Skip to main content
Log in

Marker-assisted gene introgression for resistance to Xanthomonas oryzae pv. oryzae in rice for the control of bacterial leaf blight

  • Research
  • Published:
Euphytica Aims and scope Submit manuscript


Bacterial leaf blight, sometimes known as BLB, is one of the most damaging diseases that may jeopardize the world’s supply of rice. It is caused by the bacterium Xanthomonas oryzae pv. oryzae (Xoo). It has caused sharp decline in production in regions of the globe that produce rice. More than 40 previously characterized resistance (R) genes enable host tolerance for diverse Xoo strains. In this study, three BLB resistant genes, including xa5, xa13, and Xa21, which have been crucial in disease prevention in Bangladesh, were introgressed into populations. These populations were created by crossing IRRI 154, a popular rice variety with a modern genetic background, with IRBB66 (resistant to BLB). Fifteen virulent bacterial isolates were used for BLB infection, and promising recombinants from the F5 and BC2F4 generations were found to be resistant. Using marker assisted selection (MAS) with gene-specific primers on generations F5 and BC2F4, we were able to find that 60 recombinant introgressed lines (RILs) had a pyramiding of BLB resistance genes. In terms of agronomic performance, the RILs outperformed both their donor and recipient parents, demonstrating that the RILs had pyramided three resistance genes, therefore conferring broad-spectrum BLB resistance. The produced BLB-resistant RILs offer substantial future development potential, either as cultivable crops or as BLB resistance donor material for use in boosting the yields of other rice lines.

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

Access this article

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

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

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

Data availability

The datasets generated during and/or analysed during the current study are available from the corresponding author on reasonable request.


  • Alam MS, Islam MR, Hossain I, Bhuiyan M, Khan M (2016) Pathotypic variation of Xanthomonas oryzae pv. oryzae in Bangladesh. Arch Phytopathol Plant Prot 49(1–4):31–42

  • Atlin GN, Cairns JE, Das B (2017) Rapid breeding and varietal replacement are critical to adaptation of cropping systems in the developing world to climate change. Glob Food Sec 12:31–37

    Article  PubMed  PubMed Central  Google Scholar 

  • BBS (2016) Yearbook of Agricultural Statistics of Bangladesh 2016. Bangladesh Bureau of Statistics, Dhaka, Bangladesh

  • Bharani M, Nagarajan P, Rabindran R, Saraswathi R, Balasubramanian P, Ramalingam J (2010) Bacterial leaf blight resistance genes (Xa21, xa13 and xa5) pyramiding through molecular marker assisted selection into rice cultivars. Archives of Phytopathology and Plant Protection 43(10):1032–1043

    Article  CAS  Google Scholar 

  • Bhuiyan N, Paul D, Jabber M (2002) Feeding the extra millions. In: Proceedings of the BRRI-DAE workshop on experiences of HYV rice production in Bangladesh, Bangladesh Rice Research Institute, Gazipur-1701, 2002

  • Cha K, Kim Y, Kim H, Lee D, Kim M (1982) Effects of application levels of fertilizer on the susceptibility to bacterial leaf blight, yield and quality of grains in nineteen rice cultivars in Jeonnam Region. Korean Journal of Applied Entomology 21(4):216–221

    Google Scholar 

  • Chunwongse J, Martin G, Tanksley S (1993) Pre-germination genotypic screening using PCR amplification of half-seeds. Theor Appl Genet 86(6):694–698

    Article  CAS  PubMed  Google Scholar 

  • Collard BC, Mackill DJ (2008) Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Philos Trans R Soc B: Biol Sci 363(1491):557–572

    Article  CAS  Google Scholar 

  • Das G, Rao G (2015) Molecular marker assisted gene stacking for biotic and abiotic stress resistance genes in an elite rice cultivar. Front Plant Sci 6:698

    Article  PubMed  PubMed Central  Google Scholar 

  • Das G, Rao GJ, Varier M, Prakash A, Prasad D (2018) Improved Tapaswini having four BB resistance genes pyramided with six genes/QTLs, resistance/tolerance to biotic and abiotic stresses in rice. Sci Rep 8(1):1–16

    Google Scholar 

  • Dash AK, Rao RN, Rao G, Verma RL, Katara JL, Mukherjee AK, Singh ON, Bagchi TB (2016) Phenotypic and marker-assisted genetic enhancement of parental lines of Rajalaxmi, an elite rice hybrid. Front Plant Sci 7:1005

