Simple sequence repeats for genetic studies of alpaca

Trace sequences from the 2X alpaca genome sequencing effort were examined to identify simple sequence repeats (microsatellites) for genetic studies. A total of 6,685 repeat-containing sequences were downloaded from GenBank, processed, and assembled into contigs representing an estimated 4,278 distinct sequences. This sequence set contained 2,290 sequences of length > 100 nucleotides that contained microsatellites of length > or = 14 dinucleotide or 10 trinucleotide repeats with purity equal to 100%. An additional 13 sequences contained a GC microsatellite of length > or = 12 repeats (purity = 100%) were also obtained. Primer pairs for amplification of 1,516 putative loci are presented. Amplification of genomic DNA from alpaca and llama by PCR was demonstrated for 14 primer sets including one from each of the microsatellite repeat types. Comparative chromosomal location for the alpaca markers was predicted in the bovine genome by BLAT searches against assembly 4.0 of the bovine whole genome sequence. A total of 634 markers (41.8%) returned BLAT hits with score > 100 and Identity > 85%, with the majority assignable to unique locations. We show that microsatellites are abundant and easily identified within the alpaca genome sequence. These markers will provide a valuable resource for further genetic studies of the alpaca and related species.