PMC:4502373 / 33921-46474 JSONTXT

{"target":"http://pubannotation.org/docs/sourcedb/PMC/sourceid/4502373","sourcedb":"PMC","sourceid":"4502373","source_url":"https://www.ncbi.nlm.nih.gov/pmc/4502373","text":"Discussion\n\nCSS for complex traits\nThe CSS approach demonstrates that the test is generally applicable for the identification of trait-specific genomic regions for complex traits by comparing phenotypically contrasting populations. The CSS test combines multiple pieces of evidence from the rank distribution of different selection tests in a weighted index of signatures of selection. The power of the test and its constituents (FST, ΔDAF, and XP-EHH) depends on the phenotypic and genetic divergence between the candidate and reference populations, as we demonstrated with simple binary monogenic (Randhawa et al. 2014) and complex polygenic traits (this study).\nUse of multibreed cohorts has increased the discovery of trait-specific regions because of shared linkage disequilibrium between the causal mutations and neighboring SNPs (Kemper and Goddard 2012) arising from long-term historical selection. Contrasting patterns of genomic variation at the putative regions under selection across groups increases the likelihood of capturing the signatures of selection linked to stature. In our approach, signals of selection are amplified at candidate regions across breeds within groups, whereas background noise (false-positive signals) is reduced in the rest of the genome. Such noise is usually expected from the demographic history of breed formation and random genetic drift (Seichter et al. 2012). Overall, application of the CSS method combined with grouping breeds according to their wither height identified candidate regions in the bovine genome for this complex trait.\nDetection of signatures of selection is valuable in the discovery of potential genomic regions of functional mutations affecting quantitative traits (Hayes et al. 2008). Recent investigations suggest that, in the absence of classic selective sweeps, signatures of selection for complex traits are less likely to be detected by using individual selection tests on single breed data (Kemper et al. 2014). Our approach combines multiple selection tests and grouping of phenotypically alike breeds, and has been found to be highly efficient at detecting signatures of selection and identifying candidate gene regions for complex traits. This approach makes use of existing resources under long-term historical selection and provides a relatively inexpensive entry for more detailed follow-up studies in the genetic architecture of complex traits.\n\nDetection of signatures of selection for bovine stature\nIn 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).\nWe 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.\nIt 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).\nSeveral 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.\nThe 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.\n\nValidation of known stature-associated genomic regions in cattle\nThis study validated two important candidate gene regions (regions 6 and 10) linked to stature in European breeds of cattle. Region 6 harboring NCAPG and LCORL genes located on BTA-6 has frequently shown strong signatures of selection in multiple breeds of cattle (Barendse et al. 2009; Druet et al. 2013; Flori et al. 2009; Gibbs et al. 2009; Kemper et al. 2014; Mancini et al. 2014; Pintus et al. 2013; Porto-Neto et al. 2013; Rothammer et al. 2013; Stella et al. 2010; Qanbari et al. 2014; Perez et al. 2014). Region 10 harboring PLAG1 and CHCHD7 genes on BTA-14 has been associated with height in humans (Gudbjartsson et al. 2008; Soranzo et al. 2009; Okada et al. 2010; Lettre et al. 2008; Lango Allen et al. 2010) and stature in cattle (Nishimura et al. 2012; Pryce et al. 2011; Karim et al. 2011; Fortes et al. 2013; Bolormaa et al. 2014). This locus was also identified as a candidate region based on selective sweeps in several cattle breeds that have been under strong selection for body size (Druet et al. 2013; Ramey et al. 2013; Kemper et al. 2014).\n\nGenomic regions associated with stature in European Bos taurus\nBased on strong recent selection for stature in European Bos taurus, our comparison of the large cohort with the small cohort successfully localized height-related genes at all significant regions (regions 1, 6, 10, and 11). Regions 1 and 11 can be considered novel and may contain functional variants contributing to the genetic control of bovine stature, because they harbor DUSP23 (BTA-3: 10.02-10.03 Mb) and POLR2A (BTA-19: 27.78-27.80) as candidate genes, respectively (Lanktree et al. 2011).