    Article  PubMed  PubMed Central  Google Scholar 

  • Dokku P, Das K, Rao G (2013) Pyramiding of four resistance genes of bacterial blight in Tapaswini, an elite rice cultivar, through marker-assisted selection. Euphytica 192(1):87–96

    Article  Google Scholar 

  • Finatto T, de Oliveira AC, Chaparro C, Da Maia LC, Farias DR, Woyann LG, Mistura CC, Soares-Bresolin AP, Llauro C, Panaud O (2015) Abiotic stress and genome dynamics: specific genes and transposable elements response to iron excess in rice. Rice 8(1):1–18

    Article  Google Scholar 

  • Gautam RK, Singh PK, Sakthivel K, Srikumar M, Kumar N, Kumar K, Singh AK, Roy SD (2015) Analysis of pathogenic diversity of the rice bacterial blight pathogen (Xanthomonas oryzae pv. oryzae) in the Andaman Islands and identification of effective resistance genes. J Phytopathol 163(6):423–432

  • Goulden C (1939) Problems in plant selection. In: Proc Seventh Genet Cong Cambridge University Press, pp 132–133

  • Hasan MM, Rafii MY, Ismail MR, Mahmood M, Rahim HA, Alam MA, Ashkani S, Malek MA, Latif MA (2015) Marker-assisted backcrossing: a useful method for rice improvement. Biotechnol Biotechnol Equip 29(2):237–254

    Article  PubMed  PubMed Central  Google Scholar 

  • Horino O, Siwi BH, Miah SA, Mew TW (1983) Virulence of Xanthomonas campestris pv. oryzae isolated in Indonesia and Bangladesh. Japanese J Phytopathol 49(2):191–199

  • Islam MR, Alam MS, Khan AI, Hossain I, Adam LR, Daayf F (2016) Analyses of genetic diversity of bacterial blight pathogen, Xanthomonas oryzae pv. oryzae using IS1112 in Bangladesh. Comptes Rendus Biol 339(9–10):399–407

  • Jabeen R, Iftikhar T, Batool H (2012) Isolation, characterization, preservation and pathogenicity test of Xanthomonas oryzae pv. oryzae causing BLB disease in rice. Pak J Bot 44(1):261–265

  • Kauffman H (1973) An improved technique for evaluat-ing resistance of rice varieties to Xanthomonas oryzae. Plant Dis Rep 57:537–541

    Google Scholar 

  • Ke Y, Hui S, Yuan M (2017) Xanthomonas oryzae pv. oryzae inoculation and growth rate on rice by Leaf clipping method. Bio Protoc 7(19): e2568

  • Khush GS (2005) What it will take to feed 5.0 billion rice consumers in 2030. Plant Mol Biol 59(1):1–6

  • Khush GS, Jena K (2009) Current status and future prospects for research on blast resistance in rice (Oryza sativa L.). In: Advances in genetics, genomics and control of rice blast disease, pp 1–10

  • Kumar GS, Kumari KA, Rani CVD, Sundaram R, Vanisree S, Jamaloddin M, Swathi G (2013) Study of simple sequence repeat (SSR) polymorphism for biotic stress resistance in elite rice variety JGL 1798. Afr J Biotechnol 12(40)

  • Laha GS, Reddy CS, Krishnaveni D, Sundaram RM, Prasad MS, Ram T, Muralidharan K and Viraktamath BC (2009) Bacterial blight of rice and its management. DRR Techn Bull No. 41. Directorate of Rice Research (ICAR), Rajendranagar, Hyderabad, 37p

  • Lee K, Rasabandith S, Angeles E, Khush G (2003) Inheritance of resistance to bacterial blight in 21 cultivars of rice. Phytopathology 93(2):147–152

    Article  CAS  PubMed  Google Scholar 

  • Luo Y, Ma T, Zhang A, Ong KH, Li Z, Yang J, Yin Z (2016) Marker-assisted breeding of the rice restorer line Wanhui 6725 for disease resistance, submergence tolerance and aromatic fragrance. Rice 9(1):1–13

    Article  Google Scholar 

  • Mew T (1987) Current status and future prospects of research on bacterial blight of rice. Annu Rev Phytopathol 25(1):359–382

    Article  Google Scholar 

  • Mundt CC (2018) Pyramiding for resistance durability: theory and practice. Phytopathology 108(7):792–802

