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ARS Home » Pacific West Area » Pullman, Washington » WHGQ » Research » Research Project #424575

Research Project: Genetic Improvement of Wheat and Barley for Resistance to Biotic and Abiotic Stresses

Location: Wheat Health, Genetics, and Quality Research

2013 Annual Report

Objective 1. Identify and develop wheat germplasm adapted to the Pacific Northwest of the United States with improved tolerance to pre-harvest sprouting, drought stress, cold temperatures, rusts, and soil-borne diseases. 1A. Identify sources of drought, cold, and disease tolerance by phenotyping subsets of the National Small Grains Collection as well as international and regional nurseries. 1B. Reduce production risk by developing germplasm with increased resistance to stripe and stem rust. 1C. Breeding club wheat and hard white winter wheat. Objective 2: Develop more efficient wheat and barley breeding approaches based on high throughput phenotyping and genotyping methods as well as genomic selection models. 2A. Identify and apply SNP markers for basic biology and MAS in wheat and barley. 2B. Develop high-throughput phenotyping methods for measuring freezing and drought tolerance. 2C. Develop statistical models for genotype response to environmental stress that improve the efficiency of selection and breeding. Objective 3: Investigate the mechanisms controlling drought and cold tolerance, pre-harvest sprouting, and rust resistance in wheat. 3A. Identify and combine physiological mechanisms that support yield under water stress in wheat including water-use efficiency, root architecture, and photosynthetic efficiency. 3B. Transcriptome analysis of post cold-acclimation stress response. 3C. Gene Expression profiling and biochemical pathway discovery for stripe rust resistance. 3D. Examine the role of the plant hormones ABA and GA in controlling seed dormancy, germination, and preharvest sprouting tolerance.

Objective 1. We will evaluate a total of 6,356 accessions for resistance to freezing injury, Fusarium crown rot, lesion nematodes, cyst nematodes, and stripe rust. We will conduct these evaluations using facilities at WSU, including controlled environments in the WSU Plant growth facility and at the Spillman Agronomy Farm. We will use the genomic information generated by the T-CAP for the existing core collection to link phenotypes to genotypes. We will also screen germplasm from U.S. regional nurseries. These selections will be genotyped to determine relationships and, on the theory that genetic control of resistance will be different among genetically diverse genotypes, traits from the most diverse will be introgressed into adapted cultivars, and germplasm adapted to various regions of the U.S. carrying unique new sources of resistance and molecular markers that can be used to select for these new resistance loci. Objective 2. Specific areas that are being targeted in SNP development include identification of SNP markers linked to stem and stripe rust resistance genes, and identification of SNP in wheat responsible for adaptation. The current small grains single plant core collections are being evaluated for SNP linkages to drought, stripe, leaf and stem rust response. As new, verified markers are identified, they will be made available to the customers of the genotyping laboratory as applicable to the customers’ research and breeding objectives. Our goal is to transition away from single gene selection using SSR markers and incorporate genome selection utilizing SNPs through SNP-chip platforms. Objective 3. Pathways and mechanisms controlling drought and cold tolerance, pre-harvest sprouting, and rust resistance in wheat will be elucidated. Indirect selection for tolerance to freezing and to drought based on physiological traits associated with drought and freezing tolerance will be carried out as part of the selection process. Plant lines will be selected for higher water use efficiency, deeper roots, and higher photosynthetic efficiency to develop better grain yield and grain-filling under drought stress. Transcriptome analysis will be used to identify pathways and mechanisms responding to freezing stress and stripe rust. Key genes will be identified and their expression monitored under stress conditions, thereby identifying plant lines differing in their abilities to respond to parts of the freezing or infection process. Variation in sensitivity to plant hormones will be investigated as a means to control and improve seedling emergence and preharvest sprouting tolerance. These different abilities and sensitivities will be genetically combined, resulting in improved stress tolerance.

