BARLEY BREEDING AND GENETICS

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: COMPLETE
• Funding Source: HATCH
• Reporting Frequency: Annual
• Accession No.: 1012616
• Project Start Date: Jul 1, 2017
• Project End Date: Jun 30, 2020
• Program Code: [(N/A)]- (N/A)

Recipient Organization
MONTANA STATE UNIVERSITY
(N/A)
BOZEMAN,MT 59717

Performing Department
Plant Sciences and Plant Pathology

Non Technical Summary
The goal of this proposal is to develop improved barley for Montana farmers. New varieties should have higher yield potential, quality stability, disease and pest resistance. Varieties should be useful to end-users, including maltsters, brewers, specialty food companies, and the feed or aquaculture industry. The methods for achieving improved varieties rely upon traditional plant breeding practices of crossing and selection, with field selection augmented by the use of molecular markers. Selections will also include extensive quality testing and collaboration with end-users to identify preferred varieties. Research into the genetic control of important barley traits will be applied to ensure continued barley improvement. The broader impacts of the work are a larger food supply for the world, and an improved ability of Montana farmers to compete in a global marketplace.

Animal Health Component

60%

Research Effort Categories

Basic

40%

Applied

60%

Developmental

(N/A)

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
201	1550	1081	75%
202	1550	1080	25%

Knowledge Area
202 - Plant Genetic Resources; 201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1550 - Barley;

Field Of Science
1081 - Breeding; 1080 - Genetics;

Keywords

barley

malt

forage

genetics

insect resistance

molecular genetics

genetic diversity

Goals / Objectives
The primary goal of the research is to develop superior barley varieties for Montana farmers for all end uses of malt, feed, forage and human foood. An additional goal is to contribute to the literature regarding barley breeding and genetics. Specific goals for this period include: 1) Fully establish the BarleyBreeding pipeline for Montana, 2) Empower selections through the creation of the Barley quality lab 3) Genetically dissect important barley traits, including quality, abiotic and biotic stress resistanceby making marker trait associations, 4) Explore the impact of management decisions on soil health and barley quality.

Project Methods
Breeding pipeline: The barley breeding process can be considered to consist of three main parts 1) making crosses between parents that are hoped to provide new combinations of genes in the progeny, 2) inbreeding the progeny of those crosses approaching homozygosity, and 3) selecting the best of those progeny for varietal release. Breeders can cross elite parents with positive characteristics hoping new combinations will be superior or can cross an elite by a line that has a unique and valuable characteristic. In the latter cross, fewer progeny maybe superior if the parent with unique traits is not well adapted to Montana. New crosses are made every winter in the greenhouse using a variety of parental lines. F1 seed harvested from the crosses are planted in the green house in the summer, and F2 progeny from these plants are inbred for two generations in the greenhouse during the fall and winter by single seed descent. This allows the plants to become homozygous for most genes, and genetic fixation of the lines for further testing. F4 seed from single plants grown in the greenhouse are planted in the field, and single F4 plants are selected from superior rows. Seed from these plants is grown the following summer (or the following winter) in a fully-seeded F5 row, and the superior types are selected. F6 seed from these lines is tested in an initial yield trial in Bozeman. The best lines from this trial are tested at seven environments around Montana, and the best lines from this trial are tested over at least two years in eleven environments. Lines that perform well over the years of statewide testing are candidates for release as commercial varieties. The total time investment from cross to evaluation of lines for potential release is approximately eight years. However, since new crosses are made every year, new materials are evaluated for potential release each year.With the help of various collaborators especially those at Montana Experiment Station, summer of 2015 field trials were planted and included 49 advanced lines at 11 locations, 64 advanced lines at 7 locations, 16 hull-less lines at 11 locations, 16 forage lines at 2 locations, drill strips for AMBA, the Western Regional Nursery, a genomic selection training population of 200 lines for malt, and a Nested Association Mapping Panel of almost 8,000 lines grown in one location (Bozeman, MT). In 2016 similar field trials were planted except the 8,000 line NAM panel was replaced with four graduate student projectsTable 1. Core nurseries conducted each year for the barley breeding program. For locations other than Bozeman, the work is accomplished by the Research Center faculty and staff.NurseryNumber of LinesLocationNotesCrossing Block50-75 parentsBozeman - Plant Growth CenterParents include superior varieties from MSU and other regional programs as well as diverse germplasm from around the worldF1150Bozeman - Plant Growth CenterFirst generation following crossingF2 and F312000Bozeman - Plant Growth CenterInbred lines are developed without selection via single seed descentF412000Bozeman - Post FarmIndividual plants selected for height, grain protein, kernel hardness and plant typeF52500Bozeman - Post FarmRows selected for agronomic appearance, hardness and grain proteinF6 Yield Trial400-600Bozeman - Post FarmReplicated nurseries selected for yield and qualityF7 - Preliminary Yield Trial81Bozeman, Havre, Sidney, MoccasinReplicated yield trials with full malt tests or other end-use quality testsF8-F10 Advanced Yield Trial64Bozeman, Havre, Sidney, Moccasin, Huntley, Creston, ConradReplicated yield trials with full malt or other end-use quality testsWinter nursery300BozemanHead rows scored for winter survivalSeed Increase/Variety Purification2-4 elite linesBozeman - Post FarmPure seed grown for distribution next yearWinter nursery1,000Yuma AZAdvance lines of particular interest to hasten release will be grown in a winter nursery in Yuma AZImproving selections: Selection for agronomic improvement involves growing the lines in multiple environments as described above. In the past quality testing was not instituted until late generations often only testing one to a few environments. It is our goal to get quality data in as early generation and as many environments as possible. The creation of the MSU Barley Quality lab will make this goal a reality. By summer of 2017 we will be able to run all American Society of Brewing Chemists (ASBC) recommended tests for barley and malt quality. The malt quality flow chart below indicates the malt quality analysis work flow, the equipment that has been purchased and funding sources. To empower earlier selections a research goal is to identify quality tests that can be deployed early in the breeding process e.g. NIR to predict malt and forage quality, sedimentation tests and or seed characterization tests to predict malt quality. Another way to empower selections is to use molecular makers that have identified either by other groups or by ourselves. All three graduate student projects should identify new marker trait associations that can be deployed into the breeding program. We are also collaborating on an interstate project to use genomic selection to empower breeding. We are collaborating with researchers from NDSU and University of Idaho who are screening our lines for resistance to fusarium head blight and spot form of net blotch.Genetic Dissection of traits: Currently three student projects involve making marker trait associations as well as provide information about the genetic regulation of important traits. 1) A Nested Association Mapping populations that has been genotyped is being used to dissect the relationship between seed size and shape, head morphology, germination and malt quality. 2) An Association Mapping panel consisting of 300 land races that has been genotyped is being screened for forage quality. And 3) An Association Mapping panel is being screened for resistance to root lesion nematode. In all cases positive traits will be integrated into the breeding program using marker assisted selection.Exploring management: In order to better inform growers, two graduate student projects pertain to important management decisions. 1) Four crop rotations (Continuous barley, barley fallow, barley/pea for grain, barley/pea for green manure) in till and no-till are being investigated for their impact on nematode community structure with the goal of using management to control plant parasitic nematodes in collaboration with Pat Carr and Shabeg Briar. 2) The impact of fertility and water on near isogenic lines for low or high protein is being determined to empower grower production of high quality malt in collaboration with Andreas Fischer.New populations: We are in the process of creating new populations for genetic dissection of other traits. We are particularly interested in the relationship between low protein and extended grain-fill. We have crossed lines that have low protein due to increased starch deposition with lines that have an extended time between heading date and maturity. Other studies indicate these traits could not only improve yield and malt quality but might also be involved in drought tolerance. We are also creating populations that vary for important quality traits, including beta glucans, free amino nitrogen hoping to gain more understanding about the genetic control of these important traits that we might apply to the breeding program. An advantage of breeding through single seed descent is that mapping populations can be a product of the breeding process. Therefore, populations for genetic dissection can be created in just a couple of years for traits that are important to the breeding program.?

Progress 07/01/17 to 06/30/20

Outputs
Target Audience:The audience for the variety development research is Montana farmers, and barley end?users from around the world. The audience for the genetics research is scientists working on barley improvement. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?We are training 3 graduate students and have 6 undergraduates working on the project. How have the results been disseminated to communities of interest?We have done face to face seminars, webnars and written reports. What do you plan to do during the next reporting period to accomplish the goals?Breeding pipeline: The barley breeding process can be considered to consist of three main parts 1) making crosses between parents to provide new combinations of genes in the progeny, 2) inbreeding the progeny of those crosses approaching homozygosity, and 3) selecting the best of those progeny for varietal release. Breeders can cross elite parents with positive characteristics hoping new combinations will be superior or can cross an elite by a line that has a unique and valuable characteristic. In the latter cross, fewer progeny maybe superior if the parent with unique traits is not well adapted to Montana. New crosses are made every fall in the greenhouse using a variety of parental lines. F1 seed harvested from the crosses are planted in the green house in the spring, and F2 progeny from these plants are inbred for two generations in the greenhouse during the summer and fall by single seed descent. This allows the plants to become homozygous for most genes, and genetic fixation of the lines for further testing. F4 seed from single plants grown in the greenhouse are planted in the field, and single F4 plants are selected from superior rows. Seed from these plants is grown the following summer (or the following winter) in a fully?seeded F5 row, and the superior types are selected. F6 seed from these lines is tested in an initial yield trial in Bozeman. The best lines from this trial are tested at seven environments around Montana, and the best lines from this trial are tested over at least two years in eleven environments. Lines that perform well over the years of statewide testing are candidates for release as commercial varieties. The total time investment from cross to evaluation of lines for potential release is approximately eight years. However, since new crosses are made every year, new materials are evaluated for potential release each year. The winter program has a similar scheme. However, some winter lines require 6-8 weeks cold treatment for flowering (vernalization requirement). In that case, the breeding process is slower. The winter program was initiated in 2017 with gathering of germplasm and first crosses made. Those crosses were tested for cold tolerance in 2018 with some survival. We are also testing winter germplasm from around the world to identify good parents for the program. Improving selections: Selection for agronomic improvement involves growing the lines in multiple environments as described above. In the past, quality testing was not instituted until late generations often only testing one to a few environments. It is our goal to get quality data in as early generation and as many environments as possible through the MSU Barley Quality lab. Malt quality analysis follows a set of protocols recommended by the American Society of Brewing Chemists (ASBC). The malt quality flow chart (Fig 9) indicates the malt quality analysis work flow, the necessary equipment and funding sources. Pico?malt analysis at F5, is predictive of malt quality at later generations ensuring that high?malt quality lines are not eliminated from the breeding pipeline. We are also utilizing high?throughput phenotyping to make forage barley selections and to predict lines with better root systems. Genetic Dissection of traits: Several graduate student projects involve making marker trait associations as well as provide information about the genetic regulation of important traits. 1) An Association Mapping panel consisting of 300 land races that has been genotyped and phenotyped for forage yield and quality (Hoogland et al., submitted). 2) An association mapping panel of 180 "heirloom" malt lines that have been genotyped is being phenotyped for malt quality and flavor related metabolomics. 3) A biparental population is being genotyped and phenotyped for speed of hydration, dormancy and other malt related traits. And 4) A bi? parental population, varying for stay?green, is being genotyped and screened for root archtecture. In all cases, positive traits will be integrated into the breeding program using marker assisted selection. New populations: We are creating populations that vary for important quality traits, including beta glucans, free amino nitrogen hoping to gain more understanding about the genetic control of these important traits that we might apply to the breeding program. An advantage of breeding through single seed descent is that mapping populations can be a product of the breeding process. Therefore, populations for genetic dissection can be created in just a couple of years for traits that are important to the breeding program.

Impacts
What was accomplished under these goals? The primary goal of the research is to develop superior barley varieties for Montana farmers. We released a malt barley variety and moved forward with the creation of food feed and forage varieties. We contributed journal articles and presentations to the literature regarding barley breeding and genetics and are continuing the research and creation of publications on genetic dissection of malt quality, forage quality and root archetecture.

