Skip to main content
SpringerLink
Log in

Population structure analysis and association mapping of bacterial blight resistance in indica rice (Oryza sativa L.) accessions

  • Original Paper
  • Published:
Plant Growth Regulation Aims and scope Submit manuscript

Abstract

Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is a serious disease in rice production worldwide. To understand the genetic diversity of bacterial blight resistance a population consisting of 175 indica accessions from nine countries was collected and detected their association between SSR (Simple Sequence Repeat) markers and resistance to six bacterial races. The resistance phenotypes of various rice accessions were evaluated through artificial inoculation under controlled conditions in 2013 and 2014. Association analysis showed that 17 SSR markers were significantly associated with resistance to four bacterial races and the phenotypic variations explained (PVE) ranged from 7.43 to 15.05%. Among the 17 associated SSR markers, two SSR markers located in previously reported genes regions, and 15 SSR markers were newly identified in this study. These results validated a new approach to map resistance genes of rice to bacterial blight. These markers could be used for marker-assisted selection (MAS) in rice bacterial blight resistance breeding programs.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Antony G, Zhou J, Huang S, Li T, Liu B, White F, Yang B (2010) Rice xa13 recessive resistance to bacterial blight is defeated by induction of the disease susceptibility gene Os-11N3. Plant Cell 22:3864–3876

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bhasin H, Bhatia D, Raghuvanshi S, Lore J, Sahi G, Kaur B, Vikal Y, Singh K (2012) New PCR-based sequence-tagged site marker for bacterial blight resistance gene Xa38 of rice. Mol Breed 30:607–611

    Article  CAS  Google Scholar 

  • Blair M, Garris A, Iyer A, Chapman B, Kresovich S, Mchouch S (2003) High resolution genetic mapping and candidate gene identification at the xa5 locus for bacterial blight resistance in rice (Oryza sativa L.). Theor Appl Genet 107:62–73

    Article  CAS  PubMed  Google Scholar 

  • Bradbury P, Zhang Z, Kroon D, Casstevens T, Ramdoss Y, Buckler E (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635

    Article  CAS  PubMed  Google Scholar 

  • Cao Y, Duan L, Li H, Sun X, Zhao Y, Xu C, Li X, Wang S (2007) Functional analysis of Xa3/Xa26 family members in rice resistance to Xanthomonas oryzae pv. oryzae. Theor Appl Genet 115:887–895

    Article  PubMed  Google Scholar 

  • Chen S, Liu X, Zeng L, Quyang D, Yang J, Zhu X (2011) Genetic analysis and molecular mapping of a novel recessive gene xa34(t) for resistance against Xanthomonas oryzae pv. oryzae. Theor Appl Genet 122:1331–1338

    Article  CAS  PubMed  Google Scholar 

  • Dellaporta S, Wood J, Hicks J (1983) A plant DNA minipreparation: version II. Plant Mol Biol 4:19–21

  • Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620

    Article  CAS  PubMed  Google Scholar 

  • Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567–1587

    CAS  PubMed  PubMed Central  Google Scholar 

  • Fang Z, Xu Z, Guo C (1990) The research of pathogenic types of bacterial blight of rice. Acta Phytopathol Sinica 20:81–87

  • Gu K, Yang B, Tian D, Wu L, Wang D, Sreekala C, Yang F, Chu Z, Wang GL, White FF, Yin Z (2005) R gene expression induced by a type-III effector triggers disease resistance in rice. Nature 435:1122–1125

    Article  CAS  PubMed  Google Scholar 

  • Gu K, Sangha JS, Li Y, Yin Z (2008) High-resolution genetic mapping of bacterial blight resistance gene Xa10. Theor Appl Genet 116:155–163

    Article  CAS  PubMed  Google Scholar 

  • Guo L, Guo W, Zhao H, Wang J, Liu H, Sun J, Zheng H, Sha H, Zou D (2015) Association mapping and resistant alleles’ analysis for japonica rice blast resistance. Plant Breed 134:646–652

    Article  CAS  Google Scholar 

  • Huang N, Angeles E, Domingo J, Magpantay G, Singh S, Zhang G, Kumaravadivel N, Bennett J, Khush G (1997) Pyramiding of bacterial blight resistance genes in rice: marker-assisted selection using RFLP and PCR. Theor Appl Genet 95:313–320

    Article  CAS  Google Scholar 

  • Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y, Li C, Zhu C, Lu T, Zhang Z, Li M, Fan D, Guo Y, Wang A, Wang L, Deng L, Li W, Lu Y, Weng Q, Liu K, Huang T, Zhou T, Jing Y, Li W, Lin Z, Buckler E, Qian Q, Zhang Q, Li J, Han B (2010) Genome-wide association studies of 14 agronomic traits in rice landraces accessions. Nat Genet 42:961–967

