The 'Ten billion people question' (10BPQ) posts an enormous challenge of how to maximize crop genetic gains amidst the rapid population growth and burgeoning effects of climate change. Developing the next generation of climate-resilient crops by maximizing the potential of what has been engineered, tested, and optimized by evolution (i.e. germplasm) would be critical in addressing this grand challenge to 21st century agriculture. On top of what has already been achieved during the last century of crop genetic improvements by conventional plant breeding, genomics, and biotechnology, any further enhancements in stress tolerance and yield potentials of major food crops will have to rely on the ability of modern genetic technology to create novel phenotypes or physiological attributes that were not achieved during the first Green Revolution during the 1960's.

The genus Oryza includes the Asian (O. sativa) and African (O. glaberrima) cultivated rice, and 22 wild species that collectively span ~15 million years of speciation and ~4,000 years of domestication history. The genus represents a wide spectrum of ecological niches whose real potential in stress tolerance breeding is just beginning to be unlocked through the power of genomics-enabled hypothesis-testing. With a long-term goal of contributing a possible component of the solution to the 10BPQ, current research in my laboratory is using the more exotic cultivated and wild Oryza as genetic model system to address the hypothesis that:

Transgressive traits for stress (temperature, drought, salinity) tolerance are the outcomes of regulatory network rewiring. They are manifestations of novel patterns of gene expression mediated by reconfigured genomic and epigenomic landscapes as an outcome of recombination between diverse genomes.

Transgressive segregation is a phenomenon wherein a minority of the recombinant progenies derived from two genetically diverse parents exhibit quantitative phenotypic variation that are beyond the range of the two parents. Genetics alone has not been able to fully explain the mechanistic basis of this phenomenon. Given this, the goal of my research program is to examine the phenomenon of network rewiring in genetic populations of rice exhibiting transgressive segregation for abiotic stress tolerance, by probing into the different facets of its complexity both at the level of genetic and epigenetic regulation. This research is based on the assumptions that:

1. Ideal or non-ideal complementation and/or epistatic interaction could cause transgressive phenotypes. This happens when multiple hubs of regulatory networks and their downstream targets from either parents are brought together in the same genetic background by recombination, hence regulon complementation.
2. Transgressive phenotypes (either positive or negative) may be configured by epigenomic changes mediated by non-coding regulatory RNA expression. These events lead to post-transcriptional gene silencing (PTGS) by miRNA, and/or transcriptional gene silencing (TGS) by RNA-directed DNA methylation, leading to network rewiring.
3. Transgressive phenotypes (either positive or negative) may be the result of different levels of interactions among quantitative trait loci (QTL), and between QTL and genetic background by virtue of mechanisms that involve both genetic and epigenetic regulation. These interactions may lead to either synergistic, complementary or antagonistic effects.

By comparative genomic, regulomic, and epigenomic analyses coupled with functional validation by transgenic and modern genome editing approaches, we aim to uncover patterns of genetic and epigenetic changes that reconfigure physiological and/or biochemical networks in transgressive individuals derived from genetically diverse crosses across cultivated and wild Oryza. With these strategies, we hope to explain the regulatory mechanisms behind the gain or loss of phenotypic attributes mediated by genome and epigenome shuffling that may be triggered by recombination.

Capitalizing on the transformative knowledge resulting from the investigation of a tractable evolutionary and genetic model system such as Oryza, we are also extending the same research paradigms to do translational research on crop(s) of economic importance to the water-limited agroecosystem of west Texas. Current focus of this part of my research program is to mine the natural gene pool of the cultivated Gossypium (cotton) for both major and cryptic morpho-physiometric components contributing to overall potentials for salinity and drought tolerance using similar omics-enabled research paradigm that we have established in the Oryza project. In the long term, we aim to use the information generated from the omics-enabled research to model the ideal combinations of major and cryptic physiological traits and their underlying genomic and epigenomic mechanisms.

Dr. Benildo de los Reyes

Professor of Plant Genomics,
Bayer Crop Science Endowed Chair,
Graduate Programs Director
Department of Plant and Soil Science
Texas Tech University

Experimental Sciences Building
Room 215, Mail Stop 2122
Lubbock, TX 79409-2122
Phone: +1 (806) 834-6421;
Fax: 806-742-0775
Email: benildo.reyes@ttu.edu