Detection of signatures of selection for bovine stature
In this study, we used bovine wither height (stature) measures from an online resource, namely the FAO database (DAD-IS 2014), recorded as averages for both males and females across multiple countries. Height and body size have generally been considered important traits in cattle during domestication. During early stages of domestication, selection favored animals with lower stature compared to wild ancestors (Karim et al. 2011). However, during the recent past, strong selection for increased stature has been applied in selected breeds of modern cattle (Ajmone-Marsan et al. 2010).
We found 26 bovine genomic regions in European and African Bos taurus carrying distinctive signatures of selection. Of these, 12 (46%) contained 30 stature-associated candidate genes derived from comparative mapping. We showed that when cohorts of randomly permuted animals were tested, a much lower proportion (8.3%) of the significant regions contained candidate genes, which is consistent with random expectations (∼7%). This suggests that our approach was powerful in capturing bovine genomic regions related to stature. Several of these should be considered novel because they were not previously reported in cattle.
It is noteworthy why different genomic regions are detected in the large and small cohorts within European and African cattle. The cohorts within each cattle type were compared against each other to compute the constituent (FST, ΔDAF, and XP-EHH) selection tests of CSS. Two selection tests (ΔDAF and XP-EHH) provide directional signatures of selection. This implicates that different gene variants are regulating stature in large and small breeds of cattle (Visscher and Goddard 2011).
Several traits, such as birth weight, growth rate, adult weight, and stature, are found to be correlated with each other and have pleiotropic effects. Some of the genes in the validation regions (see below) have been previously found to be associated with multiple correlated traits. The FAO data on stature have been used to objectively classify cohorts of cattle, and the data were not adjusted for other traits given the nonavailability of FAO records for the correlated traits. Multibreed classification is expected to minimize the breed sampling effects; however, some of the candidate regions may not be directly reflecting selection of stature but could be confounded by some of the other correlated traits.
The significant CSS outside the candidate gene regions (Table S5 and Table S6) may indicate putative genes associated with height or targets of selection for traits other than stature (Utsunomiya et al. 2013; Druet et al. 2013; Ramey et al. 2013; Stella et al. 2010; Kemper et al. 2014; Perez et al. 2014; Porto-Neto et al. 2013; Rothammer et al. 2013; Gautier et al. 2009). Moreover, several additional significant CSS regions in African cattle have not been reported previously, given the limited reports on selective sweep analyses in the African breeds.