Simple Sequence Repeats for Genetic Studies of Alpaca

Abstract

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.

Identification of simple sequence repeat markers in the dromedary(Camelus dromedarius) genome by next-generation sequencing

“…This was likewise observed in several other eukaryotes (26). Camel SSRs with dimer and trimer motifs were compared with those of the related alpaca (19). The most abundant dimer in camel was AG/GA/CT/TC, with 50.1% compared to 30% in alpaca.…”

“…Putative camel homologs were found on each chromosome of bovine genome, except for BTA 25, 28, and Y. One camel SSR locus was placed on BTA 6,7,8,12,16,19,24, and 26, while BTA 11 and 14 reached 5 SSRs each with an average of 2 loci per chromosome. Conversely, 3 markers showed matches to unassigned contigs (UN).…”

“…This coverage includes more SSR markers, as recorded in this study. The Illumina platform is very important for delivering good sequence depth and confidence, as shown in the SSR markers identified in alpaca (19). However, the Roche GS FLX platform is equally important in extending contig length, thus capturing long repeats flanked by unique signature sequences.…”

“…The abundance of specific SSR repeat motifs was investigated in several animals such as chicken (29) and alpaca (19). When studying the abundance of certain SSR motifs in any genome, all equivalent motifs in a grouping in different reading frames or on a complementary strand should be considered (26).…”

“…The latter was also the most abundant trimer in alpaca (21.8%), whereas the former was very rare (1.7%) (19). Molecular markers have provided new opportunities to assess animal genetic variability at the DNA level.…”