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ARS Home » Pacific West Area » Aberdeen, Idaho » Small Grains and Potato Germplasm Research » Research » Research Project #424532

Research Project: Genetic Improvement of Barley and Oats for Enhanced Quality and Biotic Stress Resistance

Location: Small Grains and Potato Germplasm Research

2014 Annual Report

Objective 1: Identify and develop barley and oat germplasm with improved stress resistance (rust resistance, winter-hardiness) and enhanced end-use quality (malt, ß-glucan content). Subobjective 1A: Improve productivity and quality of barley and oat germplasm, with emphasis on malting quality (barley) and food quality (oat). Subobjective 1B: Develop winter malting cultivars with improved quality and winter survival. Subobjective 1C: Introgress resistance to barley stripe rust (BSR) into improved barley germplasm. Objective 2: Develop methods to facilitate accelerated breeding for adaptive traits and utilization of germplasm diversity in barley and oat. Subobjective 2A: Identify SNP markers linked to resistance genes for BSR and oat crown rust (OCR) for use in marker-assisted selection (MAS). Subobjective 2B: Validation of SNP markers linked to ß-glucan content, malt extract, and diastatic power. Objective 3: Develop novel biotechnological approaches for the production of genetically engineered barley and oat. Subobjective 3A: Develop Ds-based and/or recombination-mediated cassette exchange (RMCE) gene delivery systems. Subobjective 3B: Develop transgenic barley lines resistant to Fusarium infection and/or deoxynivalenol (DON) accumulation

The three objectives are separate but complementary. Objective 1: Germplasm improvement is based on modified pedigree breeding with single seed descent, multi-location in-house and collaborative test locations, off-site winter nurseries, and winter greenhouse facilities to minimize time for varietal development. Multiple breeding targets, corresponding to specific end uses, include: spring malting barley, spring barley, and oat for food and feed. The process is similar for barley and oat, except for the specific set of targeted characteristics. Procedures are based primarily on phenotypic measurements and laboratory analyses of grain quality. Markers are being developed for key traits to enable more efficient allelic selection for trait improvement and will be used as they are developed. Failure to make adequate progress will be corrected by incorporating alternative germplasm, increasing numbers of crosses, and by increasing test environment numbers and/or quality to increase the frequency of obtaining superior progeny. Objective 2: Based on the hypothesis that SNP markers closely linked to genes for OCR and BSR resistance genes, and for malting quality, will exist. OCR resistance will be assessed and mapped within five oat populations with markers from the oat 6K SNP iSelect Illumina array. BSR resistance will be assessed and mapped within four barley populations, and malting quality in two barley populations, with markers from the barley 9K SNP iSelect Illumina array. Phenotyping will be based on multi-year, multi-location field and/or greenhouse trials. Markers identified will be validated as useful by examination of allelic effects in alternative existing or newly-created populations. Multiple genomic databases will be examined to assist the identification of candidate genes underlying QTLs. Failure to identify useful QTLs or candidate gene may require development and testing of additional populations, novel markers, or analysis of new genomic resources as they become available. Objective 3: Based on the hypothesis that Ds-mediated transposition will produce plants with single-copy loci in regions suitable for high expression, the goal is to produce "clean" transgenic plants without with intact, single-copy transgenes free of extraneous DNA derived from bacterial vectors or selectable markers genes. This system utilizes two very short (~600 bp in total length) sequences derived from another food crop, maize, that when flanking other sequences can transpose--along with the intervening sequences--to new location. Transposition is controlled by introducing the relevant enzymatic activity via crosses to Ac transposase--expressing plants. Vectors will be constructed and introduced via Agrobacterium-mediated delivery. Research will concentrate on commercial cultivars, and genes with activity against Fusarium head blight or that suppress mycotoxin production will be introduced. Failure of proper gene expression is guarded against by using. The use of Ds transposition to deliver genes tends to promote good expression, and multiple candidate genes are available, some of which have imparted useful levels of resistance in preliminary work.

