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Marker-Assisted Simultaneous and Stepwise Pyramiding of Broad-Spectrum Bacterial Leaf Blight Resistance Genes, Xa33 and Xa38, into Salt-Tolerant Rice Variety “CO43”

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Bacterial leaf blight (BLB) disease is one of the most important diseases of rice in India and worldwide. The management of this disease becomes extremely challenging due to the presence of Xoo races with varying level of virulence and diversity. The development of BLB-resistant rice lines with the help of marker-assisted selection has been proven as one of the most effective strategies to sustain rice cultivation. This study demonstrates marker-assisted introgression and pyramiding of two broad-spectrum BLB genes (Xa33 and Xa38) into the background of “CO43,” a popular fine white-grained rice cultivar, tolerant to saline coastal areas in southern India. Two separate marker-assisted backcrossing schemes were used, and at each stage of backcrossing, foreground, recombinant, and background selection were carried out. Backcross-derived lines possessing either Xa33 or Xa38 along with maximum genome recovery of “CO43” were identified at BC2F1 generation, intercrossed with each other to pyramid the genes, and selfed to identify homozygous lines for the pyramided genes. The performance of the improved “CO43” lines, such as lines # 2_7_78, 2_7_102, 6_9_65, and 6–8-76 exhibited enhanced broad-spectrum resistance to BLB (lesion length, LL 0.0 ± 0.0 to 0.9 ± 0.1 cm). Furthermore, the improved “CO43” lines maintained the agro-morphological features of the recurrent parent along with enhanced BLB resistance. These lines with effective and durable resistance would contribute to sustainable rice production in coastal areas of southern India.

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The datasets utilized and analyzed during this investigation are available upon reasonable request from the author.


  • Abdul Fiyaz R, Shivani D, Chaithanya K, Mounika K, Chiranjeevi M, Laha GS, Viraktamath BC, Subba Rao LV, Sundaram RM (2022) Genetic improvement of rice for bacterial blight resistance: present status and future prospects. Rice Sci 29(118):132.

    Article  Google Scholar 

  • Abhilash Kumar V, Balachiranjeevi CH, Bhaskar Naik S, Rambabu R, Rekha G, Harika G, Hajira SK, Pranathi K, Vijay S, Anila M, Mahadevaswamy HK (2016) Marker-assisted improvement of the elite restorer line of rice, RPHR-1005 for resistance against bacterial blight and blast diseases. J Gen 95(4):895–903.

  • Ahmed A, Ramalingam J, Isong A, Mala KK, Mbe JO (2021) Marker-assisted gene pyramiding for bacterial blight resistance in some improved rice genotypes. Badeggi J Agri Res Env 03(01):10–21.

  • Balachiranjeevi C, Naik B, Kumar A, Harika G, Hajira S, Kumar D, Anila M, Kale R, Yugender A, Pranathi K, Koushik M (2018) Marker-assisted pyramiding of two major, broad-spectrum bacterial blight resistance genes, Xa21 and Xa33 into an elite maintainer line of rice, DRR17B. PLoS One 13(10):e0201271.

  • Baliyan N, Malik R, Rani R, Mehta K, Vashisth U, Dhillon S, Boora KS (2018) Integrating marker-assisted background analysis with foreground selection for pyramiding bacterial blight resistance genes into Basmati rice. C r Biologies 341:1–8.

    Article  PubMed  Google Scholar 

  • Bhasin H, Bhatia D, Raghuvanshi S, Lore LJ, Sahi GK, 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 

  • Cheema KK, Grewal NK, Vikal Y, Sharma R, Lore JS, Das A, Bhatia D, Mahajan R, Gupta V, Bharaj T, Sing K (2008) A novel bacterial blight resistance mapped to 38 kb region on chromosome and transferred to Oryza sativa L. Genet Res Cambridge 90:397–407.

    Article  CAS  Google Scholar 

  • Chen S, Lin XH, Xu CG, Zhang QF (2000) Improvement of bacterial blight resistance of ‘Minghui 63’, an elite restorer line of hybrid rice, by molecular marker-assisted selection. Crop Sci 40:239–244.

    Article  Google Scholar 

  • Chen S, Wang C, Yang J, Chen B, Wang W, Su J, Feng A, Zeng L, Zhu X (2020) Identification of the novel bacterial blight resistance gene Xa46(t) by mapping and expression analysis of the rice mutant H120. Sci Rep 10:12642.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dellaporta SL, Wood J, Hicks JB (1983) A plant DNA Minipreparation version 2. Plant Mol Biol Repor 1:19–22.

    Article  CAS  Google Scholar 

  • Ellur RK, Khanna A, Krishnan G, Bhowmick PK, Vinod KK, Nagarajan M, Mon KK (2016) Marker-aided Incorporation of Xa38, a novel bacterial blight resistance gene, in PB1121 and comparison of its resistance spectrum with xa13+Xa21. Sci Rep 6:29188.

    Article  PubMed  PubMed Central  Google Scholar 

  • Gidamo GH, Kumaravadivel N (2015) Marker-assisted introgression of broad spectrum bacterial blight resistance gene Xa33 into CO43, salt and alkaline soil tolerant Indica rice variety. Trends in Biosciences 8:2136–2142

    Google Scholar 

  • Gidamo GH, Kumaravadivel N, Rabindran R, Ramanathan A (2015) Identification and validation of microsatellite marker linked to the putative bacterial blight resistance gene Xa33 in rice. Trends in Biosciences 8:1069–1073

    Google Scholar 

  • Gomez KA, Gomez AA (1984) Statistical procedures for agricultural research. New York. John Wiley and Sons, NY

  • IRRI-SES (International Rice Research Institute) (2013) Standard evaluation system for rice. 5th edition, Manila, Philippines: IRRI

  • Joseph M, Gopalakrishnan S, Sharma RK, Singh VP, Singh AK, Singh NK, Mohapatra T (2004) Combining bacterial blight resistance and basmati quality characteristics by phenotypic and molecular marker-assisted selection in rice. Mol Breed 13:377–387.

