Detecting the footprint of selection on the genome of Girgentana goat, a popular ancient breed

Girgentana goats are an ancient breed with distinctive morphological, adaptive, and production traits, making this population an interesting model for studying the genetic architecture underlying these traits. These special features result from natural and human-mediated selection. In this study, we aimed to detect potential signatures of selection in the Girgentana genome by combining the following statistical methods: the integrated haplotype score (iHS), the standardised log-ratio of the integrated site-specific extended haplotype homozygosity test between pairs of populations (Rsb), the runs of homozygosity (ROH) islands and the population differentiation index (FST). A composite dataset of 206 Girgentana and 334 animals from 13 goat populations across Northern and Southern Italy was analysed. All animals were genotyped using an Illumina Goat medium-density BeadChip. Multidimensional scaling and neighbour-joining analyses revealed a clear separation of the three major clades, coinciding with Girgentana, Northern, and Southern Italian goats. Twelve regions putatively under selection were detected using iHS and Rsb, whereas 16 hotspot regions were identified using FST and ROH. Notably, a candidate region on chromosome 01 was consistently identified in all four tests. This region, along with other candidate regions, includes several genes associated with adaptive immunity, reproduction, and body size traits. The Girgentana breed showed signals of ongoing selection in a region of chromosome 6 encompassing several milk quality genes, such as caseins (CSN2, CSN1S2, and CSN3). Our study provides a glimpse into the genomic regions harbouring genes that presumably affect the desired features of Girgentana. This highlights the importance of ancient breeds in providing essential genetic traits for adapting livestock to increasing climate change challenges.