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Identification and fine-mapping of a new resistance gene, Xa40, conferring resistance to bacterial blight races in rice (Oryza sativa L.)

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A new bacterial blight resistance gene has been identified through fine-mapping, which confers high levels of resistance to all Korean Xanthomonas oryzae pv. oryzae ( Xoo ) races, including the new Xoo race K3a.

Abstract

Rice bacterial leaf blight (BB) disease caused by Xanthomonas oryzae pv. oryzae (Xoo) is a serious constraint to rice production in Asia and Africa. The japonica advanced backcross breeding lines derived from the indica line IR65482-7-216-1-2 in the background of cultivar Junam are resistant to all Korean BB races, including K3a. To identify the gene(s) involved in resistance to Korean Xoo races, the association of genotypic and phenotypic variations was examined in two F2 populations derived from the crosses between 11325 (IR83261-3-7-23-6-2-1-1-2-1-2)/Anmi and 11325/Ilpum. The segregation ratios of F2 individuals from the crosses of 11325/Anmi and 11325/Ilpum were 578 resistant:209 susceptible and 555 resistant:241 susceptible, respectively, which is consistent with the expected allelic frequency of a 3:1 ratio. Genetic analysis using graphical mapping indicated that resistance (R) was controlled by a new resistance gene linked with the flanking markers RM27320 and ID55.WA18-5 within an approximately 80-kb region between 28.14 and 28.22 Mbp on chromosome 11. The eight candidate genes functionally predicted were included in the target region. Examination of the candidate genes by RT-PCR analysis only corroborated with the significant difference in transcript levels of the WAK3 gene in the presence or absence of pathogen infection. Allelism tests performed with other known BB R-genes revealed that the allele was distinct from others having a similar chromosomal location.

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Acknowledgments

This research was supported in part by a grant to the Agenda Program (Code No. PJ00926202) of the Rural Development Administration, Republic of Korea, and Global Rice Science Partnership program of IRRI. We thank the IRRI communication team for carefully editing the manuscript.

Conflict of interest

The authors declare that they have no conflict of interest.

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The experiments comply with the current laws of the country in which they were performed.

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Correspondence to Kshirod K. Jena.

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Communicated by Y. Xu.

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Supplementary Fig. 1

Pedigree of Anmi and its sister lines used in this study, which is developed by marker-assisted backcrossing. Supplementary material 1 (TIFF 1069 kb)

Supplementary Fig. 2

Leaf reactions of 11325, Ilpum, and F1 plants to Korean Xanthomonas oryzae pv. oryzae race K3a. Supplementary material 2 (TIFF 4263 kb)

Supplementary Fig. 3

Distribution of lesion length after inoculation of race K3a into 787 F2 individuals from a cross between Anmi and 11325. Supplementary material 3 (TIFF 1594 kb)

Supplementary Fig. 4

PCR analysis using CAPs marker ID55.WD3/HpCH4III for haplotype test. A indicates amplicon patterns of A1 allele among tested lines before enzyme treatment. B shows the difference between A1_A (#1, 5, 6, 7) and A1_G(#2, 3, 4) type by HpCH4III, which digests specific ACNGT sequence. L: 100-bp ladder, #1 IR65482-7-216-1-2, #2 IR17494, #3 IRBB4, #4 IRBB57, #5 11325, #6 11327, #7 11328. Supplementary material 4 (TIFF 505 kb)

Supplementary material 5 (DOCX 18 kb)

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Kim, SM., Suh, JP., Qin, Y. et al. Identification and fine-mapping of a new resistance gene, Xa40, conferring resistance to bacterial blight races in rice (Oryza sativa L.). Theor Appl Genet 128, 1933–1943 (2015). https://doi.org/10.1007/s00122-015-2557-2

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