    Article  CAS  Google Scholar 

  • Ke Y, Hui S, Yuan M (2017) Xanthomonas oryzae pv. oryzae inoculation and growth rate on rice by leaf clipping method. Bio-Protocol 7(19).

  • Kim SM, Kim CS, Jeong JU, Reinke RF, Jeong JM (2019) Marker-assisted breeding for improvement of anaerobic germination in japonica rice (Oryza sativa). Plant Breed 138:810–819.

    Article  CAS  Google Scholar 

  • Korinsak S, Darwell CT, Wanchana S, Praphaisal L, Korinsak S, Thunnom B, Patarapuwadol S, Toojinda T (2021) Identification of bacterial blight resistance loci in rice (Oryza sativa L.) against diverse Xoo Thai strains by genome-wide association study. Plants 10:518.

  • Kumar M, Singh RP, Jena D, Singh V, Rout D, Arsode PB, Choudhary M, Singh P, Chahar S, Samantaray S, Mukherjee AK, Mohan C, Bohra A, Das G, Bola S, Singh ON, Verma B (2023) Marker-Assisted improvement for durable bacterial blight resistance in aromatic rice cultivar HUR 917 popular in Eastern parts of India. Plants 12(6):1363.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kumar PN, Sujatha K, Laha GS, Rao KS, Mishra B, Viraktamath BC, Hari Y, Reddy CS, Balachandran SM, Ram T, Madhav MS (2012) Identification and fine mapping of Xa33, a novel gene for resistance to Xanthomonas oryzae pv. oryzae. Phyto Path 102:222–228.

  • Luo Y, Sangha JS, Wang S, Li Z, Yang J, Yin Z (2012) Marker-assisted breeding of Xa4, Xa21 and Xa27 in the restorer lines of hybrid rice for broad-spectrum and enhanced disease resistance to bacterial blight. Mol Breed 30:1601–1610.

    Article  CAS  Google Scholar 

  • Marè C, Zampieri E, Cavallaro V, Frouin J, Grenier C, Courtois B, Brottier L, Tacconi G, Finocchiaro F, Serrat X, Nogués S, Bundó M, San Segundo B, Negrini N, Pesenti M, Sacchi GA, Gavina G, Bovina R, Monaco S, Tondelli A, Cattivelli L, Valè G (2023) Marker-assisted introgression of the salinity tolerance locus saltol in temperate Japonica rice. Rice 16(1):2.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Noh TH, Lee DK, Park JC, Shim HK, Choi YM, Kang MH, Kim DJ (2007) Effect of bacterial leaf blight occurrence on rice yield and grain quality in different rice growth stage. Res Plant Dis 13:20–23.

    Article  Google Scholar 

  • 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 

  • Subramanian S, Balasubramanian KM, Ranganathan TB, Sivasubramanian V, Chandramohan J (1984) CO43, a salt tolerant variety for Tamil Nadu. IRRN 9:3

    Google Scholar 

  • Sundaram RM, Vishnupriya RM, Biradar SK, Laha GS, Ashok Reddy G, Shobha Rani N, Sarma NP, Sonti RV (2008) Marker assisted introgression of bacterial blight resistance in Samba Mahsuri, an elite indica rice variety. Euphytica 160:411–422.

    Article  Google Scholar 

  • Wang S, Liu W, Lu D, Lu Z, Wang X, Xue J, He X (2020) Distribution of bacterial blight resistance genes in the main cultivars and application of Xa23 in rice breeding. Front Plant Sci 11:555228.

    Article  PubMed  PubMed Central  Google Scholar 

  • Xing J, Zhang D, Yin F, Zhong Q, Wang B (2021) Identification and fine-mapping of a new bacterial blight resistance gene, Xa47(t), in G252, an introgression line of Yuanjiang common wild rice (Oryza rufipogon). Plant Dis 105:4106–4112.

    Article  CAS  PubMed  Google Scholar 

  • Yugander A, Sundaram RM, Singh K, Senguttuvel P, Ladhalakshmi D, Kemparaju KB, Madhav MS, Prasad MS, Hariprasad AS, Laha GS (2018) Improved versions of rice maintainer line, APMS 6B, possessing two resistance genes, Xa21 and Xa38, exhibit high level of resistance to bacterial blight disease. Mol Breed 38:100.

    Article  CAS  Google Scholar 

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The authors gratefully acknowledge the financial support of AU, ICAR, and DBT, Government of India.


This work was funded by the Department of Biotechnology, Government of India (DBT, Grant No. BT/PR11705/ AGR/02 /646/2008), funding provided for N Kumaravadivel.

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GHG performed the experiment, analyzed data, and prepared the manuscript, and KN conceived the project. All authors reviewed the manuscript.

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Correspondence to Gizachew Haile Gidamo.

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Gidamo, G.H., Nachimuthu, K. Marker-Assisted Simultaneous and Stepwise Pyramiding of Broad-Spectrum Bacterial Leaf Blight Resistance Genes, Xa33 and Xa38, into Salt-Tolerant Rice Variety “CO43”. Plant Mol Biol Rep (2024).

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