Witsenboer, H., Vogel, J., Michelmore, R.W.

Genome 40:923-936 (1998).

SAMPL (Selectively amplified microsatellite polymorphic locus) analysis is a method to amplify microsatellite loci using generic PCR primers. SAMPL analysis uses one AFLP primer in combination with a primer complementary to microsatellite sequences. SAMPL primers based on compound microsatellite sequences provided the clearest amplification patterns. We explored the potential SAMPL analysis in lettuce to detect PCR-based codominant microsatellite markers. Fifty eight SAMPL were identified and placed on the genetic map. Seventeen were codominant. SAMPL were dispersed with RFLP markers on 11 of the 12 main linkage groups in lettuce, indicating that they have a similar genomic distribution. Some but not all fragments amplified by SAMPL analysis were confirmed to contain microsatellite sequences by Southern hybridization. Forty five cultivars of lettuce and five wild species of Lactuca were analyzed to determine the allelic diversity for codominant SAMPL. Three to 11 putative alleles were found for each SAMPL; two to six alleles were found within L. sativa and one to three alleles were found among the crisphead genotypes, the most genetically homogeneous plant type of L. sativa. This allelic diversity is greater than for RFLP markers. Numerous new alleles were observed in the wild species; however, there were frequent null alleles. Therefore, SAMPL analysis is more applicable to intra-specific than inter-specific comparisons. A phenetic analysis based on SAMPL resulted in similar dendrograms to those based on RFLP and AFLP markers.