The genome-wide relationships of the critically endangered Quadricorna sheep in the Mediterranean region

Abstract

Livestock European diffusion followed different human migration waves from the Fertile Crescent. In sheep, at least two diffusion waves have shaped the current breeds’ biodiversity generating a complex genetic pattern composed by either primitive or fine-wool selected breeds. Nowadays most of the sheep European breeds derive from the second wave which is supposed to have largely replaced oldest genetic signatures, with the exception of several primitive breeds confined on the very edge of Northern Europe. Despite this, some populations also in the Mediterranean region are characterised by the presence of phenotypic traits considered ancestral such as the policeraty, large horns in the ram, short tail, and a moulting fleece. Italy is home of a large number of local breeds, albeit some are already extinct, others are listed as critically endangered, and among these there is the Quadricorna breed which is a four-horned sheep characterised by several traits considered as ancestral. In this context we genotyped 47 individuals belonging to the Quadricorna sheep breed, a relict and endangered breed, from Central and Southern Italy. In doing so we used the Illumina OvineSNP50K array in order to explore its genetic diversity and to compare it with other 41 breeds from the Mediterranean region and Middle-East, with the specific aim to reconstruct its origin. After retaining 32,862 SNPs following data filtering, the overall genomic architecture has been explored by using genetic diversity indices, Principal Component Analysis (PCA) and admixture analysis, while the genetic relationships and migration events have been inferred using a neighbor-joining tree based on Reynolds’ distances and by the maximum likelihood tree as implemented in treemix. The Quadricorna breed exhibit genetic diversity indices comparable with those of most of the other analysed breeds, however, the two populations showed opposing patterns of genetic diversity suggesting different levels of genomic inbreeding and drift (FIS and FROH). In general, all the performed genome-wide analyses returned complementary results, indicating a westward longitudinal cline compatible with human migrations from the Middle-East and several additional genetic footprints which might mirror more recent historical events. Interestingly, among the Italian breeds, the original Quadricorna (QUAD_SA) first separated showing its own ancestral component. In addition, the admixture analysis does not suggest any signal of recent gene exchange with other Italian local breeds, highlighting a rather ancestral purity of this population. On the other hand, both the neighbor-joining tree and the treemix analysis seem to suggest a proximity of the Quadricorna populations to breeds of South-Eastern Mediterranean origin. Although our results do not support a robust link between the genetics of the first wave and the presence of primitive traits, the observed genetic uniqueness together with the inferred phylogeograpic reconstruction would suggest an ancient presence of the Quadricorna breed in the Italian Peninsula. Because of this singularity, urgent conservation actions are needed in order to keep the breed and all related cultural products alive.