InDels in an intronic region of gene Ccsmd04 coding for dormancy/auxin-associated protein control sterility mosaic disease resistance in pigeonpea
Sterility mosaic disease (SMD) presents a significant challenge to pigeonpea cultivation in the Indian subcontinent, potentially leading to total crop failure. The development of diagnostic molecular markers for SMD resistance can aid in developing SMD-resistant varieties. In this context, a QTL-seq...
| Main Authors: | , , , , , , , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Elsevier
2025
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/179403 |
| _version_ | 1855535812730421248 |
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| author | Rangari, Sagar Krushnaji Dube, Namita Sharma, Vinay Gangurde, Sunil S. Sharma, Mamta Gangashetty, Prakash I. Saxena, Rachit Kumar Moghiya, Abhinav Sharma, Vinay K. Bhutia, Karma L. Kant, Ravi Thudi, Mahendar Satheesh Naik, S.J. Pratap, Aditya Dixit, Girish Prasad Mayes, Sean Pandey, Manish K. |
| author_browse | Bhutia, Karma L. Dixit, Girish Prasad Dube, Namita Gangashetty, Prakash I. Gangurde, Sunil S. Kant, Ravi Mayes, Sean Moghiya, Abhinav Pandey, Manish K. Pratap, Aditya Rangari, Sagar Krushnaji Satheesh Naik, S.J. Saxena, Rachit Kumar Sharma, Mamta Sharma, Vinay Sharma, Vinay K. Thudi, Mahendar |
| author_facet | Rangari, Sagar Krushnaji Dube, Namita Sharma, Vinay Gangurde, Sunil S. Sharma, Mamta Gangashetty, Prakash I. Saxena, Rachit Kumar Moghiya, Abhinav Sharma, Vinay K. Bhutia, Karma L. Kant, Ravi Thudi, Mahendar Satheesh Naik, S.J. Pratap, Aditya Dixit, Girish Prasad Mayes, Sean Pandey, Manish K. |
| author_sort | Rangari, Sagar Krushnaji |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Sterility mosaic disease (SMD) presents a significant challenge to pigeonpea cultivation in the Indian subcontinent, potentially leading to total crop failure. The development of diagnostic molecular markers for SMD resistance can aid in developing SMD-resistant varieties. In this context, a QTL-seq approach identified genomic regions associated with SMD resistance using a recombinant inbred line population generated from ICP8863 × ICPL87119. In total, 6105 high-confidence variants were identified in the genomic region, smdCc04 based on the ΔSNP index. A genomic region smdCc04 on chromosome Cc04 spans 3.2 Mb (9.3–12.5 Mb) comprises 5 missense variants and 9 Indels. A total of 211 candidate genes were identified from this region. 1 bp insertion, 21 bp insertion, 9 bp deletion, and 3 bp insertion at different intronic positions in 22 susceptible genotypes leads to downregulation of Dormancy/auxin associated protein (Ccsmd04 gene) resulting in loss of signaling in disease resistance pathways. The identified sites recognize four important disease and plant growth related transcription factors. A total of 4 InDels and 8 SNPs were validated from smdCc04 genomic region using whole genome re-sequencing data and kompititive allele specific polymerase chain reaction (KASP) genotyping in resistant and susceptible pigeonpea genotypes. Gene-based markers snpCC00149 and snpCC00150 present in the genomic region smdCc04 can be used in pigeonpea breeding programs for developing SMD resistant varieties. |
| format | Journal Article |
| id | CGSpace179403 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| publisher | Elsevier |
| publisherStr | Elsevier |
| record_format | dspace |
