Research Project: Improvement of Barley and Oat for Enhanced Productivity, Quality, and Stress Resistance

Location: Small Grains and Potato Germplasm Research

2022 Annual Report

Objectives
This project intends to produce improved barley and oat germplasm, and new information and techniques to facilitate increased efficiencies. The objectives below will be the specific focus for the next five years: Objective 1: Develop barley and oat germplasm with increased yield, better quality, and superior or novel resistances to biotic and abiotic stresses. • Subobjective 1A: Develop low protein barley lines suitable for all-malt brewing. • Subobjective 1B: Develop improved winter food barley varieties. • Subobjective 1C: Develop facultative malting barley. • Subobjective 1D: Develop barley varieties with improved Fusarium head blight resistance. Objective 2: Translate new, sequence-based information into breeder-friendly tools for crop improvement in barley and oats. • Subobjective 2A: Map Fusarium head blight (FHB) resistance and develop germplasm resistant to multiple diseases via marker-assisted selection. • Subobjective 2B: Map quantitative trait loci (QTL) from new sources of adult plant resistance to oat crown rust disease (OCR) and develop milling oat germplasm resistant to crown rust. Objective 3: Develop and implement novel biotechnological tools to produce barley germplasm with unique traits and enhance understanding of the genetic mechanisms underlying key traits. Subobjective 3A: Deliver a site-specific recombination (TAG) platform via Ds-mediated transposition, and demonstrate functionality for RMCE in barley. • Subobjective 3B: Construct and deliver Ds-bordered RNAi constructs that are transposition competent and that confer resistance to Fusarium head blight. • Subobjective 3C: Perform genetic analyses of seed total phosphorus and phytic acid in barley.

Approach
Objective 1: Productive varieties will be developed that are improved for agronomic performance, protein and beta-glucan contents, winter survival, and Fusarium head blight (FHB) resistance. Hybridization with generation advance in greenhouses, New Zealand, and by doubled haploids will be used for population development. Breeding efficiency will be enhanced by investigating the genetics of key traits to enable genomic selection and the development of novel selection schemes. Agronomic performance and FHB resistance will be assessed in multi-location field trials. Grain quality will be assessed by physical examination and chemical analysis of grain for malt quality, protein and beta-glucan contents, and mycotoxin content. Objective 2: Research will relate genetic sequence to disease resistance. Incorporating resistance to diseases that constrain oat and barley production outside of the Intermountain West will make Aberdeen germplasm more valuable. Since Idaho locations have low disease, direct selection for resistance is difficult. Indirect selection of sequence-based markers associated with resistance will combine good agronomic performance and grain quality with resistance to rusts and blotches. For diseases with established markers, development of new lines with specific markers will precede field screening in disease-prone sites outside of Idaho and in greenhouses using artificial inoculation. For other diseases, such as oat crown rust, screening in disease-prone sites will measure disease in multiple test lines, and statistical associations between specific sequences and resistances will identify and “map” new markers. Hybridization, generation advance, and genotypic and phenotypic screens will establish new populations from which lines that have improvements in disease resistance, yield, and quality will be selected. Objective 3: Research will develop tools for experimental genetic manipulations and knowledge of how phosphorus is stored in seeds. Phosphorus is a critical nutrient and a major water pollutant. The hypothesis that the gene lpa-M955 is responsible for reduced seed phosphorus will be investigated by investigating statistical associations between the gene and different levels of seed phosphorus as measured by chemical assays. The hypothesis that new mutations can be found that result in 25% less phosphorus but without negative impact on plant performance will be examined by finding low-phosphorus mutant seeds, and growing them and selecting healthy plants that will then be tested in greenhouses and fields. To facilitate future genetic engineering experiments to identify additional genes of importance, the hypothesis that causing test genes to “jump” (transpose) into specific locations will help answer genetic questions will be tested by attempts to move a test gene into a specially designed receiver site. To test the hypothesis that this process can be harnessed to produce a non-chemical method of controlling a fungus that produces toxins in crop seeds, transposition will deliver an antifungal gene, followed by greenhouse and growth chamber screening for the reduced ability of the fungus to grow and produce toxins.

