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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

2018 Annual Report


Objectives
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


Approach
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
This is the final report for project 2050-21000-031-00D, which has been replaced by new project 2050-21000-034-00D. Two spring barley varieties were released with improved productivity, agronomic traits, and grain quality. ‘Merem’ features improved yield in combination with higher levels of malt extract, which improves use efficiency. ‘Gemcraft’ is the first barley variety released in North America specifically to address the unique needs of all-malt brewers. Gemcraft combines good productivity with the lower enzymatic and protein content traits desired for all-malt brewing. To meet the demand for barley with high beta (ß)-glucan content, ‘Kardia’ and ‘Goldenhart’ hulless barleys were released. Both have improved combinations of performance and ß-glucan content compared to currently-popular varieties. To facilitate future progress, new variability for ß-glucan content in barley was created by inducing low and high ß-glucan mutants with altered CslF6 activity. The high ß-glucan mutant was patented (U.S. Patent 9,681,620 B2) and has potential as a parent of novel high ß-glucan food varieties. The low ß-glucan mutant may be useful for malting, where high beta-glucan is undesirable. Winter (fall-planted) barley, compared to spring barley, has higher yield and better water-use characteristics. Increased water-use efficiency is a critical need in water-limited production areas. Expanding production of winter barley requires increased winter hardiness for dependable production. Progress was made in several areas. Additional testing sites in key production areas were developed to enable more rapid identification of superior germplasm. Collaborative, multi-location testing identified 77 lines with excellent winter survival within a set of lines from the Vavilov Center. Three candidate varieties were identified that are undergoing industry testing. All represent improvements over previous winter barley releases, ‘Charles’ and ‘Endeavor’, and two are resistant to barley stripe rust. Sustainable production was addressed by the release of ‘Sawtooth’ (hulless) and ‘Harrrington’ low-phytate spring barleys. They have better yield and reduced phytate compared to previously-released low-phytate varieties. Phytate is a phosphorus storage compound that is associated with ground and surface water contamination and reduced non-ruminant animal nutrition. Disease resistance is complicated to assess because of year-to-year variation in pathogen populations and weather. Tools to enable direct genetic selection of disease resistance were developed for oat crown rust (OCR) and barley stripe rust (BSR). The goal is to discover genetic markers for resistance to allow more efficient selection and faster development of improved varieties. For OCR, the Pc58 resistance trait was mapped to two distinct genetic loci in the ‘Ogle x ‘Tam O-301’ population. Sequence-based single nucleotide polymorphism (SNP) markers were developed for both loci. SNP markers for other OCR seedling resistance loci were mapped in four additional populations. In addition, adult plant resistance—conferred by multiple genes and thought to be a more stable resistance than that conferred by single seedling resistance genes was studied in a population developed from ‘94197A1-9-2-2-2-5’, ‘CDC Boyer’, ‘TAM O-301’ and ‘MN841801’ that combined multiple resistance genes. Lines within this population were characterized for the number and origin of resistance genes using SNP markers developed by this project. Initial evaluation of field OCR resistance showed that these markers were effective for selection of resistant lines, and that these genes are more effective in combination than they are alone. Some of these lines will be used to contribute crown rust resistance to the breeding program. In addition, an approach called ‘bulk segregant analysis’ was used to identify molecular markers in oat that are likely associated with resistance to an important disease called stem rust. Markers for two single stem rust resistance genes and one two-gene combination were tentatively identified in cooperation with ARS scientists in St. Paul, Minnesota. The next step will be to verify these markers in a second genetic background and design markers. Progress on BSR resistance included the advancement of two candidate winter malting barley varieties (one with adult plant resistance derived from the previously-released ‘95SR316A’), and the development of lines with resistance derived from a landrace sourced out of the National Small Grains Collection, ‘Grannenlose Zweizeilige’ (GZ). GZ has seedling resistance genes that confer high levels of BSR resistance. Four GZ resistance loci were mapped, and SNP markers were developed and used to develop an advanced backcross population composed of multiple lines that include all possible combinations of GZ-derived resistance alleles on a genetic background derived primarily from 95SR316A. This population will enable validation of the location and magnitude on resistance of these SNP markers. This population will be a valuable source of parents, with 95SR316A contributing adult plant resistance combined with good agronomic and malting qualities, and GZ contributing high levels of seedling resistance. To facilitate the transfer of adult plant resistance from 95SR316A to other backgrounds, lines derived from the crosses 95SR316A x ‘Lenetah’ (susceptible to BSR) and 95SR316A x GZ were genotyped for thousands of SNP markers across the genome. Genetic mapping is underway to identify markers for adult plant resistance to BSR contributed by 95SR316A. BSR resistance work has benefitted from cooperative agreements with Oregon State University and University of California, Davis, and from cooperation with ARS in Pullman, Washington. The progress reported above was made possible by field data collected from these cooperators. In addition to data on lines from this program, data was provided on elite breeding lines from the California, Oregon, and Washington barley breeding programs. This collaboration directly contributed to the identification and deployment of stripe rust resistance genes in the context of the varieties ‘Alba’ and ‘Buck’, and multiple germplasm lines (#STRKR and BISON genetic stocks). The BISON stocks include lines with resistance QTL in all possible combinations on the susceptible, elite background of ‘Baronesse’. The #STRKR germplasm line is a bulk of three lines with winter/facultative growth habit. Educational opportunities for graduate students and staff have been provided at all cooperating institutions and opportunities for life-long learning have been offered to stakeholders at field days, and via online resources (e.g. http://barleyworld.org/bsr), and in the popular press. Biochemical assessment of malting quality is expensive and slow. ARS scientists in Aberdeen made four backcross-derived populations to test the utility of quality selection with those identified in the variety ‘Stellar’ for improving malting quality in the Aberdeen program. These crosses have placed two targeted combinations of Stellar-derived markers onto two different Aberdeen genetic backgrounds that were chosen to provide genetic and phenotypic contrasts. All four populations are being advanced and will be ready for further study next year. Genetic engineering of barley can produce mutants useful for understanding genetic control of traits and for producing useful germplasm. Collaborative work with the University of California, Berkeley, Oregon State University, and McGill University produced a barley transposon tagging system, a new genetic tool for barley based on maize Dissociation (Ds) transposons. Transposons are small, mobile DNA sequences that can be modified to carry additional genes. When inserted into a gene, transposons cause a mutation that alter plant characteristics, thus revealing gene function. Out of a population of thousands of lines containing transposon insertions, 131 were identified with a single transposon in a known location. These lines were released as genetic stocks, and characterizations of the altered sequence were documented in the National Center for Biotechnology Information GenBank database. One line had a mutation of a gene involved in floral development, and is being used for genetic studies by colleagues in Japan and Scotland. Ds transposons tend to move into locations in or near genes, and if they are modified to include a gene, it will be moved into a location that supports good gene expression. In collaboration with ARS researchers in Albany, scientists are using transposon-mediated delivery of novel genes into spaces between native genes to improve the precision of transgene insertion using a two-step process. In the first step, a “recombination platform” is being delivered that contains specific sequences that will allow the second step. After plants are identified where this platform has been properly delivered (the platform is intact and not causing a mutation in a native gene) they are ready for step two, the introduction of genes with new functions to enable genetic studies or to produce a useful characteristic, such as disease resistance. Improved control of transgene insertion is achieved because the recombination is precise and the location of the introduced gene is into a known, characterized location. Such precision is expected to increase the utility and safety of genetically engineered barley plants. We have introduced these recombination platforms into barley and identified plants where step one has been successful. Scientists are initiating step-two experiments that will introduce genes for resistance to Fusarium head blight resistance. This disease produces a toxic substance that can contaminate barley grain and cause human illness. The products of this research are expected to increase our understanding of how to produce barley plants resistant to Fusarium head blight.


