ROH and HRR patterns across the genome of European goat and sheep breeds

Runs of Homozygosity (ROH) constitute continuous homozygous genomic segments widely studied in farmed animals. Increased levels of homozygosity are usually formed by founder effects and geographic isolation, management practices and demographic history. Frequent ROH may indicate inbreeding events, reduced reproduction success and fitness. Heterozygosity Rich Regions (HRR), which represent consecutive single nucleotide differences between paternal and maternal chromosomes, are also studied. HRR provide insights into evolutionary history and genetic diversity, while facilitating the identification of genomic regions related to survival rate, immune response and fertility. The present study focuses on the exploration of these genomic patterns in 5 goat breeds (Fosses, Provencale, Eghoria, Skopelou, Swedish Landrace) and 6 sheep breeds (Bizet, Castellana, Churra, Chios, Solognote, Tsigai) from North, Central and South Europe, including Greek native populations. Altogether, 50K species-specific genotypes were obtained from the SMARTER global database. ROH and HRR were detected with the ‘detectRUNS’ R package. Most goat breeds exhibited predominantly short ROH, indicating ancient inbreeding events. The Swedish Landrace was characterized by high inbreeding coefficient (FROH) as well as the highest ROH number and length in contrast to the French Provencale and Fosses, which displayed this pattern in HRR. Greek breeds showed divergent patterns between each other due to the geographic isolation of Skopelos compared to the mainland Eghoria goats. A common HRR island was found across all goat populations in chromosome 1, previously associated with embryonic development, whereas other shared islands between breeds have been related to immune response (chromosomes 3, 8, 12), survival in arid environments (chromosome 12) and meat and wool-related traits. The Swedish Landrace shared an island (ROH and HRR) with nearly every other breed, possibly due to historical connections to Viking trade. In sheep, Solognote displayed the highest ROH count and Churra the highest HRR count and length. Additionally, Bizet exhibited particularly high FROH. All sheep breeds studied here share an island (ROH or HRR) with the Spanish Castellana sheep. This could be potentially attributed to two demographic events. First, sheep migration from the Balkans to Spain along the Mediterranean route during the Roman period linked Chios sheep with Spanish breeds. Second, the post-domestication dispersal of the close relative Merino sheep in Europe connected Castellana to French and Hungarian breeds. SNP annotation revealed 93 genes associated with common islands in goats and 71 genes in sheep. Following functional enrichment analysis, numerous adaptive traits were related to HRR islands. Several of them participate in immune response regulation and inflammation. Meanwhile, ROH islands contained some traits requiring conservation. Adaptive traits were more prevalent in goats, numbering 13 versus 5 in sheep. Sheep were mainly associated with production and behavioral traits. Overall, the characterization of the goat genome indicated environmental adaptation to harsh conditions compared to sheep where more signals related to artificial selective pressure were identified. These findings could be utilized for management strategies of small ruminants within breed level.