A long-term selection experiment for high (HWS) and low (LWS) BW at 8 wk of age (BW8) was conducted in White Plymouth Rock chickens. Over 54 generations of selection, responses to bidirectional selection were profound. Increase in BW8 in line HWS was linear, and there was a significant quadratic response in line LWS for BW at both 4 and 8 wk of age. Although there is no indication that line HWS has come close to approaching a selection limit in more than 50 generations, selection limits occurred in line LWS chickens at generation 48 for females and generation 50 for males. Evidence also exists that one or more beneficial mutations have occurred in line HWS, aiding in progressive increases in BW8 over generations. Analyses of ratios of BW at 4 wk of age with those at 8 wk of age (ratio 4/8) revealed that LWS females grew proportionately faster through 4 wk of age than LWS males or HWS chickens. Comparisons of the selected lines with contemporary lines in which selection had been relaxed (discontinued) indicated that, in line HWS, the relaxed lines generally regressed toward original (preselection) values, suggesting that the linear response to single-trait selection was at least partially due to continued genetic variance. In LWS chickens, a series of plateaus in selection response occurred, but relaxed contemporary lines still regressed toward preselection values for BW8. In spite of the length of this selection experiment (54 generations), genetic variance and beneficial mutations have allowed continued, linear response to selection for increased BW8. Response to selection for decreased BW8 has been tempered by physiological barriers that have decreased survival of young chicks or the ability of females to reproduce. These findings are discussed in a historical perspective.

The ability of a population to adapt to changes in their living conditions, whether in nature or captivity, often depends on polymorphisms in multiple genes across the genome. In-depth studies of such polygenic adaptations are difficult in natural populations, but can be approached using the resources provided by artificial selection experiments. Here, we dissect the genetic mechanisms involved in long-term selection responses of the Virginia chicken lines, populations that after 40 generations of divergent selection for 56-day body weight display a 9-fold difference in the selected trait. In the F15 generation of an intercross between the divergent lines, 20 loci explained >60% of the additive genetic variance for the selected trait. We focused particularly on fine-mapping seven major QTL that replicated in this population and found that only two fine-mapped to single, bi-allelic loci; the other five contained linked loci, multiple alleles or were epistatic. This detailed dissection of the polygenic adaptations in the Virginia lines provides a deeper understanding of the range of different genome-wide mechanisms that have been involved in these long-term selection responses. The results illustrate that the genetic architecture of a highly polygenic trait can involve a broad range of genetic mechanisms, and that this can be the case even in a small population bred from founders with limited genetic diversity.

The abundance of gut microbiota can be viewed as a quantitative trait, which is affected by the genetics and environment of the host. To quantify the effects of host genetics, we calculated the heritability of abundance of specific microorganisms and genetic correlations among them in the gut microbiota of two lines of chickens maintained under the same husbandry and dietary regimes. The lines, which originated from a common founder population, had undergone >50 generations of selection for high (HW) or low (LW) 56-day body weight and now differ by more than 10-fold in body weight at selection age. We identified families of Paenibacillaceae, Streptococcaceae, Helicobacteraceae, and Burkholderiaceae that had moderate heritabilities. Although there were no obvious phenotypic correlations among gut microbiota, significant genetic correlations were observed. Moreover, the effects were modified by genetic selection for body weight, which altered the quantitative genetic background of the host. Heritabilities for Bacillaceae, Flavobacteriaceae, Helicobacteraceae, Comamonadaceae, Enterococcaceae, and Streptococcaceae were moderate in LW line and little to zero in the HW line. These results suggest that loci associated with these microbiota families, while exhibiting genetic variation in LW, have been fixed in HW line. Also, long term selection for body weight has altered the genetic correlations among gut microbiota. No microbiota families had significant heritabilities in both the LW and HW lines suggesting that the presence and/or absence of a particular microbiota family either has a strong growth promoting or inhibiting effect, but not both. These results demonstrate that the quantitative genetics of the host have considerable influence on the gut microbiota.

BackgroundArtificial selection provides a powerful approach to study the genetics of adaptation. Using selective-sweep mapping, it is possible to identify genomic regions where allele-frequencies have diverged during selection. To avoid false positive signatures of selection, it is necessary to show that a sweep affects a selected trait before it can be considered adaptive. Here, we confirm candidate, genome-wide distributed selective sweeps originating from the standing genetic variation in a long-term selection experiment on high and low body weight of chickens.ResultsUsing an intercross between the two divergent chicken lines, 16 adaptive selective sweeps were confirmed based on their association with the body weight at 56 days of age. Although individual additive effects were small, the fixation for alternative alleles across the loci contributed at least 40 % of the phenotypic difference for the selected trait between these lines. The sweeps contributed about half of the additive genetic variance present within and between the lines after 40 generations of selection, corresponding to a considerable portion of the additive genetic variance of the base population.ConclusionsLong-term, single-trait, bi-directional selection in the Virginia chicken lines has resulted in a gradual response to selection for extreme phenotypes without a drastic reduction in the genetic variation. We find that fixation of several standing genetic variants across a highly polygenic genetic architecture made a considerable contribution to long-term selection response. This provides new fundamental insights into the dynamics of standing genetic variation during long-term selection and adaptation.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0785-z) contains supplementary material, which is available to authorized users.

SummarySex-linked barring, a common plumage colour found in chickens, is characterized by black and white barred feathers. Previous studies have indicated that the white bands are caused by an absence of melanocytes in the feather follicle during the growth of this region. Here, we show that Sex-linked barring is controlled by the CDKN2A ⁄ ⁄ B locus, which encodes the INK4b and ARF transcripts. We identified two non-coding mutations in CDKN2A that showed near complete association with the phenotype. In addition, two missense mutations were identified at highly conserved sites, V9D and R10C, and every bird tested with a confirmed Sex-linked barring phenotype carried one of these missense mutations. Further work is required to determine if one of these or a combined effect of two or more CDKN2A mutations is causing Sex-linked barring. This novel finding provides the first evidence that the tumour suppressor locus CDKN2A ⁄ ⁄ B can affect pigmentation phenotypes and sheds new light on the functional significance of this gene. IntroductionThe diversity of pigmentation in both natural populations and domesticated animals is one of the most studied traits in biology. Pigmentation diversity became a subject for scientific studies in the beginning of the 20th century after the rediscovery of Mendelian genetics (Bateson, 1902;Haldane et al., 1915). Hundreds of genes have been discovered that influence pigmentation in a range of species. In just the mouse, 159 genes affecting pigmentation have been reported (Montoliu et al., 2009). Many of the described causative mutations alter the coding sequence and thus have been straightforward to pinpoint. However, the genetic basis for the bewildering diversity of pigmentation patterns among species, particularly among birds, is poorly understood and is unlikely to be determined by simple loss-of-function mutations. Plumage colour and patterning show great variation among breeds of chickens. To date, five loci controlling SignificanceThe CDKN2A ⁄ B locus has a key role in cell cycle regulation. It encodes both the ARF protein, which binds the p53-stabilizing protein MDM2, and the INK4 protein, a cyclin-dependent kinase inhibitor. Loss-of-function mutations in CDKN2A are responsible for familiar forms of human melanoma. Our study establishes a new animal model for functional studies of CDKN2A because it provides conclusive evidence that mutation(s) in this gene underlies the Sex-linked barring plumage colour in chickens. A barred feather pattern is very common among birds, and to our knowledge, this is the first time that a gene controlling such a pigmentation pattern has been identified.ª