Integrating association mapping, linkage mapping, fine mapping with RNA Seq conferring seedling vigor improvement for successful crop establishment in deep sown direct-seeded rice
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 ai...
| Autores principales: | , , , , , , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2023
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/163894 |
| _version_ | 1855517803253071872 |
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| author | Sandhu, Nitika Ankush, Ade Pooja Singh, Jasneet Raigar, Om Prakash Bains, Sutej Jindal, Taveena Singh, Mohini Prabha Sethi, Mehak Pruthi, Gomsie Augustine, Gaurav Verma, Vikas Kumar Goyal, Shivani Kumar, Aman Panwar, Harsh Sihag, Manvesh Kumar Kaur, Rupinder Kurup, Smita Kumar, Arvind |
| author_browse | Ankush, Ade Pooja Augustine, Gaurav Bains, Sutej Goyal, Shivani Jindal, Taveena Kaur, Rupinder Kumar, Aman Kumar, Arvind Kurup, Smita Panwar, Harsh Pruthi, Gomsie Raigar, Om Prakash Sandhu, Nitika Sethi, Mehak Sihag, Manvesh Kumar Singh, Jasneet Singh, Mohini Prabha Verma, Vikas Kumar |
| author_facet | Sandhu, Nitika Ankush, Ade Pooja Singh, Jasneet Raigar, Om Prakash Bains, Sutej Jindal, Taveena Singh, Mohini Prabha Sethi, Mehak Pruthi, Gomsie Augustine, Gaurav Verma, Vikas Kumar Goyal, Shivani Kumar, Aman Panwar, Harsh Sihag, Manvesh Kumar Kaur, Rupinder Kurup, Smita Kumar, Arvind |
| author_sort | Sandhu, Nitika |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | 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. |
| format | Journal Article |
| id | CGSpace163894 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1638942024-12-19T14:12:04Z Integrating association mapping, linkage mapping, fine mapping with RNA Seq conferring seedling vigor improvement for successful crop establishment in deep sown direct-seeded rice Sandhu, Nitika Ankush, Ade Pooja Singh, Jasneet Raigar, Om Prakash Bains, Sutej Jindal, Taveena Singh, Mohini Prabha Sethi, Mehak Pruthi, Gomsie Augustine, Gaurav Verma, Vikas Kumar Goyal, Shivani Kumar, Aman Panwar, Harsh Sihag, Manvesh Kumar Kaur, Rupinder Kurup, Smita Kumar, Arvind breeding linkage mapping candidate genes root length introgression lines alleles germination 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. 2023-12 2024-12-19T12:53:10Z 2024-12-19T12:53:10Z Journal Article https://hdl.handle.net/10568/163894 en Open Access Springer Sandhu, Nitika; Ankush, Ade Pooja; Singh, Jasneet; Raigar, Om Prakash; Bains, Sutej; Jindal, Taveena; Singh, Mohini Prabha; Sethi, Mehak; Pruthi, Gomsie; Augustine, Gaurav; Verma, Vikas Kumar; Goyal, Shivani; Kumar, Aman; Panwar, Harsh; Sihag, Manvesh Kumar; Kaur, Rupinder; Kurup, Smita and Kumar, Arvind. 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, Volume 16, no. 1 |
| spellingShingle | breeding linkage mapping candidate genes root length introgression lines alleles germination Sandhu, Nitika Ankush, Ade Pooja Singh, Jasneet Raigar, Om Prakash Bains, Sutej Jindal, Taveena Singh, Mohini Prabha Sethi, Mehak Pruthi, Gomsie Augustine, Gaurav Verma, Vikas Kumar Goyal, Shivani Kumar, Aman Panwar, Harsh Sihag, Manvesh Kumar Kaur, Rupinder Kurup, Smita Kumar, Arvind Integrating association mapping, linkage mapping, fine mapping with RNA Seq conferring seedling vigor improvement for successful crop establishment in deep sown direct-seeded rice |
| title | Integrating association mapping, linkage mapping, fine mapping with RNA Seq conferring seedling vigor improvement for successful crop establishment in deep sown direct-seeded rice |
| title_full | Integrating association mapping, linkage mapping, fine mapping with RNA Seq conferring seedling vigor improvement for successful crop establishment in deep sown direct-seeded rice |
| title_fullStr | Integrating association mapping, linkage mapping, fine mapping with RNA Seq conferring seedling vigor improvement for successful crop establishment in deep sown direct-seeded rice |
| title_full_unstemmed | Integrating association mapping, linkage mapping, fine mapping with RNA Seq conferring seedling vigor improvement for successful crop establishment in deep sown direct-seeded rice |
| title_short | Integrating association mapping, linkage mapping, fine mapping with RNA Seq conferring seedling vigor improvement for successful crop establishment in deep sown direct-seeded rice |
| title_sort | integrating association mapping linkage mapping fine mapping with rna seq conferring seedling vigor improvement for successful crop establishment in deep sown direct seeded rice |
| topic | breeding linkage mapping candidate genes root length introgression lines alleles germination |
| url | https://hdl.handle.net/10568/163894 |
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