Integrating association mapping, linkage mapping, fine mapping with RNA Seq conferring seedling vigor improvement for successful crop establishment in deep sown direct-seeded rice

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dc.creatorSandhu, Nitika
dc.creatorAnkush, Ade Pooja
dc.creatorSingh, Jasneet
dc.creatorRaigar, Om Prakash
dc.creatorBains, Sutej
dc.creatorJindal, Taveena
dc.creatorSingh, Mohini Prabha
dc.creatorSethi, Mehak
dc.creatorPruthi, Gomsie
dc.creatorAugustine, Gaurav
dc.creatorVerma, Vikas Kumar
dc.creatorGoyal, Shivani
dc.creatorKumar, Aman
dc.creatorPanwar, Harsh
dc.creatorSihag, Manvesh Kumar
dc.creatorKaur, Rupinder
dc.creatorKurup, Smita
dc.creatorKumar, Arvind
dc.date2023-12
dc.date2024-12-19T12:53:10Z
dc.date2024-12-19T12:53:10Z
dc.date.accessioned2026-06-27T04:08:34Z
dc.descriptionOngoing 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.
dc.identifierhttps://hdl.handle.net/10568/163894
dc.identifier.urihttp://hdl.handle.net/123456789/22924
dc.languageen
dc.publisherSpringer
dc.rightsOpen Access
dc.sourceSandhu, 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
dc.subjectbreeding
dc.subjectlinkage mapping
dc.subjectcandidate genes
dc.subjectroot length
dc.subjectintrogression lines
dc.subjectalleles
dc.subjectgermination
dc.titleIntegrating association mapping, linkage mapping, fine mapping with RNA Seq conferring seedling vigor improvement for successful crop establishment in deep sown direct-seeded rice
dc.typeJournal Article

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Instituto Internacional de Investigación del Arroz (IRRI)