\nThere can be some advantages of limiting body size in smaller breeds, for instance, in relation to ease of calving or resource-limited production systems. As noted above, early domestication favored selective breeding to reduce body size for ease of management (Karim et al. 2011; Ajmone-Marsan et al. 2010). With very few exceptions (e.g., Dexter), recent history of European Bos taurus breeds do not document selective breeding for smaller size. Interestingly, 60% of all significant regions can be considered novel in the small cohort and harbor stature-associated genes, namely PKN2 at region 3 (Lanktree et al. 2011), ATP5G2 and ATF7 at region 5 (Okada et al. 2010), and CAMLG, DDX46, TXNDC15, CATSPER3, and PITX1 at region 7 (Gudbjartsson et al. 2008). The functional role of these candidate genes in relation to stature is not well-documented.\n\nGenomic regions associated with stature in African Bos taurus\nFive candidate regions (2, 4, 8, 9, 12) in the African cohorts harbor nine candidate genes associated with human height identified by GWAS (Gudbjartsson et al. 2008; Soranzo et al. 2009; Okada et al. 2010; Lanktree et al. 2011; Kim et al. 2010; Weedon et al. 2008). Previously, FBP2 and PTCH1 genes underlying region 8 (BTA-8) have been associated with stature in European dairy and beef breeds, respectively (Weedon et al. 2008; Kim et al. 2010; Lanktree et al. 2011; Pryce et al. 2011). In region 12 (BTA-19), the growth hormone genes (GH1, GH2) are strong candidates for dairy production traits (Hayes et al. 2009; Rothammer et al. 2013; Mullen et al. 2010). Moreover, three genes (WDR68, MAP3K3, and LYK5) neighboring growth hormone genes have also been associated with human height in multiple GWAS reports (Gudbjartsson et al. 2008; Soranzo et al. 2009; Lanktree et al. 2011). The remaining three candidate regions, i.e., regions 2, 4, and 9, harbor the stature-associated SPAG17, SCMH1, and CYP19A1 genes, respectively (Weedon et al. 2008; Kim et al. 2010; Okada et al. 2010; Lanktree et al. 2011).\nOverall, four of the five candidate regions identified in the African cohorts are novel for their association with bovine stature. This suggests that the strategy of combining CSS and multibreed panels showed utility in the African cohorts also, although the overall proportion of candidate gene regions detected was lower compared to European cohorts. High levels of Bos indicus admixture, smaller sample size, and ascertainment bias of the Illumina BovineSNP50 chip in the African Bos taurus breeds may have impacted the power to detect regions under selection (Randhawa et al. 2014; Decker et al. 2009; Gautier et al. 2010; Gautier and Naves 2011).\n\nComparison of significant CSS regions between European and African Bos taurus\nNo candidate gene regions were found in common across the European and African cattle types. This may be due to the long-term differences in natural and production-oriented selective pressures in these diverse genetic archetypes (Edea et al. 2014; Gautier et al. 2009; Gautier and Naves 2011; Gibbs et al. 2009; Randhawa et al. 2014). Recent attempts to find the transferability of height-associated loci across human populations have shown comparable results (low consistency) for finding the same genetic variants when discoveries made in non-African ethnicities were compared in populations of African ancestry (Kang et al. 2010; Shriner et al. 2009). Our results indicate that there may be a persistent trend of dissimilarities for African genealogies across species, and some environmental factors would have shaped a comparatively different genetic architecture. We suggest that investigation of several other African breeds with sufficient sample sizes can further elaborate the nature of different candidate gene regions.\nA region on BTA-13 harboring UQCC and GDF5 genes, which we putatively linked to bovine stature (Randhawa et al. 2014), was also not detected in this study. The absence of BTA-13 genes (UQCC and GDF5) as the possible candidate for bovine stature in this study are due to the sensitivity of CSS (and its constituent tests of selection) to the sample composition because the cohort composition between the two papers is quite different regarding inclusion and exclusion of several breeds. Moreover, another gene, ASIP (related to coat color), was also located at the BTA-13 peak, and ASIP may also be another plausible candidate of the signatures of selection detected in the previous study.\nIn comparison to previous findings in cattle, we note that some of the known genes and regions related to bovine stature were not detected here, mainly because they were identified in Bos indicus and composite breeds (Pryce et al. 2011). Moreover, genetic architecture of stature is not considered fully analogous in cattle and human; our results suggest that many common genes might be participating in the physiological control of stature in the two species (Pryce et al. 2011).\nCharacterization of biological function of candidate genes could help our understanding of mechanisms underlying stature diversity. Future research should focus on regional genomic sequencing (involving multiple genes) rather than single gene-centric approaches. In addition, gene networks and functional pathway analyses on subsets of genes identified by genome-wide association or selection scans can help uncover the biological processes in complex 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