Genomic Analysis of Adaptability and Genetic Structure of Jabal Akhdar Goats: Evidence of Positive Selection in an Indigenous Omani Breed

TL;DR

This study explores the genetic makeup of Jabal Akhdar goats in Oman to understand how they adapt to harsh mountain conditions.

Contribution

The study identifies genomic regions under positive selection linked to environmental adaptability in an indigenous Omani goat breed.

Findings

Jabal Akhdar goats show moderate inbreeding and distinct genetic structure compared to Egyptian desert breeds.

93 genomic regions were found to be under positive selection, including genes related to hypoxia tolerance, muscle function, and fertility.

The findings can guide conservation and breeding strategies to improve productivity in this unique goat breed.

Abstract

Goats are a vital source of food and income for people living in harsh environments, particularly in mountainous and dry regions. In Oman, a unique breed of goat lives in the high-altitude Jabal Akhdar mountain range, where temperatures can drop below freezing and vegetation is scarce. These goats are known for their ability to survive and grow well under such difficult conditions, but little is known about the genetic traits that help them do so. In this study, we examined the genetic makeup of these goats to understand how they have adapted to their environment over time. We looked for signs of inbreeding and explored which genes may be responsible for helping the goats adapt to low oxygen levels, limited food, and temperature extremes. We also compared their genetic patterns to other desert-adapted goat breeds from Egypt. Our results identified key genetic regions that may play a role in traits like growth, reproduction, and resistance to environmental stress. This information is valuable for designing breeding programs to preserve and improve these local goat breeds. Understanding how animals adapt to tough conditions can help communities raise highly productive livestock and ensure food security in challenging climates.

Jabal Akhdar goats, native to Oman’s high-altitude Jabal Akhdar mountain range, are recognized for their high growth rate, remarkable twinning rate, and adaptability to harsh environmental conditions. This study assesses the genetic structure, inbreeding levels, effective population size (Ne), and linkage disequilibrium (LD) of Jabal Akhdar goats while identifying genomic regions under positive selection that may contribute to their environmental adaptation. The SNP genotypes from 72 Jabal Akhdar goats and two desert breeds from Egypt (153 Barki and 60 Saidi) revealed a clear genetic distinction between both groups. Within the Jabal Akhdar goats, genetic differentiation was also identified among the three sampled villages, indicating a village-specific genetic structure. The Jabal Akhdar breed exhibited a moderate level of inbreeding (FROH = 0.16), greater than that of the Barki and Saidi breeds. Additionally, Jabal Akhdar goats displayed greater LD and lower Ne levels compared to the Egyptian breeds. Analysis of runs of homozygosity (ROH) and extended haplotype homozygosity-based statistics (iHS and Rsb) identified 93 genomic regions exhibiting signatures of positive selection (80 from ROH, 5 from iHS, and 8 from Rsb). These regions harbor genes associated with traits essential for environmental adaptability, including hypoxia tolerance (SUCNR1, ANGPTL1, MITF, MTUS2), muscle development and function (MBNL1, ACTC1, CAPN5), fertility (GNRHR, CCNA1, SPAG1), UV radiation resistance (UVRAG, BRCA1), bone development (SOST, MEOX1), and lipid metabolism for energy utilization (DGAT2, G6PC, SUCLG2). The results of this study provide valuable insights for identifying causative variants and haplotypes underlying the Jabal Akhdar goat’s superior adaptability. These findings can guide breeders in designing conservation strategies and improving the productivity of this unique indigenous breed.

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