Publications

• Type: Journal Articles Status: Published Year Published: 2020 Citation: Alptekin B., D. Mangel, D. Pauli, T. Blake, J. Lachowiec, T. Hoogland, A. Fischer, and J. Sherman. 2020. Combined effects of a glycine-rich RNA-binding protein and a NAC transcription factor extend grain fill duration and improve malt barley agronomic performance. Theor. Applied Genetics https://doi.org/10.1007 /sOOl 22-020-03701-1
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Achhami, B.B., GVP Reddy, JD Sherman, RKD Peterson, DK Weaver (2020) Effect of precipitation and temperature on Larval Survival of Cephus cinctus (Hymenoptera:Cephidae) in barley cultivars. Journal of Economic Entomology https://academic.oup.com/jee/advance-article/doi/10.1093/jee/toaa097/5840374?guestAccessKey=c000c695-0576-4fc8-b35d-09701e0d46b9
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Vetch J.M., J. G. Walling, J. Sherman, J. M. Martin, M. J. Giroux. (2020) Mutations in the HvMKK3 and HvAlaAT1 genes affect barley pre?harvest sprouting and after?ripened seed dormancy. Crop Science https://doi.org/10.1002/csc2.20178

Progress 10/01/17 to 09/30/18

Outputs
Target Audience:The audience for the variety development research is Montana farmers, and barley end-users from around the world. The audience for the genetics research is scientists working on barley improvement. Three graduate students and six undergraduates were trained. We have provided data to growers, and the craft malt industry. We have provided tours of the malt quality lab to stakeholders. We have connected growers with endusers. We have provided growers and end-users an opportunity to evaluate lines and give us feedback to help guide selections. Changes/Problems:A challenge this year was the late spring and early winter, which hampered production. We lost an environment due to hail. Rain during harvest resulted in pre-harvest sprouting. The wet year caused disease isssues. However, these problems provide opportunities for different selection pressure, empowering the breeding program. What opportunities for training and professional development has the project provided?We hosted the Craft Malt Guild in 2019 and provided a week long malt class to craft maltsters. We also hosted a Brewers Association Class in 2019. We were an invited speaker for American Malting Barley Association, Craft Malt Guild, Brewers Association, and Grain Growers. How have the results been disseminated to communities of interest?Results have been disseminated through peer-reviewed publications, invited talks, stake-holder tours, and field days. What do you plan to do during the next reporting period to accomplish the goals?The primary goal of the research is to develop superior barley varieties for Montana farmers. The milestone for success will be released varieties that are widely grown in Montana, and used by maltsters, brewers, the food industry, and the livestock industry in Montana and throughout the world. Next year we hope to release a forage barley. An additional goal is to contribute to the literature regarding barley breeding and genetics. During the life of this proposal we intend to create publications on genetic dissection of malt quality, forage quality and root architecture; management of low protein lines; and malt process papers.

Impacts
What was accomplished under these goals? 1) Fully establish the BarleyBreeding pipeline for Montana The pipeline if fully flowing with new lines entering each year through crosses and we have released our first malt barley line - Buzz. 2) Empower selections through the creation of the Barley quality lab The MSU malt quality lab provided data more than 1,000 data points to the MSU breeding program for malt selections. The lab is also providing forage quality data and DON analysis. The lab also provided data for student research projects and publications. Finally the lab provides data to growers and end-users. 3) Genetically dissect important barley traits, including quality, abiotic and biotic stress resistanceby making marker trait associations Genetic dissection of malt quality, forage agronomics and quality and root development are in progress. 4) Explore the impact of management decisions on soil health and barley quality. Resulted in a paper about nematode community structure in preparation. Fertility management studies informed the release of Buzz and will result in a publication

Publications

• Type: Journal Articles Status: Published Year Published: 2019 Citation: Turner, H., Elmore, L., Walling, J., Lachowiec, J., Mangel, D., Fischer, A., Sherman, J. D. (2019). The effect of steeping regime on barley malt quality and its impacts on breeding program selection. Journal of the American Society of Brewing Chemists https://doi.org/10.1080/03610470.2019.1629794.
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Neyhart, J. L., Sweeney, D., Sorrells, M., Kapp, C., McFarland, A., Kephart, K., Sherman, J., Stockinger, E. J., Fisk, S., Hayes, P., Daba, S., Mohammadi, M., Hughes, N., Lukens, L., Barrios, P. G., Gutierrez, L., Smith, K. P. (2019). Registration of the S2MET Barley Mapping Population for Multi- Environment Genomewide Selection. Journal of Plant Registrations/Crop Science Society of America, 13(2), 270-280.
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Burkhardt, A., Briar, S., Martin, J., Carr, P., Lachowiec, J. A., Zabinski, C., Roberts, D., Miller, P., Sherman, J. (2019). Perennial crop legacy effects on nematode community structure in semi-arid wheat systems. Applied Soil Ecology 136:93-100