Progress Report
These research objectives continue and expand on objectives initiated under the previous project, 5348-21000-023-00D. Objective 1A: Seventy-eight Iranian Landrace accessions were characterized for agronomic traits, and for resistance to root lesion nematodes & stripe rust. Regional nurseries were characterized for agronomic performance, frost tolerance, and resistance to stripe rust & cereal cyst nematodes. Objective 1B: Germplasm adapted to the Great Plains & Eastern USA were developed with sources of stripe rust resistance from the USDA-ARS club wheat breeding program. Objective 1C: Six advanced club & common soft white breeding lines were entered into cooperative nurseries as a final step to assess competitive performance in the northwestern USA. Objective 2A: 90,000 single nucleotide polymorphism discovery done on panel of PNW wheat which includes 5 mapping populations, consensus map being developed. Genotyping by sequencing done on northwest winter, spring & club wheat mapping populations. The Western Regional Small Grains Genotyping Lab processed 547,045 datapoints for marker assisted selection in multiple crops over the entire year (includes 6 months of 5348-21000-023-00D). Objective 2B: Improved sampling method was developed and carbon isotope discrimination was used as a metric for water use efficiency. Objective 2C: A genetic model that predicts wheat frost tolerance was developed based on genotype and phenotype data. The Vernalization1 (Vrn-A1) & C-repeat Binding Factor genes were sequenced in over 150 accessions; one haplotype at C-repeat binding factor #12 and #15 interacted with copy number variation at the Vrn-A1 locus to increase frost tolerance of winter and spring wheat. Objective 3A: Two spring recombinant inbred line populations, Louise/Alpowa and Louise/AUS28451 were characterized for water use & photosynthesis traits at multiple locations. Louise/AUS28451 was characterized for resistance to root lesion nematodes. Objective 3B: Transcriptomes were analyzed from plants (1) cold-acclimated for 5 weeks, then (2) frozen to -3C for 24 hours, or (3) as in (2) plus thawed at +3C for 24 hrs. Freezing tolerance was significantly greater & transcriptomes were greatly different at successive time points, indicating gene expression cascades involved in enhanced freezing tolerance. Objective 3C: Developed 6 mapping populations containing introgressions from wheat landraces with dual resistance to stem and stripe rust, three have seedling resistance and 3 have adult plant resistance. Sequencing transcriptomes of 90 individuals for Electronic Quantitative Trait Loci mapping of High Temperature Adult Plant stripe rust resistance from the cultivar “Louise” Objective 3D: Examined how the hormone gibberellic acid & its receptor GID1 (GA-Insensitive Dwarf1) stimulates seed germination. GID1 lifts repression of germination by blocking expression of abscisic acid (ABA) biosynthesis gene XERICO, leading to decreased ABA levels and increased germination potential.

1. The plant hormone Gibberellic Acid (GA) controls loss through after-ripening. The problem is that no one yet understands how dry dormant seeds are able to acquire the ability to germinate through a period of dry storage, called after-ripening. ARS researchers in Pullman, Washington, found that levels of the plant hormone GA increase with seed after-ripening of an Arabidopsis mutant called sly1. Increased GA levels block DELLA gene activation of ABA hormone biosynthesis, thereby preventing ABA from repressing seed germination. This research has the potential to provide new strategies to control the timing of seed dormancy loss in crops.

2. Lesion nematodes reduced wheat yields in many dryland wheat producing areas including the Pacific Northwest of the US. Our objectives were to assay a set of Iranian landrace accessions to determine if they possessed resistance to two species of lesion nematode. Methods included greenhouse and field assays for disease. We identified 21 accessions with resistance to both Pratylenchus thorneii and P. neglectus. These accessions will be useful to breed for resistance to both species.

3. Freezing injury reduces yields in winter wheat in many locations thoughout the US. Our objectives were to determine if specific allele variation at two loci on chromosome 5A, FrA2 and Vrn-A1, were associated with frost survival in wheat. We assayed 150 spring and winter wheat accessions from around the world as well as a population segregating for the two loci using controlled artificial freezing tests in programmeable freezers. Our results indicate that copy number variation at CBF12, CBF14 and at Vrn-A1 are all associated with frost tolerance in winter and in spring wheat and that these loci interact to regulate frost tolerance in wheat. These results are important for breeders who want to manipulate and improve frost tolerance in wheat.