TY - JOUR
T1 - Genome variation in tick infestation and cryptic divergence in Tunisian indigenous sheep
AU - Ahbara, Abulgasim M.
AU - Khbou, Médiha Khamassi
AU - Rhomdhane, Rihab
AU - Sassi, Limam
AU - Gharbi, Mohamed
AU - Haile, Aynalem
AU - Rekik, Mourad
AU - Rischkowsky, Barbara
AU - Mwacharo, Joram M.
N1 - © 2022. The Author(s).
PY - 2022/2/28
Y1 - 2022/2/28
N2 - 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.
AB - 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.
KW - Animals
KW - Cattle
KW - Genome
KW - Genotype
KW - Mosquito Vectors
KW - Polymorphism, Single Nucleotide
KW - Sheep/genetics
KW - Tick Infestations/genetics
UR - http://www.scopus.com/inward/record.url?scp=85125648092&partnerID=8YFLogxK
U2 - 10.1186/s12864-022-08321-1
DO - 10.1186/s12864-022-08321-1
M3 - Article
C2 - 35227193
AN - SCOPUS:85125648092
SN - 1471-2164
VL - 23
JO - BMC Genomics
JF - BMC Genomics
IS - 1
M1 - 167
ER -