Fine mapping and sequence analysis reveal a promising candidate gene encoding a novel NB-ARC domain derived from wild rice (Oryza officinalis) that confers bacterial blight resistance

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dc.creatorSinha, Pragya
dc.creatorKumar T., Dilip
dc.creatorSk, Hajira
dc.creatorSolanki, Manish
dc.creatorGokulan, C.G.
dc.creatorDas, Ayyappa
dc.creatorMiriyala, Anila
dc.creatorGonuguntala, Rekha
dc.creatorElumalai, Punniakoti
dc.creatorKousik, M.B.V.N.
dc.creatorS. K., Masthani
dc.creatorKumboju, Chaitra
dc.creatorArra, Yugander
dc.creatorG. S., Laha
dc.creatorChirravuri, N. Neerja
dc.creatorPatel, Hitendra Kumar
dc.creatorGhazi, Irfan Ahmad
dc.creatorKim, Sung-Ryul
dc.creatorJena, Kshirod K.
dc.creatorHanumanth, Surekha Rani
dc.creatorOliva, Ricardo
dc.creatorMangrauthia, Satendra K.
dc.creatorSundaram, Raman Menakshi
dc.date2023-08-25
dc.date2023-11-06T02:59:35Z
dc.date2023-11-06T02:59:35Z
dc.date.accessioned2026-06-27T04:12:36Z
dc.descriptionBacterial blight disease of rice caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most serious constraints in rice production. The most sustainable strategy to combat the disease is the deployment of host plant resistance. Earlier, we identified an introgression line, IR 75084-15-3-B-B, derived from Oryza officinalis possessing broad-spectrum resistance against Xoo. In order to understand the inheritance of resistance in the O. officinalis accession and identify genomic region(s) associated with resistance, a recombinant inbred line (RIL) mapping population was developed from the cross Samba Mahsuri (susceptible to bacterial blight) × IR 75084-15-3-B-B (resistant to bacterial blight). The F2 population derived from the cross segregated in a phenotypic ratio of 3: 1 (resistant susceptible) implying that resistance in IR 75084-15-3-B-B is controlled by a single dominant gene/quantitative trait locus (QTL). In the F7 generation, a set of 47 homozygous resistant lines and 47 homozygous susceptible lines was used to study the association between phenotypic data obtained through screening with Xoo and genotypic data obtained through analysis of 7K rice single-nucleotide polymorphism (SNP) chip. Through composite interval mapping, a major locus was detected in the midst of two flanking SNP markers, viz., Chr11.27817978 and Chr11.27994133, on chromosome 11L with a logarithm of the odds (LOD) score of 10.21 and 35.93% of phenotypic variation, and the locus has been named Xa48t. In silico search in the genomic region between the two markers flanking Xa48t identified 10 putatively expressed genes located in the region of interest. The quantitative expression and DNA sequence analysis of these genes from contrasting parents identified the Os11g0687900 encoding an NB-ARC domain-containing protein as the most promising gene associated with resistance. Interestingly, a 16-bp insertion was noticed in the untranslated region (UTR) of the gene in the resistant parent, IR 75084-15-3-B-B, which was absent in Samba Mahsuri. The association of Os11g0687900 with resistance phenotype was further established by sequence-based DNA marker analysis in the RIL population. A co-segregating PCR-based INDEL marker, Marker_Xa48, has been developed for use in the marker-assisted breeding of Xa48t.
dc.formatapplication/pdf
dc.identifierhttps://hdl.handle.net/10568/132733
dc.identifier.urihttp://hdl.handle.net/123456789/25180
dc.languageen
dc.publisherFrontiers Media
dc.rightsOpen Access
dc.sourceSinha, Pragya, Dilip Kumar, Hajira Sk, Manish Solanki, C. G. Gokulan, Ayyappa Das, Anila Miriyala et al. "Fine mapping and sequence analysis reveal a promising candidate gene encoding a novel NB-ARC domain derived from wild rice (Oryza officinalis) that confers bacterial blight resistance." Frontiers in Plant Science 14 (2023).
dc.subjecthost plant resistance
dc.subjectintrogression line
dc.subjectinheritance
dc.subjectphenotypic variation
dc.subjectblight
dc.subjectxanthomonas oryzae
dc.subjectsequence analysis
dc.subjectdisease resistance
dc.subjectdominant genes
dc.titleFine mapping and sequence analysis reveal a promising candidate gene encoding a novel NB-ARC domain derived from wild rice (Oryza officinalis) that confers bacterial blight resistance
dc.typeJournal Article

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Instituto Internacional de Investigación del Arroz (IRRI)