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

Abstract

AbstractImproving 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 F3:4:5and BC2F2:3populations. 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_Os07g25150codes forMyb-30-related transcription factor. TheLOC_Os07g25150codes forMyb 30-related transcription factor,LOC_Os07g17689annotated as protein translation factor,LOC_Os07g17770as tryptophanyl-tRNA synthetase,LOC_Os07g15440as alanyl-tRNA synthetase family protein,LOC_Os07g24100as retrotransposon protein and the remaining others as expressed proteins. The antagonistic relationship betweenMyb-30and ethylene-mediated signalling (EIN-3) in regulating mesocotyl elongation have been observed. The functional characterization and knocking ofLOC_Os07g25150codes forMyb 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.