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

Italy hosts a rich biodiversity of local goat breeds, shaped by its wide variety of climates, landscapes, and traditional farming systems, making the preservation of these locally adapted populations critical for maintaining genetic resources. This study aimed to explore the genomic biodiversity of Italian goats, track recent temporal changes through comparison with samples collected about two decades ago, and investigate the genomic mechanisms underlying environmental adaptation, as well as identify hotspots of possible climatic vulnerability. Demographic data over the last 15 years show that only five breeds are currently considered not at risk of extinction according to FAO criteria, while 22 breeds are classified as critical or formally extinct (no registered animals in 2024). Medium-density single-nucleotide polymorphism (SNP) data from 685 goats representing 31 populations were analysed for population structure, genomic background, and genetic diversity. Comparison with historical samples revealed changes over time, exemplified by Bianca Monticellana and Capestrina, which now display a highly similar and uniform genetic background and higher inbreeding. Genomic analyses revealed a clear separation between northern and central-southern breeds, with northern populations exhibiting more distinct genomic backgrounds while central-southern populations are generally more admixed. Landscape genomic analyses were conducted on a subset of 693 goats from 32 populations, using latent factor mixed model and partial redundancy analysis approaches together with present and projected (SSPs 2-4.5 and 5-8.5, 2080-2100) climatic variables from WorldClim 2.1. A total of 468 SNPs were identified as putatively adaptive, including five detected by both methods, encompassing genes such as KPNA1, PARP9, and LRP8. Genomic offset analyses highlighted vulnerable areas in the northern fringes of the Alpine region, the eastern Po Valley (unsampled due to limited presence of local goat populations), and the Murgia-Gargano region of Apulia, home to the Garganica breed. Overall, these results reveal the impact of breeding practices and environmental pressures on Italian goat genomes, provide insights into adaptive genetic variation of goat species, and identify populations and regions at greatest risk, emphasising the need for targeted conservation and management strategies to preserve this unique component of livestock biodiversity.