Progress Report
Progress towards objective 1, subobjective B, winter malting barley development, was achieved in two areas: improved testing facilities, and development of potential new products. Efficient determination of winter hardiness—a key characteristic of commercial utility—had been suboptimal because of an insufficient number of appropriate test environments. In 2014, an additional nursery was established in Idaho Falls, an area that is a major producer of malting barley. This nursery will increase the efficiency of winter malting barley cultivar development. Potential products of the program continued to move towards release. Six lines that showed good agronomic and quality characteristics are in various stages of industry quality testing by the American Malting Barley Association. Three of these lines were evaluated in pilot scale tests, and three lines previously approved based on pilot scale testing moved into more comprehensive plant scale tests. Related to Objective 1, subobjective 1A, program resources are being directed to respond to changes in the marketplace by identifying and advancing towards release barley lines with specific quality characteristics desired by the growing 'all-malt' brewing industry. The problem to solve is that all-malt brewing involves recipes and processes that differ significantly to those used in adjunct (non-barley sources of carbohydrate) brewing, and past selections have produced malt barley varieties that are suboptimal for the needs of all-malt brewing. Lines with variability in key quality traits were identified, and we provided seed of these lines to industry partners for testing. Six lines were identified based on these tests that have favorable quality characteristics for all-malt brewing. Marker assisted selection for complex characteristics such as malting quality and agronomic performance (Objective 2, subobjective 2B) will require a comprehensive understanding of genetic variability in the elite germplasm used at Aberdeen. A first step towards this goal was taken by establishing collaboration with researchers at Brigham Young University. In 2014, 156 elite breeding lines were genotyped using a marker system known as ‘KASPar’. These data will be used to guide further investigations of genetic variability for key traits, and to design strategies for marker assisted selection for complex traits. The North American Collaborative Oat Research Enterprise is a global research partnership represented by 28 oat research sites, the United States Department of Agriculture, the North American Millers' Association, and the Prairie Oat Growers’ Association. As part of its focus on research innovation in oat, this partnership has completed genotyping of a sample of current North American elite oat varieties. During this year, we made progress towards Objective 2 by using these data to evaluate the genetic diversity among these oat accessions with an eye towards elucidating the population structure. Our analyses have yielded insight into the genetic similarities and differences among oat accessions developed in different parts of the United States. This understanding will enable oat breeders to choose parents with the maximum potential for unique gene combinations that may result in new cultivars with novel characteristics. These findings will also be used to compensate for the effects of a structured population on the genome-wide association analyses that have just begun. Developing oat and barley germplasm with resistance to abiotic (environment) and biotic (insects, disease) stress is essential for economically and environmentally sustainable production. We made progress on Objective 2, subobjective 2A by advancing our understanding of the genetic control of oat crown rust resistance based on a locus known as ‘Pc58’. Using a ‘recombinant inbred’ population of 283 lines developed from a cross of oat cultivars Ogle and TAM O-301 and molecular markers known as ‘SNPs’, we discovered that Pc58 is composed of at least two distinct loci located on chromosomes 9D and 15A. In another study of crown rust resistance, using three other populations developed from crosses with ‘CDC Boyer’ and breeding line 94197A1-9-2-2-2-5, we identified quantitative trait loci for partial resistance on chromosomes 19A, 12D, and 13A. The SNP markers enabled for the first time the assignment of chromosomal locations to crown rust resistance loci and these markers provide a basis for further work to develop marker-assisted selection protocols. In progress also related to Objective 2, subobjective 2A, 14 stripe rust-resistant barley lines derived from crossing Lenetah with 95SR316A were selected based on good agronomic performance in preliminary trials and tested in advanced yield trials in 2014. Lenetah is a high-yielding feed cultivar and 95SR316A is a stripe rust resistant germplasm line, both products of the ARS breeding program at Aberdeen. Progress was made also in the identification of locations in the barley genome, known as ‘QTL’, associated with resistance. Analysis of seedling resistance data of a population derived from Lenetah/Grannenlose Zweizeilige (GZ) identified a major QTL for resistance on chromosome 4H. Marker assays have been developed for this QTL and are currently being validated in a population derived from 95R316A/GZ, setting the stage for marker assisted selection for the GZ-derived resistance. GZ contains a single QTL conferring resistance to many races of barley stripe rust. Field data for stripe rust resistance was also collected. In collaboration with researchers at Pullman, Washington (ARS), and Corvallis, Oregon (Oregon State), two mapping populations, 95SR316A/GZ and Lenetah/GZ, were evaluated. Finally, a coordinated plan for screening mapping and breeding populations for stripe rust resistance was established involving ARS researchers (Aberdeen and Pullman), Oregon State University, and the University of California, Davis. A mapping study, using SNP markers, of the genetics of Russian wheat aphid resistance was completed. This work contributed to Objective 2, subobjective 2A, and included Russian wheat aphid-resistant germplasm identified from screening the National Small Grains Collection as well as improved, Russian wheat aphid resistant germplasm lines and cultivars developed by ARS researchers at Aberdeen, Idaho, and Stillwater, Oklahoma. The study confirmed previous mapping results based on molecular markers known as ‘RFLPs’ and ‘DArTs’, and improved on these prior studies by using the more-useful SNP markers. Since these markers are based on variation in expressed sequences, that is, variation in genes, QTLs associated with these markers were related to recently-available barley sequence data, and genes potentially associated with stress resistance in the region the QTLs were identified. These data will assist in understanding the genetics of Russian wheat aphid resistance and of the diversity of resistance in the Collection, and enable marker assisted selection for Russian wheat aphid resistance. Fusarium head blight, most often associated with the more-humid regions of the Midwest, has been increasingly prevalent in the arid Intermountain West. In 2014, in cooperation with researchers at the University of Idaho, a mist-irrigation nursery was established and barley germplasm was tested for resistance to the disease. Germplasm selection was based on the results of prior, limited testing in North Dakota that identified useful levels of resistance in the Aberdeen breeding program. Development of head blight resistant germplasm via biotechnological approaches also progressed. To enable the use of RNA interference, a natural system of gene regulation involving RNA sequence recognition, we designed fungal and plant expression vectors, and initiated experiments to identify specific sequences with activity against Fusarium genes.

