Genome variation in tick infestation and cryptic divergence in Tunisian indigenous sheep
Abulgasim M. Ahbara,
Médiha Khamassi Khbou,
Rihab Rhomdhane,
Limam Sassi,
Mohamed Gharbi,
Aynalem Haile,
Mourad Rekik,
Barbara Rischkowsky,
Joram M. Mwacharo
Affiliations
Abulgasim M. Ahbara
Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA)
Médiha Khamassi Khbou
Lab. of Infectious Animal Diseases, Zoonosis and Sanitary Regulation, Univ. Manouba, Institution of Agricultural Research and Higher Education, National School of Veterinary Medicine of Sidi Thabet
Rihab Rhomdhane
Laboratoire de Parasitologie, Institution de La Recherche et de L’Enseignement Supérieur Agricoles, Univ. Manouba, Ecole Nationale de Médecine Vétérinaire de Sidi Thabet
Limam Sassi
Laboratoire de Parasitologie, Institution de La Recherche et de L’Enseignement Supérieur Agricoles, Univ. Manouba, Ecole Nationale de Médecine Vétérinaire de Sidi Thabet
Mohamed Gharbi
Laboratoire de Parasitologie, Institution de La Recherche et de L’Enseignement Supérieur Agricoles, Univ. Manouba, Ecole Nationale de Médecine Vétérinaire de Sidi Thabet
Aynalem Haile
Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA)
Mourad Rekik
Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA)
Barbara Rischkowsky
Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA)
Joram M. Mwacharo
Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA)
Abstract Background Ticks are obligate haematophagous ectoparasites considered second to mosquitos as vectors and reservoirs of multiple pathogens of global concern. Individual variation in tick infestation has been reported in indigenous sheep, but its genetic control remains unknown. Results Here, we report 397 genome-wide signatures of selection overlapping 991 genes from the analysis, using ROH, LR-GWAS, XP-EHH, and FST, of 600 K SNP genotype data from 165 Tunisian sheep showing high and low levels of tick infestations and piroplasm infections. We consider 45 signatures that are detected by consensus results of at least two methods as high-confidence selection regions. These spanned 104 genes which included immune system function genes, solute carriers and chemokine receptor. One region spanned STX5, that has been associated with tick resistance in cattle, implicating it as a prime candidate in sheep. We also observed RAB6B and TF in a high confidence candidate region that has been associated with growth traits suggesting natural selection is enhancing growth and developmental stability under tick challenge. The analysis also revealed fine-scale genome structure indicative of cryptic divergence in Tunisian sheep. Conclusions Our findings provide a genomic reference that can enhance the understanding of the genetic architecture of tick resistance and cryptic divergence in indigenous African sheep.
