Insights into Genomic Patterns of Homozygosity in the Endangered Dülmen Wild Horse Population

Background/Objectives: Dülmen wild horses are kept in a fenced wooden and marsh area around Dülmen in Westphalia, Germany, since 1856. Previous analyses supported early genetic divergence from other domesticated horse populations and the Przewalski horse. Therefore, the objective of this study was to evaluate genetic diversity using high-density genomic data. Methods: We collected 337 one-year-old male Dülmen wild horses, captured at 12 annual auctions, for genotyping on the Illumina GGP Equine Plus Beadchip. All analyses were performed for 63,123 autosomal SNPs. Results: On average, each horse had 27.96 ROH with an average length of 8.237 Mb, resulting in an average genomic inbreeding coefficient FROH of 0.107. ROH with a length of 2–4 Mb were most frequent, and the next frequent ROH fall into the length categories of 4–8 and 8–16 Mb. The effective population size (Ne) steadily decreased in the last 100 generations by 4.57 individuals per generation from 498 to 41. We identified 10 ROH islands on equine chromosomes 1, 4, 5, 7, 9, and 10. Only one ROH island on ECA 1 was shared by 45% of the horses. Overrepresented genes of ROH islands were associated with glycerophospholipid catabolism through phospholipase A2 genes, skeletal muscle contraction (TNNI3, TNNT1), synapse activity and structure (CTTNBP2), regulation of inflammatory response (NLRP genes), and zinc finger protein genes, which are involved in many cellular processes and may also act as tumor suppressors and oncogenes. Conclusions: This study highlights the development of genomic inbreeding and shows the importance of the stallions selected for breeding on the genetic diversity of the Dülmen wild horses. The results of this study should be used to develop strategies to slow down increase in inbreeding and prevent transmitting unfavorable alleles from the stallions to the next generation.