Genomic and epigenomic analysis of transgressive segregation in rice

Transgressive segregation is a phenomenon wherein the phenotypes of a few recombinant individuals are outside the phenotypic range of the parents. In this project, we are testing the hypothesis that transgressive stress (salinity, low temperature) tolerance phenotypes in rice are created through epistatic or complementation effects when portions of two divergent genomes are brought together in the same nuclear genomic background (i.e., genome and epigenome shuffling) by homologous recombination. By integrated use of various next-generation sequencing applications, our aims are to: 1) Discover stress-regulated miRNAs and siRNAs that are transgressively expressed in intraspecies and interspecies recombinants with transgressive stress tolerance phenotypes; 2) Establish meaningful correlations between mRNA, miRNA and siRNA transcriptome signatures among recombinants and their respective parents, for hypotheses on how global gene expression is altered and how they relate to the acquired physiological properties in transgressive segregants; and 3) Establish meaningful correlations between transcriptome signatures and genome methylation profiles among recombinants and their parents for hypotheses on how epigenomic changes alter gene regulation in transgressive segregants and how those trends relate to the acquired physiological properties. Outcomes of this exploratory research are expected to advance our understanding of biological networks, towards novel applications of network biology and epigenetics to stress tolerance breeding in major cereal crops.