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 ۲۰۰۰ sequencing, we generated ۵۸۹,۳۲۶,۱۵۸ clean ۱۵۰ bp paired-end reads at ۵۰x coverage. De novo assembly produced ۲۳۵,۹۷۸ contigs (N۵۰= ۸,۵۲۶ bp) from which ۱۵۱,۵۵۶ SSR motifs were identified, primarily ۲-mer (۳۸.۸۰%), ۴-mer (۲۱.۸۵%), and ۱-mer (۱۶.۲۰%) motifs. Primer pairs were designed for ۱۴۴,۱۸۴ loci (۹۵%) (amplicon sizes of ۱۰۰-۱۸۰ bp). The Turkmen camel exhibited high SSR diversity (۶,۲۰۱ unique motifs), significantly exceeding than of Arabian and Bactrian camels (χ² = ۷.۱۴, p= ۰.۰۰۷, df= ۱) with an estimated ۷۸ to ۵۱۰ additional unique motifs. These markers enable genetic diversity analysis, historical demography studies, and identification of breed-specific motifs (e.g., ۱,۱۷۹ novel motifs in Turkmen camels). Additionally, ۱۹,۴۲۵ codon-repeat loci, predominantly leucine-rich repeats (۴۲%), 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 ۱۹,۴۲۵ codon-repeat loci, particularly leucine-rich repeats (۴۲%).

کلیدواژه ها:

Primer ، SSR marker ، Turkmen camel ، Whole genome sequencing