Genomic and Phenotypic Differentiation of Ardi Goat Lines with Distinct Facial Pigmentation in Bahrain: Implications for Conservation.

Indigenous goat populations are valuable genetic resources for livestock production in arid and semi-arid environments, yet many remain insufficiently characterized at the phenotypic and genomic levels. This study investigated phenotypic variation and genome-wide associations in two local Ardi goat lines in Bahrain: Ardi Bahraini and Ardi Mu'atar, the latter being distinguished by a characteristic facial marking pattern. A total of 280 goats were phenotypically characterized for qualitative traits and body measurements, and 76 animals were genotyped using the Illumina Caprine 60K single nucleotide polymorphism (SNP) BeadChip. After quality control, 49,716 autosomal SNPs were retained for genome-wide association analysis. Phenotypic analysis showed that the two lines differed significantly in body weight, body length, hip height, face width, tail length, ear width, and tail circumference, while discriminant analysis identified tail length, ear width, tail circumference, and facial patterns differentiating the lines. Principal component analysis (PCA) showed partial genomic clustering of the two lines, and genome-wide significant and suggestive SNPs based on Bonferroni and false discovery rate (FDR) thresholds on chromosomes 6, 13, 14, and 29. The strongest association was observed for rs268277393 on chromosome 13, located near