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United States Department of Agriculture

Agricultural Research Service

Research Project: CHARACTERIZATION OF STRESS RESISTANCE GENES AND MECHANISMS, & IMPROVEMENT AND GENOTYPING OF WHEAT AND BARLEY GERMPLASM FOR THE WESTERN U.S.
2012 Annual Report


1a.Objectives (from AD-416):
Investigate the genetic mechanisms by which the plant hormones abscisic acid (ABA) and gibberellin (GA) control pre-harvest sprouting stand establishment, and drought and cold tolerance in wheat and model organisms. Develop and utilize molecular markers for the western region wheat and barley breeding programs for resistance to stem rust, other biotic and abiotic stresses, and end-use quality. Develop wheat cultivars with durable resistance to stripe rust, stem rust, soilborne diseases, cold and drought, and improved end-use quality for Western Region cropping systems using wheat germplasm resources from the USDA-ARS National Small Grains Germplasm Collection (NSGC) and other national and international sources.


1b.Approach (from AD-416):
Determine whether ABA sensitivity controls grain dormancy and tolerance to preharvest sprouting. Determine whether degree of drought tolerance and cold tolerance tend to correlate with each other and depend upon ABA sensitivity. Determine how GA signaling controls seed dormancy and plant height. Identify and use new and existing molecular markers linked to genes for biotic stress resistance, specifically for stripe rust resistance. Identify and use new molecular markers for genes linked to abiotic and end-user quality. Establish and use high-throughput molecular marker analysis systems to track the segregation of important genes in wheat and barley breeding programs. Characterize core wheat germplasm sets for use in identifying haplotypes important in Western Regional germplasm adaptation. Use molecular markers to link genotypes to phenotypes while maintaining critical haplotypes for enhancement, disease resistance and end-use quality in Western Region wheat breeding programs. Identify new sources of genes giving superior end-use quality, disease resistance, and resistance to cold and drought.


3.Progress Report:
Objective 1A addresses whether the plant hormone ABA controls wheat grain dormancy and preharvest sprouting tolerance. Higher ABA sensitivity correlated with higher preharvest sprouting tolerance in soft white and hard red wheat varieties. ABA hypersensitive mutant ZakERA8 is a semi-dominant mutation that causes higher seed dormancy and slower dormancy loss. Increased seed dormancy provides ZakERA8 with better preharvest sprouting tolerance than normal Zak. Objective 1B examined whether ABA controls wheat resistance to drought stress. ABA hypersensitive mutant Warm4 has increased vegetative ABA sensitivity in leaf dip experiments. Warm4 causes decreased transpiration rate and increased water use efficiency. Objective 1C examines how the hormone GA controls seed dormancy. GA and its receptor GID1 stimulate seed germination by lifting DELLA gene repression of germination. GID1-DELLA protein interaction is associated with loss of seed dormancy. Mutations that interfere with GID1-DELLA interaction lead to increased seed dormancy via DELLA-repression of seed germination.

Objective 2A Identify and use molecular markers for biotic stress resistance, abiotic stress and end-use quality. The Western Regional Small Grains Genotyping laboratory coordinated SNP discovery efforts on 1,824 wheat lines including 6 mapping populations, produced 7504 polymorphic markers of which 7160 were mapped to chromosomes. Objective 2B 518264 datapoints were scored using SSR molecular marker analysis systems to track the segregation of important genes in the 5 state breeding programs. 334,148 SNP datapoints were obtained in research for stripe rust traits. Objective 2C Characterize core wheat germplasm for use in identifying haplotypes important in Western Regional germplasm: Germplasm from the NSGC that was screened in Kenya for UG99 resistance was characterized with SSR and SNP markers, a molecular phylogeny was developed which was used to indicate novel resistance germplasm Sthapit et al. 2012 PAG P0156. Six mapping populations have been developed for introgression into adapted material and for gene discovery.