Accomplishments
1. Release of ‘Goldenhart’ two-rowed, spring hull-less food barley. A new food barley with high beta-glucan content was developed and released by ARS researchers in Aberdeen, Idaho, collaborating with the University of Idaho. It has shown better yield under irrigated conditions and similar yield in dryland areas compared to other popular high beta-glucan barley varieties, ‘Julie’, ‘Transit’, and ‘CDC Alamo’. Beta-glucan intake is associated with improved cardiovascular health, but the majority of the U.S. population consumes less than is recommended. The availability of ‘Goldenhart’ as an ingredient in food will lead to enhanced human health, and contribute to producer profitability by providing a commodity with marketplace demand.

2. Release of ‘Gemcraft’ two-rowed, spring malt barley. A new barley variety, the first to be developed and released specifically for the “all-malt” sector of the brewing industry, was developed and released by ARS researchers in Aberdeen, Idaho, in collaboration with the University of Idaho. Gemcraft has yield equal to or better than popular malt barley varieties. It was developed using a novel collaborative model with the Brewer’s Association, which represents craft brewers who do not use adjunct (non-barley) sources of starch, such as rice or corn. All-malt brewers require specific alterations of enzymatic activities and protein content compared to brewers who use adjunct sources of starch. By providing a malt specifically tailored to the all-malt industry, Gemcraft will contribute to producer and brewer profitability by providing an in-demand commodity crop and by enabling the efficient production of an improved, premium malt product to consumers.


Review Publications
Gines, M.C., Baldwin, T.T., Rashid, A., Bregitzer, P.P., Jellen, E., Maughan, J., Esvelt Klos, K.L. 2018. In silico selection of expression reference genes with demonstrated stability in barley among a diverse set of tissues and cultivars. Crop Science. 58(1):332-341. https://doi.org/10.2135/cropsci2017.07.0443.
Baldwin, T.T., Basenko, E., Harb, O., Brown, N., Hammond-Kosack, K.E., Bregitzer, P.P. 2018. Sharing mutants and experimental information prepublication using FgMutantDB. Fungal Genetics and Biology. 115:90-93. https://doi.org/10.1016/j.fgb.2018.01.002.
Bjornstad, A., He, X., Tekle, S., Esvelt Klos, K.L., Huang, Y., Tinker, N.A., Dong, Y., Skinnes, H. 2017. Genetic variation and associations involving Fusarium head blight and deoxynivalenol accumulation in cultivated oat (Avena sativa L.). Plant Breeding. 136:620-636. https://doi.org/10.1111/pbr.12502.