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ARS Home » Pacific West Area » Albany, California » Western Regional Research Center » Crop Improvement and Genetics Research » Research » Research Project #443932

Research Project: New Genetic and Genomics Resources to Improve Wheat Quality and Resilience to Biotic and Abiotic Stresses

Location: Crop Improvement and Genetics Research

Project Number: 2030-21430-015-000-D
Project Type: In-House Appropriated

Start Date: Mar 12, 2023
End Date: Mar 11, 2028

The primary objective of this project is to enhance the grain yield, end-use quality, and pest resilience of wheat by creating novel genetic and genomics resources. The specific objectives and sub-objectives are listed in the following. Objective 1: Enhance wheat for high yields and resistance to fungal and insect pests through identification and exploitation of genetic variation in primary gene pool. Sub-objective 1.A: Identify genes conferring resistance to Hessian fly and greenbug as well as tan spot in a sequenced Ae. tauschii panel. Sub-objective 1.B: Identify and map genes for resistance to stem rust, leaf rust, stripe rust, tan spot and Septoria nodorum blotch in cultivated emmer wheat using association mapping. Sub-objective 1.C: Identify and map genes conferring resistance to tan spot in hexaploid wheat line PI 277012. Sub-objective 1.D: Improve yield potential in elite durum and bread wheat germplasm with salinity tolerance. Sub-objective 1.E: Develop elite breeding lines of durum and bread wheat with enhanced resistance to Fusarium head blight, sawfly, and Hessian fly. Objective 2: Discover and develop novel genetic variation in wheat responsible for superior end-use quality. Sub-objective 2.A: Characterize diversity of gluten protein genes among U.S. wheat lines. Sub-objective 2.B: Develop molecular markers that are linked to prolamin alleles associated with the end-use quality and immunogenetic potential in wheat. Sub-objective 2.C: Improve gluten strength of wheat flour through conventional mutation breeding. Objective 3: Develop hypoallergenic wheat for healthier and safer food and non-food products. Sub-objective 3.A: Reduce immunogenic potential of wheat flour through conventional mutation breeding. Sub-objective 3.B: Relate gluten polyprotein composition to physical properties of novel bioproducts for applications in diverse fields. Objective 4: Validate genetically identified trait gene candidates by improving genome editing and transformation efficiency in elite wheat cultivars. Sub-objective 4.A: Improve transformation and gene editing efficiency in wheat cultivars Sub-objective 4.B: Reduce immunogenic potential of wheat flour using efficient gene editing technology Sub-objective 4.C: Validate gene candidates for resistance to Hessian fly and greenbug identified from Ae. tauschii using efficient transformation. Objective 5: Develop Triticeae genomic resources for cereal crop improvement. Sub-objective 5.A: Develop Ae. markgraffi reference C genome. Sub-objective 5.B: Develop Triticeae reference E genome. Sub-objective 5.C: Develop pan-genomes of durum wheat (AABB) and Ae. tauschii (DD), the bread wheat progenitors. The resources committed to the project include 3,500 sq. ft. of full-equipped laboratory space, 350 sq. ft. of office space, 3500 sq. ft. of greenhouse space, and field spaces for conducting yield, quality, and disease evaluation trials.

Objective 1: Three mapping populations of bread wheat, emmer wheat, and Aegilops tauschii that were previously sequenced or genotyped will be evaluated for their resistance to tan spot, Hessian fly, and greenbug. The phenotypic and genotypic data will be used to identify the quantitative trait loci (QTL) and candidate genes controlling the resistance using association or linkage mapping. Adapted and elite durum and bread wheat germplasm with enhanced grain yield, salinity tolerance, and disease (Fusarium head blight) and insect (Hessian fly and sawfly) resistance will be developed using backcross breeding coupled with phenotypic assessments and marker-assisted selection (MAS). Objective 2: The novel genetic variation in wheat responsible for superior end-use quality will be identified by using Prolamin Sequencing Capture Array (ProSeq), transcriptome sequencing, and genotyping with molecular markers targeting specific prolamin alleles. New genetic variations in prolamin components of the gluten will also be generated through mutagenesis using chemicals (ethyl methyl sulfonate) or radiation (fast neutron). Objective 3: Several radiation-mutagenized wheat lines that are deficient in glutenin proteins with epitopes responsible for inducing gluten-related disorders have been backcrossed to the wild-type line, Summit. New mutations in the glutenin and gliadin loci generated in Objective 2 will be introgressed into other elite bread and durum wheat varieties using MAS. The reduction in immunogenic potential of the identified mutant lines will be assessed using commercial kits and antibodies for detecting causal agents for immunogenicity. Both electrospinning and solution blow spinning will be used in the production of gluten fibers from wild-type and hypoallergenic wheat lines. Objective 4: The gene transformation efficiency from co-expression of multiple morphogenetic genes will be tested by generating the WOX5-GRF4-GRF1 construct and introducing it into wheat using Agrobacterium-mediated transformation. CRISPR/Cas9-based genome editing system will be used to create mutations that disrupt the expression of wheat genes encoding immunogenic proteins in Butte86 and Summit. The candidate genes for resistance to Hessian fly and greenbug identified from the Ae. tauschii panel in Objective 1 will be validated using improved gene-editing and transformation. Objective 5: The reference-quality genome assemblies for Ae. markgraffi, Thinopyrum elongatum, three durum wheat lines, and three Ae. tauschii accessions will be developed based on single-molecule real-time (SMRT) sequencing on a PacBio sequel II (HiFi/CCS mode/cell) Platform. The chromosome-scale assemblies from Ae. markgraffi and Th. elongatum will be released as the reference C and E genomes. The individual chromosome-scale assemblies from the three durum lines and three Ae. tauschii accessions will be provided to the Tetraploid Wheat Pangenome Consortium and the Open Wild Wheat Consortium, respectively, for pan-genome analysis with the individual assemblies from other durum lines and Ae. tauschii accessions under international collaborations.