Genomic diversity and selection signatures underlying tail fatness inferred from 1 genome-wide SNPs markers in local sheep in semi-arid area

In climate change perspective, the genetic make-up of local breeds showing adaptive 15 traits of particular importance, should be explored and preserved as a priority. In this 16 context, this study highlights the potential of genomic analysis to i) provide an overview 17 of fine scale genomic variability within and among local breeds and ii) explore potential 18 breed-specific selection footprints of local sheep under semi-arid conditions. Thus, we 19 sampled 65 unrelated sheep breeds from Tunisia including 26 fat tailed Barbarine 20 samples and 39 thin tailed sheep from the Noire de Thibar, the Queue fine de l’Ouest 21 Thibar and the D’man breeds which are genotyped using Illumina OvineSNP50K array 22 data. The study of intra-breed genetic diversity based on estimation of genome-wide runs 23 of homozygosity (ROH) distribution and inbreeding estimation (F ROH ) showed that 24 Barbarine samples are less affected by inbreeding than other breeds. Moreover, the 25 genomic relationships among 60 individuals based on network-based approach, using 26 46 232 genotypes confirmed the recent admixture between Barbarine and Queue Fine de 27 l’Ouest animals resulting from the uncontrolled crossbreeding between two breeds, which 28 suggest paying more attention to preserve the genetic integrity of those local breeds. As 29 expected, all samples from Noire de Thibar breed were clearly differentiated from the 30 remaining individuals explained by past introgression of European gene flow into the 31 breed. The signals of selection identified across and within breeds were detected by 32 selecting the top 10% of SNPs most commonly observed in a ROH region. For genome- 33 wide scan of selective sweeps detection, we focused on the highest signal observed 34 across and within analysis. Therefore, results across samples identified three significant 35 ROH islands on chromosome 1,10 and 13 with highest signal on OAR 13. We uncover a 36 strong signal of positive selection of an overlapping 3.03 Mb homozygous region spanning 37 46.58 – 49.61 Mb on chromosome 13 detected within Barbarine samples analysis with a 38 peak of mean frequency P=0.31 harboring 20 candidate genes. These candidate putative 39 genes preferentially selected in fat tailed Barbarine animals were CDS2 , PROKR1 and 40 BMP2 which are involved in fat deposition and lipid storage, a relevant sheep adaptive 41 trait in semi-arid area. Our findings will primarily assist policy makers and livestock 42 keepers for carrying out molecular breeding and conservation in sheep. In climate change context, fine-scale characterization of local sheep stock showing 48 specific adaptive traits are urgently needed. Using ovine 50K SNP array data, this research highlights a potential threat of genetic homogenization between most important 50 sheep breeds in Tunisia and uncover breed-specific footprints involved in fat tail formation 51 in Barbarine sheep. This case study revealed how genomic data could be used to 52 ascertain population structure, to exploit uniqueness of local sheep genetic stock to harsh 53 conditions and give relevance for the conservation of native livestock breeds.