    Article  CAS  PubMed  Google Scholar 

  • Pradhan SK, Nayak DK, Mohanty S, Behera L, Barik SR, Pandit E, Lenka S, Anandan A (2015) Pyramiding of three bacterial blight resistance genes for broad-spectrum resistance in deepwater rice variety. Jalmagna Rice 8(1):1–14

    Google Scholar 

  • Prasad R, Shivay YS, Kumar D (2017) Current status, challenges, and opportunities in rice production. In: Rice production worldwide, pp 1–32

  • Rashid MM, Nihad SAI, Khan MAI, Haque A, Ara A, Ferdous T, Hasan MAI, Latif MA (2021) Pathotype profiling, distribution and virulence analysis of Xanthomonas oryzae pv. oryzae causing bacterial blight disease of rice in Bangladesh. J Phytopathol 169(7–8):438–446

  • Ray DK, Mueller ND, West PC, Foley JA (2013) Yield trends are insufficient to double global crop production by 2050. PLoS ONE 8(6):e66428

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sanchez A, Brar D, Huang N, Li Z, Khush G (2000) Sequence tagged site marker-assisted selection for three bacterial blight resistance genes in rice. Crop Sci 40(3):792–797

    Article  CAS  Google Scholar 

  • Shankara K, Patil M, Pramesh D, Sunkad G, Yenjerappa S, Ibrahim M, Rajesh N (2017) Chikkannaswamy. Isolation and characterization of bacterial leaf blight of rice (X. oryzae pv. oryzae) isolates from Southern India. Int J Pure Appl Biosci 5(4):452–461

  • Suela MM, Lima LP, Azevedo CF, Resende MDVd, Nascimento M, Silva FF (2019) Combined index of genomic prediction methods applied to productivity. Ciência Rural 49

  • Suh JP, Jeung JU, Noh TH, Cho YC, Park SH, Park HS, Shin MS, Kim CK, Jena KK (2013) Development of breeding lines with three pyramided resistance genes that confer broad-spectrum bacterial blight resistance and their molecular analysis in rice. Rice 6(1):1–11

    Article  Google Scholar 

  • Sundaram R, Laha G, Viraktamath B, Sujatha K, Natarajkumar P, Hari Y, Srinivasa Rao K, Reddy C, Balachandran S, Madhav M (2011) Marker assisted breeding for development of bacterial blight resistant rice. Genomics Crop Improv: Relevance Reserv (Institute of Biotechnology, Acharya NG Ranga Agricultural University, Hyderabad) 500(030):154–182

    Google Scholar 

  • USDA F (2020) Livestock and Poultry: World Markets and Trade. United States Department of Agriculture. Foreign Agriculture Service

  • Xu J, Jiang J, Dong X, Ali J, Mou T (2012) Introgression of bacterial blight (BB) resistance genes Xa7 and Xa21 into popular restorer line and their hybrids by molecular marker-assisted backcross (MABC) selection scheme. Afr J Biotech 11(33):8225–8233

    CAS  Google Scholar 

  • Zhai W, Zhu L (1999) Rice bacterial blight resistance genes and their utilization in molecular breeding. Prog Biotechnol 19:9–15

    Google Scholar 

  • Zheng K, Huang N, Bennett J, Khush GS (1995) PCR-based marker-assisted selection in rice breeding. IRRI Discussion Paper Series (Philippines)

Download references


The authors would like to express their gratitude to Dr. F H Ansarey, President, ACI Limited, Dhaka 1212, Bangladesh, for providing continual emotional support, and assistance with lab equipment.


The authors declare that no funds, grants, or other support were received during the preparation of this manuscript.

Author information

Authors and Affiliations



All authors contributed to the study conception and design. Material preparation, data collection and analysis were performed by Md. Ariful Islam, Md. Moniruzzaman Hasan and Tanbin Akter. The first draft of the manuscript was written by Md. Ariful Islam and Md. Moniruzzaman Hasan and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Md. Moniruzzaman Hasan.

Ethics declarations

Competing interests

The authors declare that they have no conflict of interest regarding this manuscript and research.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Islam, M.A., Hasan, M.M., Rahman, M.A. et al. Marker-assisted gene introgression for resistance to Xanthomonas oryzae pv. oryzae in rice for the control of bacterial leaf blight. Euphytica 220, 60 (2024).

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: