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United States Department of Agriculture

Agricultural Research Service

Research Project: SMALL GRAINS GENETICS AND GERMPLASM ENHANCEMENT
2010 Annual Report


1a.Objectives (from AD-416)
Objective 1: Develop, evaluate, and apply molecular tools, including molecular genotyping and transposon tagging, to small grains genetics and germplasm enhancement research. Sub-objective 1.A. Identify and characterize genes involved in barley seed phytate content using Ds-generated (low phytate) LP insertion mutants. Sub-objective 1.B. Improve the Ogle1040/TAM O-301 (OT) genetic linkage map by.
1)developing and mapping polymerase chain reaction (PCR) based markers and.
2)physically anchoring linkage groups to chromosomes using aneuploid oat stocks. Objective 2: Identify, map, and develop molecular markers for disease resistance and quality genes, and use these resources to move favorable alleles from National Small Grains Collection (NSGC) accessions and other sources into adapted plant types. Sub-objective 2.A. Identify wheat and barley landraces from the NSGC likely to possess unexploited genes for resistance to new virulent races of the stem rust pathogen. Sub-objective 2.B. Introgress quantitative and qualitative resistance to barley stripe rust into adapted germplasm via marker assisted selection (MAS). Sub-objective 2.C. Identify, map, and develop molecular markers for quantitative trait loci (QTL) in barley cultivars Azhul and/or Falcon conditioning high ß-glucan (BG) levels. Sub-objective 2.D. Map and introgress resistance to crown rust of oat into high-yielding Aberdeen germplasm via MAS. Objective 3: Develop improved barley and oat cultivars meeting the needs of conventional and specialty markets for both dryland and irrigated production systems, including barley cultivars and/or germplasm with resistance to new races of the stem rust pathogen (Ug99). Sub-objective 3.A. Develop improved spring and winter malt barley and specialty cultivars. Sub-objective 3.B. Develop oat cultivars combining the enhanced levels of disease resistance from southern U.S. with the superior yield and quality of ARS-Aberdeen lines.

The objectives in our project are complementary and interconnected. Proven methods and existing germplasm will be used to develop commercial cultivars for growers, and innovative new resources will be developed to facilitate genetic investigations and to enhance the efficiency of future germplasm and cultivar development. These resources will be made available to other researchers and to the agribusiness community.


1b.Approach (from AD-416)
This project seeks to generate improved small grains germplasm, including barley and oat cultivars, and to develop and use genomic tools that will facilitate future germplasm improvements. Most of the work will focus on barley and oat improvement. However, wheat stem rust screening of landrace accessions from the National Small Grains Collection (NSGC) will be included as part of a coordinated ARS effort to mitigate the threat of emerging races. The germplasm improvement work for barley will focus on issues of importance in the intermountain west, such as improving winter malt barleys and developing specialty types to expand market opportunities for producers. The oat work has a more national focus with emphasis on disease resistance. The research aimed at improving methodologies and tools for genomic research and germplasm enhancement will produce new resources for researchers, such as Ds-generated mutant barley stocks, more PCR-based oat molecular, and a more complete oat genetic map. This project also seeks to integrate the work of several scientists to achieve greater efficiency and productivity by sharing facilities, materials, and ideas among the project team members. Replacing 5366-21000-016-00D. 7/2003 FY06 Program Increase $22,275 12/19/05 Replacing 5366-21000-024-00D 03/08; FY10 Program Increase $82,500 1/25/10


3.Progress Report
Under subobjective 1A, we made significant progress by identifying over 80 experimental barley lines showing increased inorganic phosphorus in the seed in a transposon tagging population. This change to the seed may be associated with the reduction of seed phytate, a phosphorus storage compound that reduces seed nutrition and contributes to phosphorus release from farms into the environment. Although previous work with chemically-induced mutants has shown that improvements to seed phosphorus are possible, the responsible genes have not been identified and the transposon tagging population may aid in their discovery. Progress was made on subobjective 2D by combining this mapping information with disease resistance data to find associations between the genetic “mile” markers on the map and genes controlling disease resistance. Currently, the associations are being used to develop genetic “road signs” for use as a selection tool for marker-assisted breeding. By comparing the oat and barley sequences, almost the entire gene controlling seed beta glucan synthesis was discovered. Based on the gene sequences between cultivars with high and low beta glucan, genetic differences have been found which could control oat beta glucan levels. Progress under subobjective 2A was made by screening more than 1000 spring landrace wheats from the National Small Grains Collection against new races of the stem rust pathogen in the field in Kenya. A number of resistant accessions were identified and are being retested to verify their resistance. Progress was made under subobjective 2B by advancing a winter and two spring barley populations segregating for high temperature adult plant resistance to barley strip rust (BSR). Two populations have also been advanced that are segregating for BSR derived from a related barley species. A new map was constructed using inbred sibling lines from a cross of BCD47, a barley line with partial resistance to BSR, and Baronesse. Genetic “map” locations controlling BSR in the population were identified. Under subobjective 2C, a new molecular “road” map was developed using inbred sibling lines from a cross of Azhul, a barely line with high soluble fiber (beta glucan), and Falcon, a cultivar with low beta glucan. The siblings were grown in seven locations and seed from each line were tested for the percentage of beta glucan in the grain. This data was combined with the map data and genetic “map” locations controlling beta glucan were identified. Progress was made under subobjective 3A by developing and releasing two spring cultivars with high levels of soluble fiber (beta glucan) in the grain. The cultivars have a significantly higher percentage of beta glucan in the grain than currently available varieties. Under subojective 3B oat lines have been developed with a specific gene (Pc58a) and quantitative trait loci that make oat plants resistant to crown rust using marker-assisted breeding. The oat lines have been advanced and resistance has been confirmed.


