2010 Annual Report
1a.Objectives (from AD-416)
This project will address in oat, one of our important cereals, the needs for an understanding of the molecular/structural organization of its large complex genome, means to effectively identify and manipulate more durable race non-specific quantitative resistance to its major disease, crown rust, and the development of new biotic and abiotic stress resistance germplasm in elite agronomic backgrounds through the following objectives: Objective 1: Characterize the complex segmental homoeologous structure of allohexaploid cultivated oat through molecular marker analysis of monosomic and nullisomic chromosome-deficient stocks. Objective 2: Identify and map key genes (quantitative trait loci or QTLs) for important traits, particularly race non-specific crown rust resistance, by developing and phenotyping mapping populations and employing new molecular markers (EST-SSR and DArT). Objective 3: Develop cultivated oat germplasm with introduced biotic and abiotic stress resistance and high-value traits through introgressing crown rust resistance from wild oat species, exploring heat stress and disease resistance from genes introduced by crosses with corn, and evaluating high-value trait sources through coordination of regional spring oat nurseries.
1b.Approach (from AD-416)
Monosomic (single chromosome deficient) oat plants needed to complete a full series of 21 lines each deficient for a different oat chromosome will be identified cytologically and with molecular markers among derivatives of oat x corn crosses. Molecular marker linkage groups will be assigned to chromosome using these monosomic lines to develop a comprehensive genomic map for cultivated oat. The QTL identification of race non-specific (partial) crown rust in oat germplasm MN841801-1 will be enhanced with additional field and molecular marker data including the use of new DArT markers, and the effectiveness of marker-assisted selection will be tested for efficiency and effectiveness in transfer of the resistance QTLs into other oat backgrounds. New oat crown rust resistance genes will be introgressed into cultivated oat from wild oat species. Previously produced oat lines containing segments of corn chromosomes will be further developed and evaluated for possible enhanced heat tolerance and disease resistance. Coordination of cooperative regional spring oat performance nurseries will be used to identify optimal current oat genotypes for use as parents in crosses for introgressions and germplasm enhancement.
An ARS postdoctoral research associate (PD) was hired in December 2009 to pursue research on oat that was not already being completed by collaborators of the project. The focus of the PD's research is to investigate how the genome sequence of the model cool season grass Brachypodium distachyon (Brachypodium) can be employed to advance genome analysis of oat, including assessing syntenic relationships between Brachypodium and oat, employing Brachypodium genome resources to examine gene expression in oat, and linking genetics and metabolomics in oat seeds. Three projects have been pursued in the 7 months that the PD has been with the Unit. First, using computational methods, syntenic relationships between Brachypodium, diploid oat, and hexaploid oat were assessed by comparison of the Brachypodium genome sequence to linkage maps of oat. Second, a pilot study was conducted to determine the utility of a Brachypodium microarray in monitoring gene expression in oat. RNA from seedling tissue of Brachypodium and oat was isolated and used for hybridizations to Affymetrix whole genome Brachypodium arrays, which contain all Brachypodium genes. The analysis of the data obtained is ongoing. In preparation for microarray studies of oat-crown rust interactions, a large greenhouse increase of two oat near-isogenic lines differing by the presence of a particular crown rust resistance gene was completed. Lastly, using oat linkage map data, microcolinearity between oat and Brachypodium was examined in particular areas of the oat linkage map that harbor important traits. Results will be used for future development of more molecular markers for oat and for oat gene cloning using Brachypodium as a surrogate.
Comparing chromosome organization of oat and Brachypodium. Oat is an important cereal crop, but it has a large polyploid genome that poses an obstacle for many types of modern genome analysis. Brachypodium, a small weedy relative of oat, has a compact genome and its gene content and organization are similar to other small grain crops such as wheat and barley. We conducted comparative analyses of oat linkage maps and the Brachypodium genome sequence to identify homoeologous chromosomes of oat and to identify oat linkage groups that may represent different regions of the same chromosome. This research unambiguously identified several homoeologous oat linkage groups and tagged particular oat linkage groups that may be co-localized on the same oat chromosome. These results will aid oat researchers in the development of complete oat linkage maps and will lead to more efficient development of improved oat cultivars.
Tinker, N.A., Kilian, A., Rines, H.W., Bjornstad, A., Howarth, C.J., Jannink, J., Anderson, J.M., Rossnagel, B.G., Wight, C.P., Stuthman, D.D., Sorrells, M.E., Scoles, G.J., Eckstein, P.E., Ohm, H.W., Jackson, E.W., Tuvesson, S., Kolb, F.L., Molnar, S.J., Olsson, O., Carson, M.L., Ceplitis, A., Bonman, J.M., Federizzi, L., Langdon, T. 2009. New DArT markers for oat provide enhanced map coverage and global germplasm characterization. Biomed Central (BMC) Genomics. 10(39):1471-2164.
Rines, H.W., Phillips, R.L., Kynast, R.G., Okagaki, R.J., Galatowitsch, M.W., Huettl, P.A., Stec, A.O., Jacobs, M.S., Suresh, J., Porter, H.L., Walch, M.D., Cabral, C.B. 2009. Addition of Individual Chromosomes of Maize Inbreds B73 and Mo17 to Oat Cultivars Starter and Sun II: Maize Chromosome Retention, Transmission, and Plant Phenotype. Theoretical and Applied Genetics. 119(7):1255-1264.
Acevedo, M., Jackson, E.W., Chong, J., Rines, H.W., Harrison, S., Bonman, J.M. 2010. Identification and Validation of Quantitative Trait Loci for Partial Resistance to Crown Rust in Oat. Phytopathology. 100(5):511-521.