Powerful detection of polygenic selection and evidence of environmental adaptation in US beef cattle

Abstract

Selection is a basic principle of evolution. Many approaches and studies have identified DNA mutations rapidly selected to high frequencies, which leave pronounced signatures on the surrounding sequence (selective sweeps). However, for many important complex, quantitative traits, selection does not leave these intense signatures. Instead, hundreds or thousands of loci experience small changes in allele frequencies, a process called polygenic selection. We know that directional selection and local adaptation are actively changing genomes; however we have been unable to identify the genomic loci responding to this polygenic, complex selection. Here we show that the use of novel dependent variables in linear mixed models (which allow us to account for population structure, relatedness, inbreeding) identify complex, polygenic selection and local adaptation. Thousands of loci are responding to artificial directional selection and hundreds of loci have evidence of local adaptation. While advanced reproduction and genomic technologies are increasing the rate of directional selection, local adaptation is being lost. In a changing climate, the loss of local adaptation may be especially problematic. These selection mapping approaches can be used in evolutionary, model, and agriculture contexts.

Development of a genetic evaluation for hair shedding in American Angus cattle to improve thermotolerance

“…Mutations in CEP290 affect cilia formation, and are believed to interact with Bardet-Biedl syndrome (BBS) proteins [62]. Recently, BBS1 was associated with local adaptation in Red Angus cattle [19].…”

“…An alternative strategy is the exploitation of standing genetic variation in the population of interest. Recently, interest has grown in augmenting national genetic evaluations with predictions of regional adaptability and suitability [17][18][19], particularly by using novel traits [20]. Here, we develop parameters for a prototype national genetic evaluation of hair shedding in American Angus cattle, a novel trait that directly influences cattle's ability to dissipate heat.…”

Development of a genetic evaluation for hair shedding in American Angus cattle to improve thermotolerance

“…Recently, BBS1 was associated with local adaptation in Red Angus cattle (18). Further, the strength of these associations on chromosome 5 could be due to multiple causal mutations (62) in this locus from 12 Mb to 28…”

Demographic history, cold adaptation, and recent NRAP recurrent convergent evolution at amino acid residue 100 in the world northernmost cattle from Russia

“…In the glass eel fixation of an alternative NRAP allele was associated with latitude and river water temperature in a landscape genomics study (71). Interestingly, in a recent environmental GWAS study (72) variants in the NRAP gene were associated with environmental adaptations in the US Simmental cattle.…”