Development and Characterization SSR Makers Based on Next-generation Sequencing Technology in Iranian Turkmen Camel

The Iranian Turkmen one-humped camel (Camelus dromedarius) is an economically and culturally significant species valued for its milk and meat production. It is well-adapted to the arid and semi-arid climates of Middle East. Despite its importance, the genetic diversity and historical demography of this species remain poorly characterized compare to two-humped camel species, which exhibit limited genetic differentiation, the genetic diversity and historical demography of one-humped camels remain poorly understood. This study developed novel simple sequence repeat (SSR) markers for the Iranian Turkmen camel genome to facilitate genetic studies and marker-assisted breeding. We aimed to identify polymorphic loci to support analyses of genetic diversity, population structure, and evolutionary biogeography. Using Illumina HiSeq 2000 sequencing, we generated 589,326,158 clean 150 bp paired-end reads at 50x coverage. De novo assembly produced 235,978 contigs (N50= 8,526 bp) from which 151,556 SSR motifs were identified, primarily 2-mer (38.80%), 4-mer (21.85%), and 1-mer (16.20%) motifs. Primer pairs were designed for 144,184 loci (95%) (amplicon sizes of 100-180 bp). The Turkmen camel exhibited high SSR diversity (6,201 unique motifs), significantly exceeding than of Arabian and Bactrian camels (χ² = 7.14, p= 0.007, df= 1) with an estimated 78 to 510 additional unique motifs. These markers enable genetic diversity analysis, historical demography studies, and identification of breed-specific motifs (e.g., 1,179 novel motifs in Turkmen camels). Additionally, 19,425 codon-repeat loci, predominantly leucine-rich repeats (42%), were identified, potentially linked to stress response genes, offering insights into functional genomics. These SSR markers support conservation genomics and breeding programs for Camelus species, enhancing their long-term sustainability. Limitations include potential bias from using short contigs rather than scaffolds, and the need for functional validation of 19,425 codon-repeat loci, particularly leucine-rich repeats (42%).