Figure 1. The development of simple sequence repeat (SSR) markers from tall fescue ESTs.



Figure 2. Amplification of tall fescue EST-SSR (NFFA155) in 12 species covering 8 genera, 4 tribes, and 2 sub-family of the grass family Poaceae.

Figure 3. Parental linkage groups for HD-8 (HD28-56 map) and R-7(R43-64 map) along with the integrated group 2-C genetic linkage map of tall fescue.



Figure 4. Genotypes with mean scores 10% above (A) or below (B) the over all means (1,000 genotypes) for osmotic potential, relative water and chlorophyll content and their cross links have been summarized.



Figure 5. SNPs appeared as a major source of sequence variation among accessions of Canada and Virginia wildrye species from their progenitor barley (Morex and Steptoe).

Molecular markers are powerful tools in modern agriculture. They have been used for genome and comparative mapping, phylogeny and population genetics, parental selection and species identification, association studies and QTL analysis. Marker-assisted selection can enhance the speed and effectiveness of plant breeding. The goal of my project is to develop and use molecular markers for genetic improvement of forage grasses and small grain species.

The PCR-based markers have become the marker class of choice. My focus is on co-dominant simple sequence repeat (SSR) and dominant amplified fragment length polymorphism (AFLP) markers. In collaboration with the Plant Biology Division of the Foundation, ~44,000 tall fescue (Festuca arundinacea Schreb). ESTs have been generated and published in public databases. We developed 780 SSR primer pairs from these ESTs. We also developed 511 SSRs from the (GA/CT)n enriched genomic libraries.

To enrich our SSR stock, we also collected conserved grass EST-SSRs from Cornell University, Ithaca, NY and Festuca x Lolium hybrid genomic SSRs from INRA, France, and analyzed their applicability across different forage, turf, and cereal grass species. Agarose and polyacrylamide gel electrophoresis and high throughput capillary system (ABI3730) are routinely used for fragment analysis. Tall fescue EST-SSRs were found to be a good resource for forage grasses with a high rate of transferability across different grass species. A set of SSR loci for different grass species have been identified. These markers were mapped in ryegrass and bentgrass in addition to tall fescue. Comparative genomics has become an important strategy for extending genetic information from model species to more complicated species. We are utilizing the vast information generated in several cereal species for the genetic improvement of forage grasses.

Tall fescue is a major cool-season forage grass in the temperate region of the world. We developed the first PCR-based genetic linkage map of tall fescue using SSRs and AFLPs. The integrated map covers 1737 cM on 17 linkage groups with an average marker density of 1. 9 cM/marker. The maps are being used for QTL analysis of important forage traits.

Drought has significant effect on forage production especially for cool-season perennial forage grasses. We have initiated a project to evaluate protocols for rapid screening of tall fescue populations for tolerance to drought stress. A total of 1,000 genotypes were screened and the most tolerant and susceptible were selected. Greenhouse and field experiments were conducted with the best and worst 25 genotypes. The most contrasting genotypes are being used for creating a mapping population. This population will be used for QTL analysis of important drought-tolerance traits and finding marker(s) associated with discovered QTLs. Contrasting genotypes from both tails are being used for candidate-gene analysis. Database and literature are searched for stress tolerant genes. Gene sequences are blasted against tall fescue unique gene sequences compiled by the Institute for Genomic Research (TIGR). Primers are designed and screened for identifying genes associated with tolerance/resistance classes.

Phylogeny, genetic diversity, and geographical distribution of forage grass species are very important for initiating effective breeding programs. DNA fingerprinting is a tool for precise germplasm identification and a quantitative estimation of genetic diversity. In my program, we used highly informative SSRs to construct an Identification Matrix that allowed the discrimination of the studied accessions/cultivars. We studied the sequence polymorphism within and among different grass species and verified the potential of Single nucleotide polymorphisms (SNPs) for large-scale genotyping.

Ongoing projects:
  • Development of a microsatellite map of tall fescue and comparative mapping with other Poaceae species.
  • Mapping QTLs for important forage traits in tall fescue.
  • Deciphering drought tolerance in tall fescue.
  • Summer dormancy and persistence in tall fescue.
  • Genetic diversity within and among tall fescue populations.
  • Switchgrass improvement (Breeding, developing genomic tools).
  • Development of small grain cultivars for early fall-winter forage.