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High-resolution genetic mapping of a novel bacterial blight resistance gene xa-45(t) identified from Oryza glaberrima and transferred to Oryza sativa

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Key message

A novel recessive bacterial blight resistance locus designated as a xa-45(t) was identified from Oryza glaberrima accession IRGC 102600B, transferred to O. sativa and mapped to the long arm of chromosome 8 using ddRAD sequencing approach. The identified QTL spans 80 kb region on Nipponbare reference genome IRGSP-1.0 and contains 9 candidate genes. An STS marker developed from the locus LOC_Os08g42410 was found co-segregating with the trait and will be useful for marker-assisted transfer of this recessive resistance gene in breeding programs.


Bacterial blight, caused by Xanthomonas oryzae pv. oryzae, is one of the major constraints of rice productivity in Southeast Asia. In spite of having 44 bacterial blight resistance genes from cultivated rice and wild species, the durability of resistance is always at stake due to the continually evolving nature of the pathogen and lack of suitable chemical control. Here, we report high-resolution genetic mapping of a novel bacterial blight resistance gene tentatively designated as a xa-45(t) from an introgression line derived from Oryza glaberrima accession IRGC 102600B. This introgression line was crossed with the susceptible rice indica cultivar cv. Pusa 44 to generate F2 and F2:3 populations for inheritance and mapping studies. The inheritance studies revealed the presence of single recessive locus controlling resistance to the Xanthomonas pathotype seven. A high-density linkage map was constructed using double-digest restriction-associated DNA sequencing of 96 F2 populations along with the parents. The QTL mapping identified a major locus on the long arm of rice chromosome 8 with a LOD score of 33.22 between the SNP markers C8.26737175 and C8.26818765. The peak marker, C8.26810477, explains 49.8% of the total phenotypic variance and was positioned at 202.90 cM on the linkage map. This major locus spans 80 kb region on Nipponbare reference genome IRGSP-1.0 and contains 9 candidate genes. A co-segregating STS marker was developed from the LOC_Os08g42410 for efficient transfer of this novel gene to elite cultivars.

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The authors gratefully acknowledge the financial support from the Department of Biotechnology, Ministry of Science and Technology, Government of India, vide Grant Nos. BT/AB/03/FG-2/2003 and BT/AB/FG-2(PH-2) (2-B)/2009 for carrying out research. The grant provided by the Indian Agricultural Research Institute (ICAR), New Delhi, under Niche Area of Excellence vide Project Number F. No. 10(9)2011-EPD is also acknowledged for providing additional financial support for carrying out extension of the research work. We are thankful to Dr. Amit Kishore and Mr. Inderjit Singh Yadav for their suggestions during the revision of the manuscript.

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KS and KN designed the experiment and performed the phenotyping and genetic mapping using F2 population. JSL provided Xanthomonas cultures and assisted in phenotyping of mapping population. KS, RM, VG, DB, BKG and RK contributed in the phenotyping and genotyping of backcrossed derivatives. KN and KS analyzed the data and wrote the manuscript. KS and GSM involved in the field trials and the release of the rice variety PR127 with xa-45(t).

Correspondence to Kuldeep Singh.

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Communicated by Dr. Takuji Sasaki.

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Figure S1: Bulk segregant analysis showing the presence of Pusa 44 allele in homozygous conditions in both resistant and susceptible bulks, Pusa 44 (P1), O. glaberrima 102600B (P2), resistant bulk (RB), Susceptible bulk (SB), C-negative control, M- 50bp ladder (Fermentas). Figure S2: Bulk segregant analysis showing association of SSR markers RM 267, RM 593 and RM 13 of rice chromosome 5 with BB resistance in O. glaberrima 102600B, Pusa 44 (P1), O. glaberrima 102600B (P2), resistant bulk (RB), Susceptible bulk (SB), C-negative control, M-50bp ladder (Fermentas). Figure S3: Genotyping of 94 F5 progenies along with susceptible and resistant parents using xa13 marker on agarose gel (2.5%). Figure S4: Multiple sequence alignment showing polymorphic sites at SWEET11 locus among IL274, IRBB13 and Pusa44 as compared to the reference sequenceLOC4346153. Arrow indicates polymorphic sites (PDF 1432 kb)

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Neelam, K., Mahajan, R., Gupta, V. et al. High-resolution genetic mapping of a novel bacterial blight resistance gene xa-45(t) identified from Oryza glaberrima and transferred to Oryza sativa. Theor Appl Genet 133, 689–705 (2020). https://doi.org/10.1007/s00122-019-03501-2

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