Polymorphic microsatellite markers in pineapple (Ananas comosus (L.) Merrill)

• Molecular characterization and diversity of 6 genotypes representing the main groups of varieties of pineapple analyzed.
• A total of 10 polymorphic SSR loci were selected both from Ananas comosus and Ananas bracteatus sequences.
• This set of SSRs can be used for fingerprinting and diversity analysis in pineapple since most of the previously reported SSRs were not valid.

Simple Sequence Repeats (SSRs), also known as microsatellites, have not been used extensively to study the genetic diversity of pineapple (Ananas comosus (L.) Merrill). In this work the performance of existing pineapple-specific microsatellite primers and of primers based on microsatellite sequence information from Ananas bracteatus (L.) Merrill are evaluated for the molecular characterization of pineapple genotypes. Of the 20 microsatellite primer pairs specifically developed for pineapple previously reported in the literature, only six were useful in this study: two could be used directly and four could be used after redesign of the primers. In addition, 10 additional new primer pairs were designed based on A. bracteatus (L.) Merrill sequences deposited in Genbank, in order to study their transferability to pineapple. A total of 10 SSRs were finally selected that allowed the detection of 26 polymorphic alleles in 6 different pineapple genotypes, representing the main groups of varieties of this crop, averaging 2.6 alleles/locus. Average expected heterozygosity (He) was 0.56, and average observed heterozygosity (Ho) was 0.47. Ho was lower than He for over half of the studied loci. According to Wright’s fixation index (F) there is a heterozygote deficit in six loci (60%). Average genetic similarity between the studied genotypes was 0.75. The use of the SSR markers described in this work will allow the optimization of pineapple cultivar fingerprinting and diversity studies in germplasm collections.