To ensure the safety of the world's food supply given the threats of rapid population growth and declining arable land and water resources, innovative strategies for breeding the next generation of high-yield potential and climate-resilient crops will have to be implemented. New research strategies should create novel crop traits that have not yet been achieved in order to substantially enhance yield potential under marginal environments. How can this enormous goal be attained? It is now fully appreciated that any further improvements in genetic potential for yield, stress tolerance and water and nutrient use efficiency will have to rely on the ability to create complex genomic configurations that lead to novel biochemical and physiological traits. This project represents the use of contemporary research tools to solve an old puzzle. It represents a closer look and more strategic examination of one of the most enigmatic and relatively unexploited concepts in plant genetics, the phenomenon of transgressive variation. Transgressive variation is observed when progeny derived from two divergent parents are superior (or inferior) to both parents. Using rice to test the concept, this project will determine which DNA segments or RNA molecules cause transgressive traits for salinity and low temperature stress tolerance.
This project will test the hypothesis that transgressive stress tolerance phenotypes in biparental cross combinations of rice are the consequences of ideal shuffling and complementation effects between two divergent parental genomes leading to genetic network rewiring. New paradigms built upon the power of regulon restructuring, regulatory non-coding RNAs (ncRNAs), and DNA methylation will be explored to understand the intricate mechanisms by which novel gene expression patterns mediate transgression from parental phenotypes. By integrated use of various next-generation DNA sequencing applications such as genome-Seq, mRNA-Seq, ncRNA-Seq, and bisulfite-Seq, this project will: 1) discover stress-regulated miRNAs/siRNAs that are transgressively expressed in intraspecific recombinants with novel salt tolerance phenotypes, and those that are transgressively expressed in interspecific recombinants with novel low temperature or other stress tolerance attributes; 2) establish meaningful correlations between mRNA and miRNA/siRNA transcriptome signatures among recombinants and their respective parents to evelop hypotheses on how global gene expression is altered in transgressive segregants; and 3) establish meaningful correlations between transcriptome signatures and genome methylation profiles between recombinants and their parents to develop hypotheses on how epigenomic changes alter gene regulation in transgressive segregants. The approach will address the possibilities that: a) stress tolerance phenotypic transgression is due to regulatory genes that acquired optimal function because of compatible regulatory clusters in their new genetic background, i.e., regulon restructuring; b) network reconfiguration in recombinants is due to coupling or uncoupling of trans-acting ncRNAs and their target regulatory genes or genomic loci from either parents; and c) genome shuffling alters the methylation profiles in recombinants leading to novel gene expression signatures. Outcomes will advance our understanding of the intricacies of genetic and epigenetic networks towards applications to stress tolerance breeding in rice and other major cereal crops. The genomics datasets to be generated will be made available to the broader scientific community through public data repositories including the Sequence Read Archive of NCBI and DDBJ. The rice genetic stocks to be characterized will be made available to other researchers through the USDA rice genetic stock maintenance and distribution center.
