Spatio-temporal genomics of goats: recent evolution, adaptation, and future vulnerability

Area of Science:

• Genomics and Conservation Biology
• Livestock Biodiversity
• Climate Change Adaptation

Background:

• Italy possesses rich local goat breed diversity, crucial for genetic resources but threatened by climate and farming practices.
• Demographic data indicate 22 out of 31 Italian goat breeds are critically endangered or extinct.
• Understanding genomic changes is vital for effective conservation strategies.

Purpose of the Study:

• To explore the genomic biodiversity of Italian goat populations.
• To track temporal genetic changes and assess inbreeding.
• To investigate genomic adaptation mechanisms and identify climate vulnerability hotspots.

Main Methods:

• Analysis of medium-density single-nucleotide polymorphism (SNP) data from 685 goats (31 populations).
• Comparison with historical samples to assess genetic diversity and temporal changes.
• Landscape genomic analyses using latent factor mixed models and climate projections.

Main Results:

• Significant genetic erosion and increased inbreeding observed in some breeds (e.g., Bianca Monticellana, Capestrina).
• Clear genomic separation between northern and central-southern breeds; northern populations show distinct backgrounds.
• 468 putatively adaptive SNPs identified, with genomic offset analyses pinpointing vulnerable regions in Alpine, Po Valley, and Apulia areas.

Conclusions:

• Breeding practices and environmental pressures have significantly impacted Italian goat genomes.
• Genomic insights reveal adaptive variation and identify high-risk populations and regions.
• Urgent, targeted conservation strategies are needed to preserve this livestock biodiversity.