| spelling | CGSpace1794032026-01-06T02:13:48Z InDels in an intronic region of gene Ccsmd04 coding for dormancy/auxin-associated protein control sterility mosaic disease resistance in pigeonpea Rangari, Sagar Krushnaji Dube, Namita Sharma, Vinay Gangurde, Sunil S. Sharma, Mamta Gangashetty, Prakash I. Saxena, Rachit Kumar Moghiya, Abhinav Sharma, Vinay K. Bhutia, Karma L. Kant, Ravi Thudi, Mahendar Satheesh Naik, S.J. Pratap, Aditya Dixit, Girish Prasad Mayes, Sean Pandey, Manish K. pigeon peas quantitative trait loci genotyping Sterility mosaic disease (SMD) presents a significant challenge to pigeonpea cultivation in the Indian subcontinent, potentially leading to total crop failure. The development of diagnostic molecular markers for SMD resistance can aid in developing SMD-resistant varieties. In this context, a QTL-seq approach identified genomic regions associated with SMD resistance using a recombinant inbred line population generated from ICP8863 × ICPL87119. In total, 6105 high-confidence variants were identified in the genomic region, smdCc04 based on the ΔSNP index. A genomic region smdCc04 on chromosome Cc04 spans 3.2 Mb (9.3–12.5 Mb) comprises 5 missense variants and 9 Indels. A total of 211 candidate genes were identified from this region. 1 bp insertion, 21 bp insertion, 9 bp deletion, and 3 bp insertion at different intronic positions in 22 susceptible genotypes leads to downregulation of Dormancy/auxin associated protein (Ccsmd04 gene) resulting in loss of signaling in disease resistance pathways. The identified sites recognize four important disease and plant growth related transcription factors. A total of 4 InDels and 8 SNPs were validated from smdCc04 genomic region using whole genome re-sequencing data and kompititive allele specific polymerase chain reaction (KASP) genotyping in resistant and susceptible pigeonpea genotypes. Gene-based markers snpCC00149 and snpCC00150 present in the genomic region smdCc04 can be used in pigeonpea breeding programs for developing SMD resistant varieties. 2025-09 2026-01-05T19:30:02Z 2026-01-05T19:30:02Z Journal Article https://hdl.handle.net/10568/179403 en Open Access application/pdf Elsevier Rangari, S. K., Dube, N., Sharma, V., Gangurde, S. S., Sharma, M., Gangashetty, P. I., Saxena, R. K., Moghiya, A., Sharma, V. K., Bhutia, K. L., Kant, R., Thudi, M., Naik, S. J. S., Pratap, A., Dixit, G. P., Mayes, S., & Pandey, M. K. (2025). InDels in an intronic region of gene Ccsmd04 coding for dormancy/auxin-associated protein control sterility mosaic disease resistance in pigeonpea. International Journal of Biological Macromolecules, 321, 145777. https://doi.org/10.1016/j.ijbiomac.2025.145777 |
| spellingShingle | pigeon peas quantitative trait loci genotyping Rangari, Sagar Krushnaji Dube, Namita Sharma, Vinay Gangurde, Sunil S. Sharma, Mamta Gangashetty, Prakash I. Saxena, Rachit Kumar Moghiya, Abhinav Sharma, Vinay K. Bhutia, Karma L. Kant, Ravi Thudi, Mahendar Satheesh Naik, S.J. Pratap, Aditya Dixit, Girish Prasad Mayes, Sean Pandey, Manish K. InDels in an intronic region of gene Ccsmd04 coding for dormancy/auxin-associated protein control sterility mosaic disease resistance in pigeonpea |
| title | InDels in an intronic region of gene Ccsmd04 coding for dormancy/auxin-associated protein control sterility mosaic disease resistance in pigeonpea |
| title_full | InDels in an intronic region of gene Ccsmd04 coding for dormancy/auxin-associated protein control sterility mosaic disease resistance in pigeonpea |
| title_fullStr | InDels in an intronic region of gene Ccsmd04 coding for dormancy/auxin-associated protein control sterility mosaic disease resistance in pigeonpea |
| title_full_unstemmed | InDels in an intronic region of gene Ccsmd04 coding for dormancy/auxin-associated protein control sterility mosaic disease resistance in pigeonpea |
| title_short | InDels in an intronic region of gene Ccsmd04 coding for dormancy/auxin-associated protein control sterility mosaic disease resistance in pigeonpea |
| title_sort | indels in an intronic region of gene ccsmd04 coding for dormancy auxin associated protein control sterility mosaic disease resistance in pigeonpea |
| topic | pigeon peas quantitative trait loci genotyping |
| url | https://hdl.handle.net/10568/179403 |
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