Development of SCAR markers for a Thinopyrum distichum chromosome that appears to be involved in salt tolerance

Abstract

Sixty-seven F-₁ plants from the backcross: Thinopyrum distichum/tetraploid ‘Henoch’ rye//diploid ‘Henoch’ rye were cloned, tested for salt tolerance (2–4 replications per genotype) and ranked. Sixty RAPD primers were tested on the parental lines. Nine of these produced Thinopyrum specific fragments and were applied to the whole population. Correlations between salt tolerance and presence of the Thinopyrum specific bands were mostly significant but small, as would be expected with a trait involving genes on several chromosomes. The nine markers were then also tested on a group of 15 B₁ F₁ plants from the same cross in which C-banding has identified the Thinopyrum chromosomes. It appeared that OPK6 (± 1060 bp) and OPK17 (± 652 bp) polymorphisms co-segregated with a chromosome putatively identified as belonging to homoeologous group 2 and implied in salt tolerance in a different study. The diagnostic RAPD bands were cloned and sequenced and specific SCAR primers were designed. These amplified DNA sequences specific for chromosome IIJ₁ ^d that will be very useful in future introgression attempts.