Objective 3 Develop wheat germplasm and cultivars adapted to Western Region cropping systems with resistance to stripe rust, soilborne disease, cold, drought, and with improved end-use quality and to coordinate the Western Regional Cooperative Wheat Nurseries. ARS-Selbu soft white winter wheat and ARS-Chrystal winter club wheat were increased for breeders seed at Othello WA. Both have excellent resistance to predominant races of stripe rust and excellent end use quality. Marker assisted selection was used to select several hundred breeding lines with combined resistance to stripe rust, barley yellow dwarf virus, pre-harvest sprouting and soil-borne disease. The Western Regional Nurseries were evaluated at ten locations in the Northwest. Data was collected on agronomic traits, resistance to stripe, stem and leaf rust, and cold tolerance. This work will benefit wheat growers and end users because competitive soft wheat cultivars can be grown with reduced inputs and marketed as premium quality products.


4.Accomplishments
1. Development of ARS Selbu soft white winter and ARS Chrystal soft white club wheat. Changes in the stripe rust population structure caused susceptible reactions on several new soft white winter wheat cultivars in the Pacific Northwest. Promising wheat lines were screened for desirable genes using marker assisted selection, leading to the new cultivars ARS Selbu and ARS Chrystal. These cultivars have excellent resistance to stripe rust, combined with soil borne disease resistance and excellent agronomic and end use quality characteristics that will reduce grower risks for production and marketing. This research will benefit growers and end users by saving money on fungicide sprays and providing wheat grain that is highly marketable.

2. Identification of climate variables that influence the distribution and severity of species causing Fusarium crown rot. The problem is that Fusarium crown rot, caused by Fusarium psuedograminearum and Fusarium culmorum are significant yield limiting diseases of wheat in dryland cropping systems and breeders need to know which species are present in order to breed for resistance. A survey of dryland wheat cropping sites was constructed in 2008 and 2009, by ARS researchers in Pullman, WA, pathogens were isolated, diseased stems were scored, and factor analysis and general linear mixed models were used to associate climate, cropping system and soil texture variables with the disease scores and presence of specific species. Isolates of Fusarium spp. were obtained from 99% of 105 fields sampled in 2008 and 97% of fields in 2009. Results of the analysis showed that the distribution of F. pseudograminearum occurred in a greater frequency in areas of the Pacific Northwest at lower elevations with lower moisture and higher temperatures, whereas F. culmorum occurred in greater frequency from areas at higher elevations with moderate to high moisture and cooler temperatures. This approach can be utilized in studies to describe the effects of climate and other environmental (soil, cropping system, etc.) factors on the distribution and severity of root diseases.

3. ARS scientists at Pullman, WA, identified the number and locations of alleles for Fusarium crown rot resistance in spring wheat. Fusarium crown rot is a major disease of wheat in the Pacific Northwest of the US that can limit yields up to 35% under severe infection. Adapted genetic sources of resistance have not been identified. Two populations segregating for resistance were scored in greenhouses, outdoor terraces and field based screening systems over multiple locations and years, and scored for molecular markers, then analyzed to determine the association between markers and resistance to Fusarium crown rot. A major QTL derived from the adapted cultivars Otis and Macon was identified on chromosome 3BL with other minor QTL located to chromosomes 2B, 3B, 4B, 4D, and 7A. This result is significant because the major QTL can be used to select for resistance to Fusarium crown rot, and resistance can be confirmed through use of the screening systems that were developed for this project, thus providing farmers with a genetic management tool for this disease.

4. Genetic improvement of wheat preharvest sprouting tolerance. Wheat varieties with low seed dormancy undergo preharvest sprouting if rain triggers germination prior to harvest, while too much seed dormancy results in poor seedling emergence or germination. The first condition causes economic loss when grain is rated as feed while the second results in reduced yield. The hormone ABA induces seed dormancy. ARS researchers in Pullman, WA, found that ABA-insensitive mutants in dormant red wheat Scarlet did not cause a decrease in initial seed dormancy or preharvest sprouting susceptibility, but did result in more rapid loss of dormancy with dry after-ripening. This rapid dormancy loss improved seed germination and emergence, and provides a genetic strategy to improve emergence of red wheat varieties.

