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Development of Genomic Tools to Dissect Regulatory Gene Networks in Wheat

Research Summary

Jorge Dubcovsky's goal is to develop functional genomics resources to empower the wheat research community and to use those resources to answer basic questions on wheat development and disease resistance.

Jorge Dubcovsky's main research contributions have been in the area of wheat development and wheat improvement. In collaboration with colleagues and students in he worked on three developmental processes that have major impacts on wheat productivity: the transition between vegetative and reproductive stages (which affects adaptation), the regulation of spike development (which affects yield), and the regulation of senescence (which affects nutrient remobilization). During the past 20 years he developed genomic for wheat including molecular maps, large insert libraries, expressed sequence tag resources, single-nucleotide polymorphism markers, and sequenced mutant populations. All these resources are publicly available and are used extensively worldwide.

In the area of reproductive development, Dubcovsky's laboratory has used these new genomic tools to clone and validate the four main vernalization genes in wheat: Vrn1, Vrn2Vrn3, and Vrn4. This work showed that the vernalization pathway in temperate cereals differs from that in the model species Arabidopsis. Dubcovsky's laboratory made also major contributions to the characterization of wheat photoperiod pathway. The molecular markers for all these developmental genes are being used extensively by wheat-breeding programs worldwide. The precise regulation of the reproductive phase is essential for wheat adaptation to changing environments.

A second developmental process that is critical for wheat productivity is the regulation of spike formation, since it determines the maximum number of grains per spike. Dubcovsky's laboratory discovered Eps1, a locus that increases spikelet number by up to 30 percent in diploid wheat and identified ELF3 as the causal gene. Allelic variants at this gene are associated with a longer spike development period and a significant increase in spikelet number. 

Dubcovsky's laboratory is also interested in terminal senescence, a highly regulated process during which nutrients are remobilized from the leaf to the wheat grain. With colleagues from University of Haifa, Dubcovsky's group cloned the high-grain protein content (GPC) gene Gpc1 from a wild wheat. This gene accelerates nutrient remobilization, increases grain protein and iron concentrations by 10 percent, and increases zinc concentrations by 5 percent. This novel allele has been incorporated into many commercial wheat varieties around the world. The Gpc1 gene is an early regulator of senescence, and the transgenic and mutant lines have been used to dissect the complex senescence regulatory network.

Dubcovsky's laboratory is also involved in the characterization of the gene networks involved in wheat resistance to rusts, a devastating group of pathogens that produce large yield losses all over the world. The slow rusting gene Yr36, that delays the progression of stripe rust in wheat, was identified and characterized in Dubcovsky's laboratory. This gene encodes a protein with a novel architecture not found before in any other known protein. The combination of a START lipid-binding domain with a kinase domain provides senses the alteration of lipids during pathogen infection and triggers a signal cascade through its kinase domain that phosphorylates the thylakoid associated ascorbate peroxidase (tAPX). Phosphorylation reduces the activity of tAPX resulting in the accumulation of reactive oxygen species (ROS) and cell death.

To advance wheat research, Dubcovsky's laboratory developed mutant tetraploid and hexaploid wheat populations with extremely high mutation density and an exome capture platform to sequence these mutant lines. The sequencing of the coding regions of 1,536 EMS mutants in tetraploid wheat revealed 4.3 million mutations, which can be used to modify or knock out the function of most wheat genes. A database (searchable by BLASTN) has been developed and is currently used by more than 200 researchers worldwide. This tool has changed the paradigm of what can be done in wheat functional genomics.

Dubcovsky's laboratory is using this new resource to dissect wheat gene networks that regulate developmental and disease resistance. These mutants were also used to generate loss-of function mutants of the Starch Branching Enzyme II and generate pasta and bread wheat varieties with a 10-fold increase in resistant starch. This increase in dietary fiber has been associated to health benefits. Commercial wheat varieties with these mutations are close to release. 

Wheat provides 20 percent of the calories consumed by humans and plays a central role in human nutrition. Better knowledge of the major developmental switches and disease resistance gene networks that affect wheat productivity is needed to engineer more productive and nutritious wheat varieties.

Grants from the United States Department of Agriculture National Institute of Food and Agriculture, tand the United States–Israel Binational Agricultural Research and Development (BARD) provided partial support for these projects.

As of March 23, 2016

Scientist Profile

Investigator
University of California, Davis
Genetics, Plant Biology