SSR marker based genetic diversity analysis and differential transcriptome in deepwater rice of Assam

Abstract

newline Deepwater rice (Oryza sativa), locally known as baodhan, is an newlineimportant crop in the flood plains of Brahmaputra valley and Barak valley of Assam. A newlinedeepwater flood is a large-scale flood lasting for a prolonged period with water levels newlinethat range from a few to several meters. Deepwater rice adapts to submergence by newlinerapidly elongating its internodes and thereby maintaining its leaves above the water newlinesurface. It hides this unique ability in its genome and uses it during a water emergency. newlineThe remarkable, rapid growth in response to water depth is a unique biological and newlineenvironmental adaptation in deepwater rice which is known as an escape strategy. At newlinepresent, there is inadequate evaluation data, no concerted effort to evaluate the genetic newlinediversity and less exploration of this traditional landraces at molecular level. A set of 92 newlinedeepwater rice germplasm of Assam were genotyped using 74 SSR markers to assess newlinethe genetic diversity and genetic relationship. A total of 139 alleles was amplified with newlinean average of 2.48 alleles per locus and the PIC value ranged from a low of 0.18 newline(RM413) to 0.69 (RM206) with a mean value of 0.39. Cluster analysis grouped these newlinevarieties into seven clusters. Analysis of molecular variance (AMOVA) revealed that newline96% of the total variation observed in this germplasm came from within the newlinepopulations, while 4% of the variation emanated among the populations. The newlinebiochemical analyses revealed the significant increased activity of anaerobically newlineinduced enzymes. Furthermore, to understand the insight of molecular mechanisms newlineunderlying the internode elongation of deep water rice, whole genome transcriptomics newlinestudy was initiated. KEGG annotation revealed the enrichment of differentially newlineexpressed genes in several metabolic pathways including plant hormonal signal, newlinesecondary metabolite, cysteine-methionine and tryptophan. Among DEGs identified, newlinemost interestingly, we found the upregulation of genes like ERFO65, ERF051, ACO2, newlineSAUR31, CYP93G2 and downregulation of ERF3(ERF076), ACO1