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


Abstract: The availability of molecular markers in camels is limited. The aim of this study was to develop new simple sequence repeat (SSR) markers. Four breeds of pooled dromedary genome were sequenced at low coverage utilizing Roche and Illumina platforms. A total of 65,746 contigs, covering approximately 52 Mb (2316 contigs > 2 kb), were assembled. The partial genome revealed 613 SSR loci with a minimum number of 5 repeat units. Comparative chromosomal location for 60 camel loci was predicted against bovine genome assembly Baylor Btau_4.6.1/bosTau7. Ten markers (16.7%) returned matches with a >100 score and >80% identity. SSR abundance was 1 in every 84.3 kb of contigs. The SSR loci mainly comprised di- (80.8%), tri- (10.8%), tetra- (7.6%), and pentamer (0.8%) motifs. (TA)n and (AC)n were the most abundant (58.6%) dimers. Thirty SSR loci were experimentally characterized for both dromedary (16 animals) and Bactrian camels. The number of alleles ranged from 1 to 3, and the average number of fragments scored per animal ranged from 0.81 to 2. Polymorphic information content ranged from 0 to 0.66 with a mean value of 0.38. These SSR markers will be a valuable resource for further genetic studies of camels and related species.

Keywords: Camel, dromedary, genome, microsatellites, next-generation sequencing

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