5. The hormone GA promotes seedling growth and development. Is important to understand mechanisms promoting the transition from seed germination to seedling growth transition is critical for vigorous early growth and establishment of crop plants. ARS researchers in Pullman, WA, found that increased accumulation of the GA hormone receptor can promote the germination of dormant seeds. However, such seedlings are underdeveloped and weak unless they are also exposed to GA hormone prior to seed germination. This suggests that increased GA hormone signaling can be used to promote early growth, development, and vigor of germinating seedlings thereby alleviating problems with poor seedling emergence, a serious problem especially in semi-arid regions where seeds must be planted deeply to reach stored soil moisture.

6. Efficient methodology developed for selection of core subsets from germplasm collection. Many germplasm collections are too large to be screened in their entirety. Efficient methods are needed to subsample and develop a core collection to represent the whole collection. Missing data present a significant barrier to efficiency. Simulated datasets were calculated based on the variables in the U.S. National Small Grains Collection that had various patterns of missing data. Core subsamples were taken to determine if using only complete data, or using all the data even when sparse, resulted in a more diverse subset. Core subsets selected using Gower’s distances estimated using all variables available, including those with more than 5% missing data; clustered using the UPGMA algorithm and sampled in proportion to the logarithm of the cluster sizes were the most diverse. This method is expected to produce core subsets that retain much of the diversity of the complete collection while excluding redundant accessions. The conclusions of this study should be broadly applicable to large germplasm collections with sparse data, including genotypic data, beyond the USDA wheat collection used in the simulation process.

7. Developing molecular markers in wheat. The need to transition away from SSR and move towards sequence based markers is essential to modern Marker Assisted Sequencing (MAS) based breeding efforts. To accomplish this, gene sequence information from relevant US germplasm was used to identify new single nucleotide polymorphisms and develop SNP based molecular markers. Outcome from this research includes; genotyping 1,824 wheat lines including 6 mapping populations treated against 9,000 SNPs (Single Nucleotide Polymorphisms), resulting in identifying 7504 polymorphic markers of which 7160 were mapped to chromosomes. Additionally, WRSGGL coordinated the current PNW germplasm set of 2,300 including additional mapping populations for 90,000 SNP discovery. These outcomes will form the core of new molecular markers that will be able to replace SSR and provide high density coverage of the wheat genome.


Review Publications
Nirmala, J., Drader, T., Lawrence, P.K., Yin, C., Hulbert, S., Steber, C.M., Steffenson, B.J., Szabo, L.J., Von Wettstein, D., Kleinhofs, A. 2011. Concerted action of two avirulent spore effectors activates Reaction to Puccinia graminis 1 (Rpg1)-mediated cereal stem rust resistance. Proceedings of the National Academy of Sciences. 108(35):14676-81.

Li, P., Chen, J., Wu, P., Zhang, J., Chu, C., See, D.R., Brown Guedira, G.L., Zemetra, R., Souza, E.J. 2011. Quantitative trait loci analysis for the effect of Rht-B1b dwarfing gene on coleoptile length and seedling root length and number of bread wheat. Crop Science. 51:2561-2568 (2011).

Poole, G., Smiley, R., Paulitz, T.C., Carter, A., See, D.R., Campbell, K. 2012. Identification of quantitative trait loci (QTL) for resistance to Fusarium crown rot (Fusarium pseudograminearum) in multiple assay environments in the Pacific Northwestern US . Theoretical and Applied Genetics. 125:91-107.

Carter, A.H., Garland Campbell, K.A., Kidwell, K.K. 2011. Chromosomes 3B and 4D are associated with several milling and baking quality traits in a soft white spring wheat (Triticum aestivum L.) population. Theoretical and Applied Genetics. 124(6):1079-96.

Schramm, E., Nelson, S.K., Steber, C.M. 2012. Wheat ABA-insensitive mutants result in reduced grain dormancy. Euphytica. 188(1),35-49. Published online March 31, 2012.

Last Modified: 11/22/2014
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