Genomic characterization of Algerian Guelmoise cattle and their genetic relationship with other North African populations inferred from SNP genotyping arrays

Understanding between and within-breeds genetic variability is essential in the choice of conservation management decisions for threatened populations. In this study we assessed the genetic diversity of the Algerian Guelmoise cattle (GUE) by analyzing data on 24 GUE individuals genotyped for the Illumina BovineSNP50 BeadChipv2. We also provided a detailed description of the population structure of GUE using comparisons with 23 worldwide cattle populations, selected as being representative of African, South European and indicine populations, in addition to four North African populations. We show that GUE is an admixed population which has strong genetic similarity to Tunisian cattle owing both to a common ancestral origin and a continuous gene flow. GUE was found to be less subject to foreign breed introgression than native Tunisian cattle. We also found support for a past admixture between GUE and the Moroccan Oulmès Zaer breed. The observed heterozygosity of GUE population was similar to that observed for the South European breeds and the other Maghreb populations (Ho∼0.30). By investigating the occurrence of Runs of Homozysosity (ROHs) in a subset of nine populations, we found that GUE had the lowest cumulative ROH length per animal with the largest proportion of their genome covered with medium and long (> 5 Mb) ROHs. This likely indicates that GUE is derived from a large ancestral population which has subsequently undergone a recent increasing levels of inbreeding. ROH islands within GUE harbored genes enriched in immune defense and transcriptional regulation functions in addition to genes related to the Pregnancy-associated proteins family. Our study is the first of its kind providing insights into the genomic structure and the phylogenetic relationships of Guelmoise cattle population. It points out the possibility to establish a common genetic management program between Algeria and Tunisia aimed at safeguarding the endangered indigenous North African cattle.