Harnessing genetic variations improving seedling vigor for successful crop establishment in deep sown direct-seeded rice

Sandhu, N.; Ankush, A. P.; Singh, J.; Raigar, O. P.; Bains, S.; Jindal, T.; Singh, M. P.; Sethi, M.; Pruthi, G.; Augustine, G.; Verma, V. K.; Goyal, S.; Kumar, A.; Panwar, H.; Sihag, M. K.; Kaur, R.; Kurup, S.

doi:10.1101/2023.03.28.534621

bioRxiv · 10.1101/2023.03.28.534621

Harnessing genetic variations improving seedling vigor for successful crop establishment in deep sown direct-seeded rice

Sandhu, N.·Ankush, A. P.·Singh, J.·Raigar, O. P.·Bains, S.·Jindal, T.·Singh, M. P.·Sethi, M.·Pruthi, G.·Augustine, G.·Verma, V. K.·Goyal, S.·Kumar, A.·Panwar, H.·Sihag, M. K.·Kaur, R.·Kurup, S.

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Abstract

Improving seedling vigour remains key objective for breeders working with direct-seeded rice (DSR). 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 was performed. 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 3.79 Mb 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 potential candidate gene, LOC_Os07g25150 codes for Myb-30-related transcription factor. The LOC_Os07g25150 codes for Myb 30-related transcription factor, LOC_Os07g17689 annotated as protein translation factor, LOC_Os07g17770 as tryptophanyl-tRNA synthetase, LOC_Os07g15440 as alanyl-tRNA synthetase family protein, LOC_Os07g24100 as retrotransposon protein and the remaining others as expressed proteins. The antagonistic relationship between Myb-30 and ethylene-mediated signalling (EIN-3) in regulating mesocotyl elongation have been observed. The functional characterization and knocking of LOC_Os07g25150 codes for Myb 30-related transcription factor may provide better understanding of the mechanism behind mesocotyl elongation. The four promising introgression lines with longer mesocotyl length, longer root length and semi-dwarf plant height have been identified.

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Sandhu, N., Ankush, A. P., Singh, J., Raigar, O. P., Bains, S., Jindal, T., Singh, M. P., Sethi, M., Pruthi, G., Augustine, G., Verma, V. K., Goyal, S., Kumar, A., Panwar, H., Sihag, M. K., Kaur, R., Kurup, S.. 2023-03-29. Harnessing genetic variations improving seedling vigor for successful crop establishment in deep sown direct-seeded rice. https://doi.org/10.1101/2023.03.28.534621

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