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United States Department of Agriculture

Agricultural Research Service


Location: Small Grains and Potato Germplasm Research

2011 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 Replacing 5366-21000-024-00D 03/08; 7/07

3. Progress Report
Under Sub-objective 1A, significant progress has been made to the application of a technique called ‘transposon tagging’ to gene discovery in barley. In this method a small piece of DNA moves into and abolishes the function of genes and it is a new tool for studying gene function in barley. Using recently-developed high-throughput and simple techniques, we isolated a line with a mutation in an inositol monophosphatase gene, which participates in the formation of phytic acid, an anti-nutrient and source of phosphorus pollution. This is one example of the use of this system; in total, 70 lines with unique transposon insertions have been developed. These lines, combined with insertion lines produced by collaborating colleagues, now comprise an impressive and growing genetic resource for the barley community. Under Sub-objective 1.B, 80,000 oat genetic “mile” markers defined in the genetic world as single nucleotide polymorphisms (SNP) and simple sequence repeats (SSR) have been identified. Over 1,100 of these genetic mile markers have been used to assemble the first complete set of genetic “road” maps for six different oat populations. Using a new strategy develop by the USDA-ARS Aberdeen molecular genetics laboratory, the maps were physically anchored to the appropriate chromosomes. Combined, this work has led to the first complete genetic atlas for cultivated oat which can now be used by oat breeders to expedite the development of new oat varieties. Under sub-objective 2.B, we made efforts to combat barley stripe rust disease by generating plant populations ready for further analysis. These populations will be used to identify locations in the barley responsible for resistance to barley stripe rust disease. We are using both spring habit and winter habit barley in this study. Under Sub-objective 2.C., field evaluations in two Idaho locations over two years have yielded key information on soluble fiber (beta glucan) development in barley grain. This information combined with a new genetic “road” map has enabled the development of genetic “signpost” for genetic regions increasing beta glucan content. This work will provide breeders a specific tool to increase soluble fiber levels in barley. Under sub-objective 2.D., field evaluations in Idaho, Louisiana, and Minnesota over two years have yielded key information on oat crown rust resistance. This information combined with the new genetic “road” map (sub-objective 1. B.) has enabled the development of genetic “signpost” for genetic regions controlling the resistance. This work will provide breeders specific tools to develop new oat varieties with improved disease resistance.

4. Accomplishments
1. New molecular markers developed for oats. Molecular markers will speed up oat breeding. ARS scientists in Aberdeen, ID, used state-of-the-art DNA sequencing technology to generate a large set of highly robust molecular markers called single nucleotide polymorphisms or SNPs. These SNP markers will make it much easier for breeders to develop new oat cultivars with disease resistance and value-added quality traits like increased soluble fiber, antioxidants, and protein. In addition, it will allow better dissection of fatty acid composition allowing development of oat products with improved shelf life and taste. Such innovations are needed to make oat production more profitable in the U.S., since oat is useful to farmers in crop rotations and valuable to consumers due to the health benefits of oat consumption.

2. First complete oat maps. Having good genetic 'road maps' will help scientists improve the oat crop. ARS scientists in Aberdeen, ID, developed the first complete maps, which means the number of 'linkage groups' equals the number of chromosomes, for the two most important oat species. This breakthrough will make it easier to find the genetic locations for important traits benefiting human health, such as fiber and antioxidant content. The new maps will enable scientists to more easily develop new varieties of oat with improved crop yield, milling quality, and disease resistance.

3. Gene discovery in barley using transposon tagging. Creating mutants in critical genes via transposon tagging is a valuable method for understanding the function of genes. ARS scientists in Aberdeen, ID, have introduced the use of simple and efficient PCR-based methods for identifying lines with novel transposon insertions. The efficiency of these methods has increased the speed and decreased the cost associated with producing mutant lines. This development will enable cost-effective development of a large number of additional mutant lines, a prerequisite to efficient use of transponson tagging resources in genetic investigations.

4. Mapping valuable genes in barley. The genetic locations of genes controlling barley soluble fiber, starch, and vitamin E content have been discovered. In addition, the locations of genes controlling height, spike length, and spike angle have been discovered. Using this information, breeders will be able to efficiently develop new barley varieties with value added traits which are agronomically acceptable for growers via molecular breeding practices. Overall, this will allow stakeholders to develop products with added health benefits for the US market.

5. Identification of diversity for Russian wheat aphid (RWA) resistance. Knowledge of the diversity among National Small Grains Collection (NSGC) accessions is necessary to efficiently and completely utilize the collection. To understand the level of diversity among accessions and improvement RWA-resistant breeding lines, an association mapping approach was used. The results showed diversity for several independent loci that conferred resistance, but also showed that multiple accessions had the same loci conferring resistance. Thus, a large (100 accessions) pool of resistance could be subset into a much smaller number of unique resistance sources. This approach demonstrates a method of identifying the fewest number of accessions, and thus reducing the breeding effort, required to maximally utilize variablity in the NSGC.

Review Publications
Verhoeven, E.C., Bonman, J.M., Bregitzer, P.P., Brunick, B., Cooper, B., Corey, A.E., Cuesta-Marcos, A., Filichkina, T., Mundt, C.C., Obert, D.E., Rossnagel, B., Richardson, K.L., Hayes, P.M. 2011. Registration of the BISON genetic stocks in Hordeum vulgare L. Journal of Plant Registrations. 5:135-140.

Oliver, R.E., Lazo, G.R., Lutz, J.D., Rubenfield, M.J., Tinker, N.A., Anderson, J.M., Wisniewski-Morehead, N.H., Adhikary, D., Jellen, E.N., Maughan, P.J., Brown Guedira, G.L., Chao, S., Beattie, A.D., Carson, M.L., Rines, H.W., Obert, D.E., Bonman, J.M., Jackson, E.W. 2011. Model SNP development based on the complex oat genome using high-throughput 454 sequencing technology. Biomed Central (BMC) Genomics. 12:77.

Oliver, R.E., Jellen, E.N., Ladizinsky, G., Korol, A.B., Kilian, A., Beard, L.J., Dumlupinar, Z., Wisniewski Morehead, N.H., Swedin, E., Coon, M.A., Redman, R.R., Maughan, P.I., Obert, D.E., Jackson, E.W. 2011. New Diversity Arrays Technology (DArT) markers for tetraploid oat (Avena magna Murphy et Terrell) provide the first complete oat linkage map and markers linked to domestication genes from hexaploid A. sativa L.. Journal of Theoretical and Applied Genetics. DOI 10.1007/s00122-011-1656-y.

Last Modified: 06/28/2017
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