Detection of selection signatures within candidate regions underlying trypanotolerance in outbred cattle populations

Abstract

Breeding indigenous African taurine cattle tolerant to trypanosomosis is a straightforward approach to control costs generated by this disease. A recent study identified quantitative trait loci (QTL) underlying trypanotolerance traits in experimental crosses between tolerant N'Dama and susceptible Boran zebu cattle. As trypanotolerance is thought to result from local adaptation of indigenous cattle breeds, we propose an alternative and complementary approach to study the genetic architecture of this trait, based on the identification of selection signatures within QTL or candidate genes. A panel of 92 microsatellite markers was genotyped on 509 cattle belonging to four West African trypanotolerant taurine breeds and 10 trypanosusceptible European or African cattle breeds. Some of these markers were located within previously identified QTL regions or candidate genes, while others were chosen in regions assumed to be neutral. A detailed analysis of the genetic structure of these different breeds was carried out to confirm a priori grouping of populations based on previous data. Tests based on the comparison of the observed heterozygosities and variances in microsatellite allelic size among trypanotolerant and trypanosusceptible breeds led to the identification of two significantly less variable microsatellite markers. BM4440, one of these two outlier loci, is located within the confidence interval of a previously described QTL underlying a trypanotolerance-related trait. Detection of selection signatures appears to be a straightforward approach for unravelling the molecular determinism of trypanosomosis pathogenesis. We expect that a whole genome approach will help confirm these results and achieve a higher resolving power.

Lack of haplotype structuring for two candidate genes for trypanotolerance in cattle

“…One issue with the current analysis is that the genes sequenced have importance in the immune response and, as repeatedly reported, may have been subject to natural selection (Freeman et al 2008;Dayo et al 2009;Gautier et al 2009). Actually, strong selection signatures have been previously reported for the TICAM1 gene in African cattle Noyes et al 2011;Flori et al 2014).…”

“…The West African cattle group, which is an unselected outbred population, had the lowest variability for the TCAM1 gene even if the European cattle group is considered. West African taurine cattle, but also trypanotolerant populations of other domestic ruminant species Traor e et al 2009Traor e et al , 2012, tend to have low diversity at neutral loci in general (Dayo et al 2009;Alvarez et al 2014). In turn, European cattle were monomorphic for the exon 1 of the INHBA gene and had the lowest variability for the exon 2 of that gene.…”

“…Selection signatures usually become strong when West African cattle is analysed together with distant (such as European or zebu) cattle samples (Freeman et al 2008;Dayo et al 2009;Gautier et al 2009). However, as suggested by our analyses as well, when the polymorphism identified is analysed in narrower subsets, the signal is weaker (Freeman et al 2008).…”

“…Hanotte et al (2003), using an experimental herd, identified several QTLs associated with trypanotolerance on 18 different autosomal bovine chromosomes. Researchers have paid major attention to the QTL identified on bovine chromosome 2 (BTA2) (Dayo et al 2009;Noyes et al 2011;Alvarez et al 2015). However, Dayo et al (2012), using 360 outbred West African cattle, confirmed the importance of a QTL previously identified on BTA4 for cattle trypanotolerance.…”

Population genetic structure of wild and farmed rusa deer (Cervus timorensis russa) in New-Caledonia inferred from polymorphic microsatellite loci

“…Furthermore, farmed populations may present low genetic diversity at the breed level (Boichard et al 1996). Depending on the breeding system and purposes and on the demographic history, large differences in genetic diversity may be observed within a species (e.g., in cattle, Freeman et al 2004;MacHugh et al 1997;Dayo et al 2009). However, genetic diversity usually decreases when the distance from the domestication centre increases (Canon et al 2001;Hanotte et al 2002).…”