Uncovering genetic diversity and inbreeding in the Saudi Shami goat through genome-wide SNP analysis

In Saudi Arabia, goats constitute a substantial component of the livestock sector, with an estimated population of approximately 7.4 million animals. In 2023, the national dairy industry produced around 2.8 billion liters of raw milk, of which goat milk contributes. Goat populations have diversified into dairy, meat, and fiber breeds, with dairy goats selected for milk yield and composition. The Shami goat is a prominent dairy breed in Saudi Arabia, primarily reared in the cooler northern regions and valued for its high milk productivity. Despite their importance, Saudi goat populations, including the Shami breed, remain underrepresented in genome-wide studies. This limits understanding of their genetic diversity, population structure, inbreeding levels, and evolutionary relationships with domestic and wild Capra species. This study aimed to evaluate the suitability of high-density SNP genotyping for the Saudi Shami goat, characterize genomic diversity and inbreeding within the population, and place the breed within a global Capra genomic context through analyses of population structure, ancestry, and evolutionary relationships. Blood samples were collected from 144 female Shami goats in the Al-Jouf region of northern Saudi Arabia. Genomic DNA was genotyped using the Illumina Goat_IGGC_65K_v2 BeadChip and mapped to the ARS1 reference genome. Quality control retained autosomal SNPs with call rates ≥95% after filtering for missingness, minor allele frequency, and linkage disequilibrium. The dataset was integrated with publicly available genotypes from domestic and wild Capra populations worldwide. Population structure was assessed using PCA and ADMIXTURE, and genetic relationships were examined using neighbor-net analysis. Genome-wide SNP genotyping produced high-quality data suitable for population genetic analyses. After quality control, 54.5k autosomal SNPs were retained, confirming the suitability of the Illumina Goat_IGGC_65K_v2 BeadChip for genomic analysis of the Saudi Shami breed. Runs of homozygosity (ROH) analysis revealed high levels of inbreeding, with an average ROH-based inbreeding coefficient (F_ROH) of 0.71. The ROH profile was dominated by long segments, with mean values of 1.15 ROH in the 4-8 Mb class, 0.61 in the 8-16 Mb class, and 0.22 exceeding 16 Mb, consistent with recent and sustained inbreeding. Comparative analyses supported five major genetic clusters. The Shami breed clustered with 69 populations from Pakistan, Iran, Tà¼rkiye, Russia, Egypt, South Africa, and Madagascar, showing particularly close affinity to Turkish breeds. Neighbor-net analysis supported these patterns, revealing shared nodes with Turkish Kilis and Ankara breeds and multiple Russian and Alpine populations. This study provides the first comprehensive genome-wide analysis of the Shami goat breed in Saudi Arabia. Comparative analyses place the Shami breed within a broader Middle Eastern and Eurasian context, revealing close genetic relationships with Turkish Kilis goats. These findings establish a genomic baseline for the Saudi Shami goat and support future conservation and genetic improvement efforts.