Progress Report
In support of Sub-objective 1A, research continued towards the development of low protein barley lines suitable for all-malt brewing as breeding lines were evaluated in multiple nurseries. All selected low protein lines were tested for malting quality and lines with promising malting quality profiles were further selected for the evaluations. Three spring lines (14ARS147-1, 15ARS019-5, and 15ARS182-1) and two winter lines (13ARS537-25 and 13ARS537-13) were tested in the American Malting Barley Association (AMBA) pilot scale evaluations using seed harvested in 2021. Breeding line 11ARS191-3 was requested by a commercial company for large-scale testing. We provided over 200 pounds of 11ARS191-3 seed to the company. In addition, we released three winter elite malting barley lines as germplasm in the Journal of Plant Registration. To address the specific needs of the distilling industry, we worked towards developing non-Glycosidic nitrile lines by obtaining 95 families for further genotype and phenotype evaluation. In support of Sub-objective 1B, we collaborated with a commercial company to comprehensively evaluate three high beta-glucan barley lines with good winter survival. The winter food barley elite lines 12ARS777-1, 12ARS777-2, and 12ARS801-1 were evaluated for agronomic and quality traits. The results will be used by the commercial company to identify whether one or more of these breeding lines should be utilized as a new variety. In support of Sub-objective 1C, the development of good quality malting barley with a facultative growth habit, we made crosses between breeding lines with good malting quality, involving at least one facultative parent. Facultative lines can be planted in either the fall or spring for a summer harvest, allowing for greater management flexibility. Lines developed from previous crosses were evaluated in winter performance nurseries and several have been identified that may exhibit facultative growth habit. Those lines will be tested in winter and spring nurseries to verify their facultative habit before evaluating them for agronomic performance and malting quality profile. The organic barley and oat evaluation nursery at Aberdeen, Idaho, achieved the requirement for three years of operation without synthesized chemical application. Collection of organic nursery evaluation data on elite breeding material was initiated. This nursery will provide growers with information on the agronomic performance and malting/milling quality of elite barley and oat cultivars under organic production in the Intermountain West. This performance nursery joins the Western Regional Spring Barley and the American Malting Barley Nurseries under coordination at Aberdeen, Idaho. To address the growing problem of Fusarium head blight (FHB) in the Intermountain West (Sub-objective 1D), elite malting and food barley breeding lines were evaluated at FHB nurseries in Idaho, North Dakota, and Minnesota. The level of FHB resistance and the resulting amount of deoxynivanol (DON) mycotoxin in the grain have been added to the characteristics on which elite germplasm is judged prior to release. DON toxin in barley grain renders it inedible by humans or animals and unusable by the malting industry. The spring malting barley genomic selection training population has been evaluated for FHB resistance at multiple locations and markers associated with resistance and DON toxin levels have been identified. In support of Sub-objective 2A, four bi-parental spring barley populations created to map genes influencing resistance to FHB were scored for FHB resistance and deoxynivalenol (DON) mycotoxin contamination after growth at two disease nurseries in North Dakota. As required for genetic mapping, the lines within these populations showed large differences in their level of resistance to FHB, especially at Fargo, North Dakota. FHB severity is highly variable from location-to-location and from year-to-year. To obtain enough data for genetic mapping, these populations will need to be further tested at multiple locations and over multiple years before enough information has been accumulated to compare the number and locations of genes influencing FHB resistance in each population. While a winter growth habit can provide some innate protection against FHB, characterization of the genetic resistance available in this type of barley is also desirable. After evaluating a sample of elite winter barley breeding lines over three years for FHB resistance and DON contamination in the FHB disease nurseries at Aberdeen and Kimberly, Idaho, four unique crosses were made between Aberdeen lines with promising levels of FHB resistance and winter habit lines from other breeding programs. The progeny from these crosses are being advanced through self-pollination to create bi-parental mapping populations. In support of Sub-objective 2B, we now have six oat populations incorporating potentially new sources of resistance to oat crown rust disease ready for gene mapping (resistant parents CIav 2272, PI 140903, PI 237090, PI 287296, PI 137599, PI 194201). Genotyping, resistance scoring and selection of lines for further breeding will be performed on a total of six adult plant resistance and three seedling resistance populations. As an enhancement of our work on oat crown rust resistance, we mapped the position of the Pc54 gene that has been used in oat variety development. Pc54 was found to be on chromosome 7D, in a region rich with seedling resistance genes and quantitative trail loci influencing disease response. The donor line of Pc54 also exhibited adult plant resistance to powdery mildew disease, so we mapped this as well. We found powdery mildew resistance to be conferred by a previously unmapped quantitative trait locus (QTL), QPm.18 on chromosome 1A, which may be useful to breeders in areas where this disease causes damage. The work on barley Ds transposon tagged lines developed in support of Sub-objective 3A has concluded. Ac/Ds (Activator/Dissociation) is a naturally occurring transposable element system first recognized in the maize genome. In a transformation system, the short Ds elements within the genome can be used to guide vectors containing the Ac element to achieve a single copy transgene at a specific genomic location. Use of this system in barley requires barley founder lines carrying Ds elements at known locations. Information on the 91 lines developed with Ds insertions at known genomic locations will be shared with the research community and the lines made available upon request. Towards Sub-objective 3B, barley has been transformed to express a fragment of a fungal gene to test the potential for this system to reduce toxin production in infected plants. Fifteen barley lines putatively transformed to express an inverted repeat of a portion of the Fusarium Tri6 gene were evaluated for proof of a transformation event and for the number of copies inserted. Five lines have been identified that are fixed for a single copy of the Tri6 insert. If expressed as expected, the double-stranded RNA produced may interfere with Fusarium’s ability to produce DON toxin on infected plants. Also, in support of Sub-objective 3B, a transformation vector containing the sequence of the FHB resistance gene Fhb7 from a wild wheat relative was designed. Transformation of barley to express this gene has begun. Barley carrying this trans-gene will be used to determine if this form of resistance can be useful in barley.

