Microsatellite markers in avocado ( Persea americana Mill.): development of dinucleotide and trinucleotide markers

Abstract

This paper compares the development of microsatellite markers from two genomic DNA libraries of avocado cultivar Hass enriched for dinucleotide and trinucleotide repeats. Sequencing showed 86 and 31% of clones from the respective libraries to contain microsatellites. However, banding profiles of trinucleotide loci were easier to interpret than those of dinucleotide loci. Of 376 dinucleotide-containing clones, 81% harbored AG repeats and 19% contained AC repeats. A subset of 104 trinucleotide-containing clones consisted of ATG repeats (44%), AGT repeats (30%), and AAG repeats (16%). Array lengths of up to 34 were attained in the dinucleotide repeat microsatellites, whereas trinucleotide arrays never exceeded 11 elements. Typing 37 genotypes at 25 loci (11 dinucleotide and 14 trinucleotide loci) revealed a total of 204 alleles, of which 60% originated from the dinucleotide loci. Average heterozygosity of the di- and trinucleotide loci was 73.4 and 52.6%, respectively. Many loci, especially dinucleotide loci, exhibited allele size differences that were not multiples of the repeat unit, suggesting nonstepwise mutational mechanisms. Several loci were additionally characterized by large gaps in the allele size distribution.