Development of SCAR markers linked to sin-2, the stringless pod trait in pea (Pisum sativum L.)

With increasing consumer demand for vegetables, edible-podded peas have become more popular. Stringlessness is one of most important traits for snap peas. A single recessive gene, sin-2, controls this trait. Because pollen carrying the stringless gene is less competitive than pollen carrying the stringy gene, there are fewer than expected stringless plants recovered in segregating generations. Marker-assisted selection (MAS) is a valuable tool to identify plants with the traits of interest at an early stage in the breeding process. The objective of this study was to identify robust, user-friendly molecular markers tightly linked to sin-2. A total of 144 target region amplification polymorphism (TRAP) primer combinations were used to screen four DNA bulks, which were constructed from 32 pea breeding lines based on their phenotypes. Sixty polymorphic TRAP primers combinations were identified between bulks of stringless and stringy pods. Five of them, F6_Trap03_168, F6_SA12_145, F10_ODD8_130, F11_GA5_850 and F12_SA12_190, showed more than 90% association with the stringless phenotype in 32 pea breeding lines. Two of the TRAP markers, F10_ODD8_130 and F12_SA12_190, were cloned, sequenced and successfully converted to sequence characterized amplified region (SCAR) markers. These two SCAR markers were validated using 20 F5 recombinant inbred lines derived from a cross between Bohatyr (a dry pea variety with strings) and S1188 (a stringless snap pea variety) and showed strong marker-trait association. The results will have direct application in marker-assisted selection of stringless edible-podded peas.