Rangari, S K and Dube, N and Sharma, V and Gangurde, S S and Sharma, M and Gangashetty, P I and Saxena, R K and Moghiya, A and Sharma, V K and Bhutia, K L and Kant, R and Thudi, M and Naik, S J S and Pratap, A and Dixit, G P and Mayes, S and 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 (TSI), 321 (3). pp. 1-12. ISSN 0141-8130
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Abstract
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.
| Item Type: | Article |
|---|---|
| Divisions: | Global Research Program - Accelerated Crop Improvement |
| CRP: | UNSPECIFIED |
| Uncontrolled Keywords: | Pigeonpea, QTL-Seq, ΔSNP-index, InDels, KASP genotyping |
| Subjects: | Mandate crops > Pigeonpea Others > Genetics and Genomics Others > Plant Pathology Others > Plant Disease |
| Depositing User: | Mr Nagaraju T |
| Date Deposited: | 24 Mar 2026 03:34 |
| Last Modified: | 24 Mar 2026 03:34 |
| URI: | http://oar.icrisat.org/id/eprint/13555 |
| Official URL: | https://www.sciencedirect.com/science/article/pii/... |
| Projects: | ICAR-ICRISAT collaborative project |
| Funders: | Bill and Melinda Gates Foundation |
| Acknowledgement: | This work was partially supported by ICAR-ICRISAT collaborative project and Bill and Melinda Gates Foundation (BMGF), USA. |
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