Progress 07/01/17 to 09/30/17

Outputs
Target Audience:The audience for the variety development research is Montana farmers, and barley end-users from around the world. The audience for the genetics research is scientists working on barley improvement. We have provided data to growers, and the craft malt industry. We have provided tours of the malt quality lab to stakeholders. We have connected growers with end-users. We have provided growers and end-users an opportunity to evaluate lines and give us feedback to help guide selections. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?We have provided training to 6 undergraduates in plant breeding and quality analysis. We have provided training to 4 graduate students in agronomic, genetic and plant breeding research. We have provided training to growers and end-users about appropriate barley varieties. We have also trained growers, maltsters and brewers in malt quality analysis so that they can be more successful How have the results been disseminated to communities of interest?Results have been disseminated through oral presentations and field days and meetings. Results have also been disseminated through written reports and published online. The project has been featured in several news articles. What do you plan to do during the next reporting period to accomplish the goals?1)Fully establish the BarleyBreeding pipeline for Montana, The Barley breeding pipeline is fully flowing, but to be successful new lines must be continually entering the pipeline so that after years of development new lines can flow out. So we will make new crosses this year that will enter the pipeline. We also plan to release a variety this year. 2) Empower selections through the creation of the Barley quality lab The MSU Barley quality lab will continue to provide data to the breeding program for selections. It will also provide data to stakeholder to empower them to be successful. We will also provide quality analysis of several populations to empower genetic dissection of malt quality. 3) Genetically dissect important barley traits, including quality, abiotic and biotic stress resistanceby making marker trait associations, Projects to make marker trait associations for head morphology, seed morphology and forage quality will be completed in 2018. A project to genetically dissect the relationship between seed traits and malt quality will be initiated. A project to genetically dissect traits that provide abiotic stress resistance will be initiated. 4) Explore the impact of management decisions on soil health and barley quality. Two management studies were continued. 1) Impact of fertility and water on malt quality of low protein lines field trial was completed this year with three locations. This project will be written up this year and information shared with growers and end-users. 2) The relationship of sulfur and nitrogen on malt quality study was grown in 3 locations. We plan to repeat in 2018.

Impacts
What was accomplished under these goals? 1)Fully establish the BarleyBreeding pipeline for Montana, The Barley breeding pipeline is fully formed with lines in all stages of development for the first time since 2010. 2) Empower selections through the creation of the Barley quality lab The MSU Barley quality lab is fully functional. We have all necessary equipment and two trained staff so that we can run all malt quality analysis as described by ASBC. We have developed and confirmed our protocols with our data matching analysis from other labs. We have begun providing data to the breeding program to empower high quality selections. We have also provided data to stake-holders to help them develop their malt process, and to ensureproduction of high-quality malt. We have also provided data to growers ensuring their grain will produce high-quality malt. 3) Genetically dissect important barley traits, including quality, abiotic and biotic stress resistanceby making marker trait associations, Projects to make marker trait associations for head morphology, seed morphology and forage quality were continued. These projects should be completed early in 2018. 4) Explore the impact of management decisions on soil health and barley quality. Two management studies were continued. 1) Impact of fertility and water on malt quality of low protein lines field trial was completed this year with three locations. This project will be written up this year and information shared with growers and end-users. 2) The relationship of sulfur and nitrogen on malt quality study was grown in 3 locations. We plan to repeat in 2018.

Publications

• Type: Journal Articles Status: Published Year Published: 2017 Citation: Varella, A. C., Weaver, D., Peterson, R., Sherman, J., Hofland, M., Blake, N., Martin, J., Talbert, L. Host plant quantitative trait loci affect specific behavioral sequences in oviposition by a stem-mining insect. 2017. Theoretical and Applied Genetics, 130, 187-197.