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
Bacterial 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, d...
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Frontiers Media S.A.
2023-08-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2023.1173063/full |
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| author | Pragya Sinha Dilip Kumar T. Hajira Sk Manish Solanki C. G. Gokulan Ayyappa Das Anila Miriyala Rekha Gonuguntala Punniakoti Elumalai Kousik M. B. V. N Masthani S. K. Chaitra Kumboju Yugander Arra Yugander Arra Laha G. S. N. Neerja Chirravuri Hitendra Kumar Patel Irfan Ahmad Ghazi Sung-Ryul Kim Kshirod K. Jena Surekha Rani Hanumanth Ricardo Oliva Satendra K. Mangrauthia Raman Menakshi Sundaram |
| author_facet | Pragya Sinha Dilip Kumar T. Hajira Sk Manish Solanki C. G. Gokulan Ayyappa Das Anila Miriyala Rekha Gonuguntala Punniakoti Elumalai Kousik M. B. V. N Masthani S. K. Chaitra Kumboju Yugander Arra Yugander Arra Laha G. S. N. Neerja Chirravuri Hitendra Kumar Patel Irfan Ahmad Ghazi Sung-Ryul Kim Kshirod K. Jena Surekha Rani Hanumanth Ricardo Oliva Satendra K. Mangrauthia Raman Menakshi Sundaram |
| author_sort | Pragya Sinha |
| collection | DOAJ |
| description | Bacterial 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. |
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| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-03-12T13:21:35Z |
| publishDate | 2023-08-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Plant Science |
| spelling | doaj.art-9cfaa35120fd47e1a18d5df03e6fb2ac2023-08-25T18:24:55ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2023-08-011410.3389/fpls.2023.11730631173063Fine 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 resistancePragya Sinha0Dilip Kumar T.1Hajira Sk2Manish Solanki3C. G. Gokulan4Ayyappa Das5Anila Miriyala6Rekha Gonuguntala7Punniakoti Elumalai8Kousik M. B. V. N9Masthani S. K.10Chaitra Kumboju11Yugander Arra12Yugander Arra13Laha G. S.14N. Neerja Chirravuri15Hitendra Kumar Patel16Irfan Ahmad Ghazi17Sung-Ryul Kim18Kshirod K. Jena19Surekha Rani Hanumanth20Ricardo Oliva21Satendra K. Mangrauthia22Raman Menakshi Sundaram23Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, IndiaDepartment of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, IndiaDepartment of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, IndiaDepartment of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, IndiaCrop Improvement, Council of Scientific & Industrial Research (CSIR)-Centre for Cellular and Molecular Biology, Hyderabad, IndiaDepartment of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, IndiaDepartment of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, IndiaSeeds/Biotech R&D Division, Rallis India Limited, Bangalore, IndiaDepartment of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, IndiaDepartment of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, IndiaDepartment of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, IndiaDepartment of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, IndiaDepartment of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, IndiaInstitute of Molecular Physiology, Heinrich Heine University, Düsseldorf, GermanyDepartment of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, IndiaDepartment of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, IndiaCrop Improvement, Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, IndiaDepartment of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, IndiaRice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Banos, PhilippinesSchool of Biotechnology, Kalinga Institute of Industrial Technology (KIIT) University, Bhubaneswar, Odisha, IndiaDepartment of Genetics, Osmania University, Hyderabad, India0Safe and Sustainable Value Chain, World Vegetable Center, Tainan, TaiwanDepartment of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, IndiaDepartment of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, IndiaBacterial 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.https://www.frontiersin.org/articles/10.3389/fpls.2023.1173063/fullbacterial blight (BB)Xanthomonas oryzae pv. oryzae(Xoo)Oryza officinalisrecombinant inbred line (RIL)mappingsingle nucleotide polymorphism (SNP) |
| spellingShingle | Pragya Sinha Dilip Kumar T. Hajira Sk Manish Solanki C. G. Gokulan Ayyappa Das Anila Miriyala Rekha Gonuguntala Punniakoti Elumalai Kousik M. B. V. N Masthani S. K. Chaitra Kumboju Yugander Arra Yugander Arra Laha G. S. N. Neerja Chirravuri Hitendra Kumar Patel Irfan Ahmad Ghazi Sung-Ryul Kim Kshirod K. Jena Surekha Rani Hanumanth Ricardo Oliva Satendra K. Mangrauthia Raman Menakshi Sundaram 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 bacterial blight (BB) Xanthomonas oryzae pv. oryzae(Xoo) Oryza officinalis recombinant inbred line (RIL) mapping single nucleotide polymorphism (SNP) |
| title | 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 |
| title_full | 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 |
| title_fullStr | 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 |
| title_full_unstemmed | 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 |
| title_short | 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 |
| title_sort | 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 |
| topic | bacterial blight (BB) Xanthomonas oryzae pv. oryzae(Xoo) Oryza officinalis recombinant inbred line (RIL) mapping single nucleotide polymorphism (SNP) |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2023.1173063/full |
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