3.4 Local adaptation by selective sweeps
The adaptation of indigenous livestock species in the SWA region to hot
and dry desert ecosystems (Middleton 1986, Vaghefi et al. 2019) may have
effect on the hair and skin traits, which directly related to heat loss
ability (Deng and Xu 2018, Berihulay et al. 2019). For example, most of
the SWA indigenous sheep breeds have coarse wool coats, whereas the
majority of local goat breeds in the cold climate of northern Asia are
cashmere-producing (Du et al. 2011). In order to gain insight into the
adaptation to desert climate, we compared the native goats from SWA with
Northeastern-Asia by calculating pairwise genetic differentiation
(F ST) and differences in nucleotide diversity (π
ln-ratio Northeastern Asia/SWA). After merging consecutive windows with
high values, we found 46 windows with the top 1% values in bothF ST and ln-ratio, spanning 72 candidate genes
(Figure 4a and Table S6 ). The top F SToutlier window contains introgressed signals related to KITLGgene on chromosome 5 (18,075–18,160 kb) which is associated with hair
follicle traits (Guenther et al. 2014). Low π and Tajima’s D values and
high composite likelihood ratio (CLR) scores suggest strong positive
selection at this locus in SWA goats (Figure 4b ). Previous
studies showed that KITLG is an important modulator of skin
pigmentation in animals, which plays a vital role in follicular survival
and the development of the melanocyte lineage in adult skin
(Yang et al. 2018). Melanin pigments have a direct
role in the protection against UV-radiation and thermoregulation, which
can pleiotropically influence a variety of behavioral and physiological
traits in mammals (Sulem et al. 2007, Yang et al.
2018, Deng and Xu 2018). We did not find any non-synonymous mutations
within the coding region, suggesting a role of regulatory mutations.