    Article  CAS  PubMed  Google Scholar 

  • Iyer-Pascuzzi A, Jiang H, Huang L, McCouch S (2008) Genetic and functional characterization of the rice bacterial blight disease resistance gene xa5. Phytopathology 98:289–295

    Article  CAS  PubMed  Google Scholar 

  • Jin L, Lu Y, Xiao P, Sun M, Corke H, Bao J (2010) Genetic diversity and population structure of a diverse set of rice germplasm for association mapping. Theor Appl Genet 121:475–487

    Article  PubMed  Google Scholar 

  • Jun T, Van K, Kim M, Lee S, Walker D (2008) Association analysis using SSR markers to find QTL for seed protein content in soybean. Euphytica 162:179–191

    Article  CAS  Google Scholar 

  • Kang H, Zhang Y, Wang G (2015) Molecular dissection of the complex genetic architecture of rice immunity to the blast fungus Magnaporthe oryzae using GWAS. Mol Plant Pathol. doi:10.1111/MPP.12340

    Google Scholar 

  • Kauffman H, Reddy P, Hsieh S, Merca S (1973) An improved technique for evaluating resistance of rice varieties to Xanthomonas oryzae. Plant Dis Rep 57:537–541

    Google Scholar 

  • Kawasaki-Tanaka A, Fukuta Y (2014) Genetic variation in resistance to blast disease (Pyricularia oryzae Cavara) in Japanese rice (Oryza sativa L.), as determined using a differential system. Breed Sci 64: 183–192

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kraakman A, Niks R, Van P, Stam P, Van Eeuwijk F (2004) Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars. Genetics 168:435–446

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu K, Muse S (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128–2129

    Article  CAS  PubMed  Google Scholar 

  • Liu Q, Yuan M, Zhou Y, Li X, Xiao J, Wang S (2011) A paralog of the MtN3/saliva family recessively confers race-specific resistance to Xanthomonas oryzae in rice. Plant Cell Environ 34:1958–1969

  • Liu W, Liu J, Triplett L, Leach J, Wang G (2014) Novel insights into rice innate immunity against bacterial and fungal pathogens. Annu Rev Phytopathol 52:213–241

    Article  CAS  PubMed  Google Scholar 

  • McCouch S, Teytelman L, Xu Y, Lobos K, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xing Y, Zhang Q, Kono I, Yano M, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L (2002) Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.) DNA Res 9:199–207

    Article  CAS  PubMed  Google Scholar 

  • Myles S, Peiffer J, Brown P, Ersoz E, Zhang Z, Costich D, Buckler E (2009) Association mapping: critical considerations shift from genotyping to experimental design. Plant Cell 21(8):2194–2202

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ni D, Yang J, Wu J, Li L, Yi C, Xu C, Wang X, Jia S, Zhang S (2004) Resistance to bacterial blight and utilization of Xa21-transgenic sterile line wan 21 A. Chin J Rice Sci 18:494–498

    CAS  Google Scholar 

  • Pritchard J, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 945–959

  • Rebecca S, Mawsheng C, Miguel E, Patrick C, Pamela C (2010) Rice Snl6, a Cinnamoyl-CoA reductase-Like like gene family member, is required for NH1- mediated immunity to Xanthomonas oryzae pv. Oryzae. PLoS Genet 6:110–117

    Google Scholar 

  • Shinada H, Yamamoto T, Sato H, Yamamoto E, Hori K, Yonemaru J, Sato T, Fujino K (2015) Quantitative trait loci for rice blast resistance detected in a local rice breeding population by genome-wide association mapping. Breed Sci 65:388–395

    Article  PubMed  PubMed Central  Google Scholar 

  • Simmonds N (1979) Principles of crop improvement. Longman, London

    Google Scholar 

  • Song W, Wang G, Chen L, Kim H, Pi L, Holsten T, Gardner J, Wang B, Zhai W, Zhu L, Fauquet C, Ronald P (1995) A receptor kinase-like protein encoded by the rice disease resistance gene Xa21. Science 270:1804–1806

    Article  CAS  PubMed  Google Scholar 

  • Tian Z, Qian Q, Liu Q Yan M, Liu X, Yan C, Liu G, Gao Z, Tang S, Zeng D, Wang Y, Yu J, Gu M, Li J (2009) Allelic diversities in rice starch biosynthesis lead to a diverse array of rice eating and cooking qualities. Proc Natl Acad Sci USA 106:21760–21765