Accomplishments

Review Publications
Sallam, A.H., Smith, K.P., Hu, G., Sherman, J., Baenziger, P.S., Wiersma, J., Duley, C., Stockinger, E., Sorrels, M.E., Szinyei, T., Loskutov, I.G., Kovaleva, O.N., Eberly, J., Steffenson, B.J. 2021. Cold conditioned: Discovery of novel alleles for low-temperature tolerance in the vavilov barley collection. Frontiers in Plant Science. 12. Article 800284. https://doi.org/10.3389/fpls.2021.800284.
Esvelt Klos, K.L., Yimer, B.A., Howarth, C., McMullen, M., Sorrells, M.E., Tinker, N.A., Yan, W., Beattie, A.D. 2021. The genetic architecture of milling quality in spring oat lines of the collaborative oat research enterprise. Foods. 10(10). Article 2479. https://doi.org/10.3390/foods10102479.
Gao, D., Nascimento, E., Leal-Bertioli, S., Abernathy, B., Jackson, S., Araujo, A., Bertioli, D. 2022. TAR30, a homolog of the canonical plant TTTAGGG telomeric repeat, is enriched in the proximal chromosome regions of peanut (Arachis hypogaea L.). Chromosome Research. 30(1):77–90. https://doi.org/10.1007/s10577-022-09684-7.
Zimmer, C.M., McNish, I.G., Esvelt Klos, K.L., Eickholt, D.P., Arruda, K.M., Pacheco, M.T., Smith, K.P., Federizzi, L.C. 2021. Genome-wide association mapping for kernel shape and its association with beta-glucan content in oats. Crop Science. 61(6):3986-3999. Article 20605. https://doi.org/10.1002/csc2.20605.