1. Commercialization of the high fiber barley cultivar of 'Transit'. Realizing the benefits of ARS research products requires their transfer to the marketplace. Transit is the first high yield and high beta-glucan food barley cultivar released from the Aberdeen barley breeding program. To promote the use of Transit high-fiber food barley, ARS researchers at Aberdeen, Idaho, presented three seminars about Transit quality and agronomic performance to trade delegates from Japan, South Korea, Brazil, and Taiwan. In addition, they produced 20,000 lbs of seed in 2013 that then enabled the Pacific Northwest Farmers Cooperative to produce 300 metric tons (MT) of Transit in 2014. U.S. producers have contracted to provide 40 MT of Transit to Japan, and other contracts are being negotiated. The acceptance of Transit as a high quality, health-promoting food barley in the international market will provide new customers to U.S. producers.

2. Release of 'Merem' malting barley. The malting industry is in constant need of barley varieties with improved agronomic and quality traits. ARS researchers at Aberdeen, Idaho, produced and released the spring malting cultivar, Merem. Merem is improved for malt extract percentage, a measure of use efficiency, and for yield. Merem will be useful to producers, maltsters and brewers, and will serve as a useful parent for ongoing breeding efforts at Aberdeen and by other public and private breeders.

3. Development of agronomically competitive low phytate barley. Low phytate barley, which confers better nutrition and seed phosphorus utilization when fed to monogastric animals, will only be commercially successful if the low phytate trait is not associated with poor performance. ARS researchers at Aberdeen, Idaho, have identified two low-phytate lines, one hulled and one hulless, that offer significant improvements in yield and quality characteristics compared to previously released low phytate cultivars. In FY14, breeder’s seed of these lines was produced in preparation for their release as cultivars. Once released as cultivars, these lines will provide producers with a simple genetic solution to increasing feed phosphorus utilization, which would reduce phosphorus levels in animal manure, thus reducing harmful releases of phosphorus into the environment.

Review Publications
Hu, G., Burton, C., Hong, Z., Jackson, E. 2014. Identification and characterization of a partially functional mutation of the cellulose-synthase-like (CslF6) gene in barley (Hordeum vulgare L.). Journal of Cereal Science. 59:189-195.
Islamovic, E., Obert, D., Budde, A.D., Schmitt, M., Brunick II, R., Kilian, A., Chao, S., Lazo, G.R., Marshall, J., Jellen, E., Maughan, P., Hu, G., Esvelt Klos, K.L., Brown, R., Jackson, E. 2014. Quantitative trait loci of barley malting quality trait components in the Stellar/01Ab8219 mapping population. Molecular Breeding. DOI: 10.1007/s11032-014-0017-3.
Brown, R., Dahleen, L.S., Lemaux, P.G., Bregitzer, P.P. 2014. Registration of the barley transposon-tagged population I:seventy lines each with a single, unique site of Ds insertion. Journal of Plant Registrations. 8:226-230.
Dahleen, L.S., Mornhinweg, D., Bregitzer, P., Vitou, J., Cakir, M. 2014. Biotype differences for resistance to Russian wheat aphid in barley. Crop Science. 54:1505-1513.
Hu, G., Chen, J., Chu, C., Wu, Y. 2014. Mapping of STS markers developed from drought tolerance candidate genes and preliminary analysis of their association with yield-related traits in common wheat (Triticum aestivum). Cereal Research Communications. 42:199-208.