Comparisons of RFLP and PCR-based markers to detect polymorphism between wheat cultivars

Previously chromosome 3A of wheat ( Triticum aestivum L.) was reported to c arry genes influencing yield, yield components, plant height, and anthesis date. The objective of current study was to survey various molecular marker systems for their ability to detect polymorphism between wheat cultivars C heyenne (CNN) and Wichita (WI), particularly for chromosome 3A. Seventy-sev en 'sequence tagged site' (STS), 10 simple sequence repeat (SSR), 40 random ly amplified polymorphic DNA (RAPD) markers, and 52 restriction fragment le ngth polymorphism (RFLP) probes for wheat homoeologous group 3 chromosomes, were investigated. Three (3.9%) STS-PCR primer sets amplified polymorphic fragments for the two cultivars, of which one was polymorphic for chromosom e 3A. Sixty percent of SSR markers detected polymorphism between CNN and WI of which 50% were polymorphic for chromosome 3A. Twenty pecent of RAPD mar kers detected polymorphism between CNN and WI in general, but none of these detected polymorphism for chromosome 3A. Of the fifty-two RFLP probes, 78. 8% detected polymorphism between CNN and WI for group 3 chromosomes with on e or more of seven restriction enzymes and 42% of the polymorphic fragement s were for chromosome 3A. These high levels of RFLP and SSR polymorphisms b etween two related wheat cultivars could be used to map and tag genes influ encing important agronomic traits. It may also be important to reconsider R FLP as the most suitable marker system at least for anchor maps of closely related wheat cultivars.