The first objective of this project was to Identify and characterize possible dwarfing (Rht) genes in canary seed. Short-statured lines were identified and evaluated over a four year period. The lines were sensitive to the plant hormone Gibberellic acid and thus height was not likely controlled by single gene. Reduced height was associated with reduced grain yield and no increase in Harvest Index. The second objective of this project was to assess the extent of disease pressure in canary seed crops, crop assess genetic variation for disease reaction to leaf mottle, fungicidal disease control and plot size effects on fungicide experiments. Leaf mottle was present in 75% percent of the fields surveyed during the course of this project; however, the severity of the disease in 69% of the fields was trace to slight.  Moderate severity was observed in 6% of fields when environmental conditions were conducive for the disease.  Fusarium spp. were isolated from seed in all years although generally at low levels. The most common species were F. graminearum and F. avenaceum, detected in up to 58% of the crops surveyed, but at generally low levels (3-4% seed infection).  Disease reaction of P. canariensis genotypes challenged with isolates of S. triseti indicated virulence was common among the S. triseti isolates on the majority of the P. canariensis accessions.  Fungicides generally reduced leaf mottle disease and fusarium seed infection. The use of larger experimental plots allowed for a more consistent detection of fungicide effects on grain yield. The main objective of the third activity of this project was to develop DNA based molecular markers for use in marker assisted selection. Genotyping by sequencing (GBS) was used to develop single nucleotide polymorphism (SNP) markers. Methods were optimized to obtain high quality DNA from young leaves. GBS identified a total of 2399 polymorphic SNPs.  Population structure using the SNP markers, revealed two sub groups of canary seed.  The glabrous brown seed and glabrous yellow seed genotypes were grouped in to one subgroup, while the pubescent gene bank accessions separated into another sub group. To assess the utility of the SNP markers, 94 canary seed accessions were evaluated for fat, protein, starch, and amylose content. General and mixed linear model analyses revealed SNP marker trait association with protein, starch and amylose concentrations.