4.Accomplishments
1. Expressed tagged sequence information development in cultivated oat. Very little genetic information exists for cultivated oat. Recently, ARS researchers at Aberdeen, ID and Albany, CA drastically increased the number of oat gene sequence fragments from 30,000 to 650,000. This information will be used to develop genetic maps and predictive assays for key traits such as soluble fiber and disease resistance. Ultimately, this will expedite the development of new oat cultivars with beneficial properties.

2. Gene discovery in barley using transposon tagging. Creating mutants in critical genes is a valuable method for understanding the role of such genes, as the mutations result in changes to the traits the genes control. Transposon tagging, where small DNA sequences (transposons) can move into (and thus mutate) genes is uniquely useful because it is the only mutagenic process that allows rapid identification of the precise sequence of the mutated gene and the product of that gene. This system has been under development for barley and its utility for creating mutations in key genes has now been demonstrated by ARS researchers in Aberdeen, ID. The first mutant to be described in detail is of a gene that is critical to the development of the barley flower, an important step in the process of creating barley seeds. This discovery will help lead to a greater understanding of one of the primary goals of agriculture: creating grain for food and feed.

3. Single nucleotide polymorphism marker development in cultivated oat. Very few genetic markers exist for cultivated oat. ARS researchers at Aberdeen, ID; Albany, CA; Fargo, ND; and Raleigh, NC recently developed the first oat-based single nucleotide polymorphism markers for molecular breeding strategies. To date, over 700 new markers have been developed. This resource will allow oat breeders and geneticist to study and expedite breeding for important traits like disease resistance and various fibers for the first time.

4. Microsatellite development in cultivated oat for genetic breeding. Very few genetic markers exist for cultivated oat. ARS researchers at Aberdeen, ID recently developed oat-based microsatellite markers. To date, over 200 new markers have been developed. This resource will allow oat breeders and geneticist to study and expedite breeding for important traits like disease resistance and various fibers for the first time.

5. Release of unique barley germplasm with highly digestible phosphorus. Phosphorus pollution of water causes excessive algal growth and oxygen depletion, and ultimately can be traced in large part to undigested phosphorus in animal manure. This is because single stomach animals such as chicken and pigs cannot digest phytate, a chemical form of stored phosphorus in seeds. Mutation breeding created alternative genes that result in more of the stored phosphorus being digestible, leading to lower levels of phosphorus in manure. These genes were initially contained in experimental lines with poor grain yields, but have been introduced into improved, higher yielding lines by ARS researchers in Aberdeen, ID. Four new germplasm lines, representing important commercial categories of barley, were released and deposited into the National Small Grains Germplasm Collection. The lines will be useful resources for plant breeders seeking to develop high yielding, commercially competitive barley varieties that contribute to long-term sustainability of agricultural systems.

6. Development of new genetic linkage maps for oat and barley improvement. Few genetic linkage maps for studying key traits in oat and barley exist. ARS researchers at Aberdeen, ID and St. Paul, MN recently developed two oat-based maps and three barley-based maps. This information will be used to make associations between the genetic markers on the linkage maps and genes controlling partial resistance to crown rust of oat, stripe rust of barley, and oat and barley grain beta glucan levels.

7. Improvement of disease assessment in oat. One limitation to breeding for disease resistance in cereal crops is the accuracy and precision of disease measurements. Better disease measurement will aid genetic mapping disease resistance genes. ARS researchers at Aberdeen, ID developed an improved method of assessing crown rust in oat by measuring pathogen DNA content relative to the DNA content in host tissues. The new method will be used in studies to map and deploy crown rust disease resistance in oat.


Review Publications
Gurung, S., Bonman, J.M., Ali, S., Patel, J., Myrfield, M., Mergoum, M., Singh, P.K., Adhikari, T.B. 2009. New and Diverse Sources of Multiple Disease Resistnace in Wheat. Crop Sci. 49:1655-1666

Acevedo, M. , Jackson, E. W. , Sturbaum, A. , Ohm, H. W. and Bonman, J. M.(2010) 'An improved method to quantify Puccinia coronata f. sp. avenae DNA in the host Avena sativa', Canadian Journal of Plant Pathology, 32(2):215-224.

Tinker, N.A., Kilian, A., Wright, C.P., Heller-Uszynska, K., Wenzl, P., Rines, H.W., Bjornstad, A., Howarth, C., Jannink, J., Anderson, J.M., Rossnagle, B.G., Stuthman, D.D., Sorrells, M.E., Jackson, E.W., Tuvesson, S., Kolb, F.L., Olsson, O., Federizzi, L.C., Carson, M.L., Ohm, H.W., Molnar, S.J., Scoles, G.J., Eckstein, P.E., Bonman, J.M., Ceplitis, A., Langdon, T. 2009. New DArT markers for oat provide enhanced map coverage and global germplasm characterization. BMC Medical Genetics. 10:39.

Oliver, R.E., Obert, D.E., Hu, G., Bonman, J.M., O'Leary-Jepsen, E., Jackson, E.W. 2010. Development of oat-based markers from barley and wheat microsatellites. Genome. 53(6): 458–471.

Mornhinweg, D.W., Bregitzer, P.P., Porter, D.R., Peairs, F.B., Baltensperger, D.D., Hein, G.L., Randolph, T.A., Koch, M., Walker, T. 2009. Registration of 'Sidney' spring feed barley resistant to Russian wheat aphid. Journal of Plant Registrations. 3(3):214-218.

Tyagi, N., Dahleen, L.S., Bregitzer, P.P. 2010. Candidate Genes Within Tissue Culture Regeneration QTL Revisited with a Linkage Map Based on Transcript Derived Markers. Crop Science. 50:1697-1707.

Last Modified: 11/27/2014
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