Sandhu, N and Ankush, A P and Singh, J and Raigar, O P and Bains, S and Jindal, T and Singh, M P and Sethi, M and Pruthi, G and Augustine, G and Verma, V K and Goyal, S and Kumar, Aman and Panwar, H and Sihag, M K and Kaur, R and Kurup, S and Kumar, A (2023) Integrating Association Mapping, Linkage Mapping, Fine Mapping with RNA Seq Conferring Seedling Vigor Improvement for Successful Crop Establishment in Deep Sown Direct‑Seeded Rice. Rice, 16. pp. 1-16. ISSN 1939-8433
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Abstract
Background Ongoing large-scale shift towards direct seeded rice (DSR) necessitates a convergence of breeding and genetic approaches for its sustenance and harnessing natural resources and environmental benefits. Improving seedling vigour remains key objective for breeders working with DSR. The present study aims to understand the genetic control of seedling vigour in deep sown DSR. Combined genome-wide association mapping, linkage mapping, fine mapping, RNA-sequencing to identify candidate genes and validation of putative candidate genes were performed in the present study. Results Significant phenotypic variations were observed among genotypes in both F3:4:5 and BC2F2:3 populations. The mesocotyl length showed significant positive correlation with %germination, root and shoot length. The 881 kb region on chromosome 7 reported to be associated with mesocotyl elongation. RNA-seq data and RT-PCR results identified and validated seven potential candidate genes. The four promising introgression lines free from linkage drag and with longer mesocotyl length, longer root length, semi-dwarf plant height have been identified. Conclusion The study will provide rice breeders (1) the pre breeding material in the form of anticipated DSR adapted introgression lines possessing useful traits and alleles improving germination under deep sown DSR field conditions (2) the base for the studies involving functional characterization of candidate genes. The development and utilization of improved introgression lines and molecular markers may play an important role in genomics-assisted breeding (GAB) during the pyramiding of valuable genes providing adaptation to rice under DSR. Our results offer a robust and reliable package that can contribute towards enhancing genetic gains in direct seeded rice breeding programs.
| Item Type: | Article |
|---|---|
| Divisions: | UNSPECIFIED |
| CRP: | UNSPECIFIED |
| Uncontrolled Keywords: | Direct seeded rice, Gene, Mesocotyl elongation, QTL mapping, Seedling vigor, Transcriptome |
| Subjects: | Others > Rice |
| Depositing User: | Mr Nagaraju T |
| Date Deposited: | 11 Mar 2024 10:50 |
| Last Modified: | 11 Mar 2024 10:50 |
| URI: | http://oar.icrisat.org/id/eprint/12560 |
| Official URL: | https://link.springer.com/article/10.1186/s12284-0... |
| Projects: | UNSPECIFIED |
| Funders: | UNSPECIFIED |
| Acknowledgement: | The work was compiled under projects funded by the Department of Biotechnology, Govt. of India (Grant No. BT/PR31462/ATGC/127/6/2019), BBSRC GCRF (BB/P023428/1) and SERB, DST (Grant No. WEA/2021/000003) |
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