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 |
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Elsevier
2025
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/180315 |
| _version_ | 1855528554632052736 |
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| author | Rangari, Sagar Krushnaji Dube, Namita Sharma, Vinay Gangurde, Sunil S. Sharma, Mamta Gangashetty, Prakash I. Saxena, Rachit K. Moghiya, Abhinav Sharma, Vinay K. Bhutia, Karma L. Kant, Ravi Thudi, Mahendar Naik, Satheesh S.J. Pratap, Aditya Dixit, Girish P. Mayes, Sean Pandey, Manish K. |
| author_browse | Bhutia, Karma L. Dixit, Girish P. Dube, Namita Gangashetty, Prakash I. Gangurde, Sunil S. Kant, Ravi Mayes, Sean Moghiya, Abhinav Naik, Satheesh S.J. Pandey, Manish K. Pratap, Aditya Rangari, Sagar Krushnaji Saxena, Rachit K. 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 K. Moghiya, Abhinav Sharma, Vinay K. Bhutia, Karma L. Kant, Ravi Thudi, Mahendar Naik, Satheesh S.J. Pratap, Aditya Dixit, Girish P. 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 | CGSpace180315 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| publisher | Elsevier |
| publisherStr | Elsevier |
| record_format | dspace |
| spelling | CGSpace1803152026-01-22T02:09:03Z 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 K. Moghiya, Abhinav Sharma, Vinay K. Bhutia, Karma L. Kant, Ravi Thudi, Mahendar Naik, Satheesh S.J. Pratap, Aditya Dixit, Girish P. Mayes, Sean Pandey, Manish K. pigeon peas genotypes resistant varieties 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. 2025-07-09 2026-01-21T17:06:59Z 2026-01-21T17:06:59Z Journal Article https://hdl.handle.net/10568/180315 en Open Access application/pdf Elsevier Rangari, Sagar Krushnaji; Dube, Namita; Sharma, Vinay; Gangurde, Sunil S.; Sharma, Mamta; Gangashetty, Prakash I.; Saxena, Rachit K.; Moghiya, Abhinav; Sharma, Vinay K.; Bhutia, Karma L.; Kant, Ravi; Thudi, Mahendar; Naik, Satheesh S.J.; Pratap, Aditya; Dixit, Girish P.; Mayes, Sean; Pandey, Manish 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, Volume 321, Part 3, https://doi.org/10.1016/j.ijbiomac.2025.145777. |
| spellingShingle | pigeon peas genotypes resistant varieties Rangari, Sagar Krushnaji Dube, Namita Sharma, Vinay Gangurde, Sunil S. Sharma, Mamta Gangashetty, Prakash I. Saxena, Rachit K. Moghiya, Abhinav Sharma, Vinay K. Bhutia, Karma L. Kant, Ravi Thudi, Mahendar Naik, Satheesh S.J. Pratap, Aditya Dixit, Girish P. 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 genotypes resistant varieties |
| url | https://hdl.handle.net/10568/180315 |
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