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tian D, Wang J, Zeng X, Gu K, Qiu C, Yang X, Zhou Z, Goh M, Luo Y, MurataHori M, White F, Yin Z (2014) The rice TAL effector–dependent resistance protein XA10 triggers cell death and calcium depletion in the endoplasmic reticulum. Plant Cell 26: 497–515

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Van D (1968) Disease resistance in plants. Academic Press, New York

    Google Scholar 

  • Virk P, Ford-Lloyd B, Jackson M, Pooni H, Clemeno T, Newbury H (1996) Predicting quantitative variation within rice germplasm using molecular markers. Heredity 76:296–304

    Article  Google Scholar 

  • Wang C, Yang Y, Yuan X, Xu Q, Feng Y, Yu H, Wang Y, Wei X (2014a) Genome-wide association study of blast resistance in indica rice. BMC Plant Biol 14:311

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang C, Fang Y, Zheng C, Qin T, Zhang X, Zhao K (2014b) High-resolution genetic mapping of rice bacterial blight resistance gene Xa23. Mol Genet Genomics 289:745–753

    Article  CAS  PubMed  Google Scholar 

  • Yoshimura S, Yamanouchi U, Katayose Y, Toki S, Wang Z, Kono I, Kurata N, Yano M, Iwata N, Sasaki T (1998) Expression of Xa1, a bacterial blight-resistance gene in rice, is induced by bacterial inoculation. Proc Natl Acad Sci USA 95:1663–1668

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhao K, Tung C, Eizenga G, Wright M, Ali M, Price A, Norton G, Islam M, Reynolds A, Mezey J, McClung A, Bustamante C, McCouch S (2011) Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat Commun 2:1020–1021

Download references

Acknowledgements

This research has been supported by Grants from Special Fund for Agro-Scientific Research in the Public Interest (201303015), the National Key Project for Transgenic Crops (2016ZX08009-003-001, 2014ZX08009-001B), the Natural Science Foundation of China (30900888,31171516) and the Fundamental Research Funds for the Central Universities (KYZ201302), Jiangsu Agriculture science and technology inovation fund (CX(12)1003-3, CX(15)1054). We would like to thank Prof. Liu Fengquan for his kindly providing all the bacterial isolates.

Author information

Author notes

    Authors and Affiliations

    1. State Key Laboratory of Crop Genetics & Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China

      Hao Chen, Yunyu Wu, Jianbo He, Changhong Guan, Nengyan Fang, Wanwan He, Ruisen Wang, Jianfei Wang, Yongmei Bao & Hongsheng Zhang

    2. Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, China

      Hao Chen, Changhong Guan, Nengyan Fang, Wanwan He, Ruisen Wang, Jianfei Wang, Yongmei Bao & Hongsheng Zhang

    3. Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou, 225007, China

      Yunyu Wu & Aihong Li

    Authors
    1. Hao Chen
      View author publications

      You can also search for this author in PubMed Google Scholar

    2. Yunyu Wu
      View author publications

      You can also search for this author in PubMed Google Scholar

    3. Jianbo He
      View author publications

      You can also search for this author in PubMed Google Scholar

    4. Changhong Guan
      View author publications

      You can also search for this author in PubMed Google Scholar

    5. Aihong Li
      View author publications

      You can also search for this author in PubMed Google Scholar

    6. Nengyan Fang
      View author publications

      You can also search for this author in PubMed Google Scholar

    7. Wanwan He
      View author publications

      You can also search for this author in PubMed Google Scholar

    8. Ruisen Wang
      View author publications

      You can also search for this author in PubMed Google Scholar

    9. Jianfei Wang
      View author publications

      You can also search for this author in PubMed Google Scholar

    10. Yongmei Bao
      View author publications

      You can also search for this author in PubMed Google Scholar

    11. Hongsheng Zhang
      View author publications

      You can also search for this author in PubMed Google Scholar

    Corresponding authors

    Correspondence to Yongmei Bao or Hongsheng Zhang.

    Additional information

    Hao Chen, Yunyu Wu and Jianbo He have contributed equally to this work.

    Rights and permissions

    Reprints and permissions

    About this article

    Check for updates. Verify currency and authenticity via CrossMark

    Cite this article

    Chen, H., Wu, Y., He, J. et al. Population structure analysis and association mapping of bacterial blight resistance in indica rice (Oryza sativa L.) accessions. Plant Growth Regul 82, 21–35 (2017). https://doi.org/10.1007/s10725-016-0234-3

    Download citation

    • Received:

    • Accepted:

    • Published:

    • Issue Date:

    • DOI: https://doi.org/10.1007/s10725-016-0234-3

    Keywords

    Search

    Navigation