2011 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 associate is conducting research on oat detailed in this report. The focus of the research has been to investigate the structural relationship between oat chromosomes and those of the model grass Brachypodium. Detailed, computationally based alignments of oat genetic linkage maps and the Brachypodium genome sequence revealed that large blocks of oat genes are organized in a similar manner in Brachypodium but that compared to Brachypodium, oat chromosomes have undergone significant structural rearrangements. Enough information was gleaned to allow the development of a model by which chromosomes evolved from an ancestor grass more than 60 million years ago. Comparing locations of genetically mapped genes influencing how much vitamin E accumulates in oat to the Brachypodium genome sequence identified a number of instances where the oat gene locations were coincident with Brachypodium genes encoding steps in the synthesis of vitamin E. Lastly, a study was initiated to develop a gene expression atlas of developing oat seeds. Oat plants were grown in replicate in a growth chamber until seeds began to form, and then developing seeds at four different time points were harvested and RNA was extracted. This RNA is being used for experiments to identify what oat genes are turned on or off at the different seed developmental time points. To tie this research in with vitamin E accumulation, a collaboration was established with an ARS colleague at Madison, Wisconsin, to characterize what vitamin E compounds are accumulating at each developmental stage of oat development; this will allow us to interrelate gene expression data with patterns of vitamin E accumulation and provide knowledge that can be used to increase the amount and type of vitamin E that accumulates in oat seeds.
Evolution of oat chromosomes from a grass ancestor revealed. Oat has a large and complex genome, which hinders genetic studies. ARS researchers in St. Paul, Minnesota, therefore aligned the oat genome to the genomes of many other domesticated grass crop species, as well as the hypothetical ancestor of all grass crops. Knowledge of the relationships between the order of genes on chromosomes in well-characterized grass crops and oat will be powerful for gene discovery in the latter crop. The ability to identify genes controlling important nutritional and agronomic traits in oat opens the door for development of oat cultivars with enhanced performance and value.
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.