The genome response to artificial selection: a case study in dairy cattle - PubMed (original) (raw)
The genome response to artificial selection: a case study in dairy cattle
Laurence Flori et al. PLoS One. 2009.
Abstract
Dairy cattle breeds have been subjected over the last fifty years to intense artificial selection towards improvement of milk production traits. In this study, we performed a whole genome scan for differentiation using 42,486 SNPs in the three major French dairy cattle breeds (Holstein, Normande and Montbéliarde) to identify the main physiological pathways and regions which were affected by this selection. After analyzing the population structure, we estimated F(ST) within and across the three breeds for each SNP under a pure drift model. We further considered two different strategies to evaluate the effect of selection at the genome level. First, smoothing F(ST) values over each chromosome with a local variable bandwidth kernel estimator allowed identifying 13 highly significant regions subjected to strong and/or recent positive selection. Some of them contained genes within which causal variants with strong effect on milk production traits (GHR) or coloration (MC1R) have already been reported. To go further in the interpretation of the observed signatures of selection we subsequently concentrated on the annotation of differentiated genes defined according to the F(ST) value of SNPs localized close or within them. To that end we performed a comprehensive network analysis which suggested a central role of somatotropic and gonadotropic axes in the response to selection. Altogether, these observations shed light on the antagonism, at the genome level, between milk production and reproduction traits in highly producing dairy cows.
Conflict of interest statement
Competing Interests: The authors have declared that no competing interests exist.
Figures
Figure 1. Population structure.
The triangle plot represents the estimated membership of each 2803 bulls in each of the 3 assumed clusters. Each bull is represented by a point colored according to its breed of origin.
Figure 2. Observed and simulated distribution of SNP FST across (A) and within each of the three breeds (B, C, D).
Figure 3. Genome map of differentiated loci.
For each SNP the across breed FST quantile estimated on the empirical distribution (Figure 2A) is reported according to its chromosomal position.
Figure 4. Whole genome map of regions under selection based on the FST across populations.
For each of the 29 bovine autosomes, the smoothed FST is plotted against the chromosomal position (green line). For significant positions (q-value<0.05), non smoothed SNP FST are indicated by a red star.
Figure 5. Representation of the gene networks N_MON (A), N_NOR (B) and N_HOL (C).
Symbols corresponding to candidate genes are colored in red. Genes colored in grey were represented in our study but did not display any evidence of selection.
Figure 6. Representation of the gene network GN.
Symbols corresponding to genes under selection are colored in red. Genes colored in grey were represented in our study but did not display any evidence of selection. Links between GH1, GHR and β-estradiol and other GN molecules are colored in light blue, blue and green respectively.
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