maizeRGA.html.

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Acknowledgments

We thank Dr. Chen Guoyue from the Triticeae Research Institute of Sichuan Agricultural University for helpful discussions during this study. The authors thank two anonymous reviewers and Dr Yann Klimentidis for critical reading. This work is supported by the grants from National Natural Science Foundation of China (No.30800687 and 31071434), Applied Basic Research Program of Sichuan Provincial Science and Technology Department (No.2008JY0096), and the ‘863’ High Technology Development Program (No.2009AA10AA03_2).

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Authors and Affiliations

  1. Institute of Maize Research, College of Agriculture, Sichuan Agricultural University, 625014, Ya-an, Sichuan, China

    Hailan Liu, Yueai Lin, Yaou Shen, Jian Liu & Suzhi Zhang

  2. Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA

    Guobo Chen

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  1. Hailan Liu
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  2. Yueai Lin
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Correspondence to Hailan Liu or Suzhi Zhang.

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H. Liu and Y. Lin have contributed equally to this work.

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Liu, H., Lin, Y., Chen, G. et al. Genome-scale identification of resistance gene analogs and the development of their intron length polymorphism markers in maize. Mol Breeding 29, 437–447 (2012). https://doi.org/10.1007/s11032-011-9560-3

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