Dermal hyperpigmentation or Fibromelanosis (FM) is one of the few examples of skin pigmentation phenotypes in the chicken, where most other pigmentation variants influence feather color and patterning. The Silkie chicken is the most widespread and well-studied breed displaying this phenotype. The presence of the dominant FM allele results in extensive pigmentation of the dermal layer of skin and the majority of internal connective tissue. Here we identify the causal mutation of FM as an inverted duplication and junction of two genomic regions separated by more than 400 kb in wild-type individuals. One of these duplicated regions contains endothelin 3 (EDN3), a gene with a known role in promoting melanoblast proliferation. We show that EDN3 expression is increased in the developing Silkie embryo during the time in which melanoblasts are migrating, and elevated levels of expression are maintained in the adult skin tissue. We have examined four different chicken breeds from both Asia and Europe displaying dermal hyperpigmentation and conclude that the same structural variant underlies this phenotype in all chicken breeds. This complex genomic rearrangement causing a specific monogenic trait in the chicken illustrates how novel mutations with major phenotypic effects have been reused during breed formation in domestic animals. The process of animal domestication has been a long and ongoing effort of the human race to cultivate beneficial traits in agriculturally productive or otherwise beneficial species. We are just now beginning to understand the effect this type of selection pressure has had on genetic variation and overall genome architecture using quickly advancing modern genetic and genomic technologies. Here we show how along the path of animal domestication a single large rearrangement involving a duplication and inversion of two distinct regions of the chicken genome occurred, likely disrupting long-range cis-regulatory elements of endothelin 3 (EDN3) and resulting in a very extreme skin pigmentation phenotype. Dermal hyperpigmentation, or Fibromelanosis (FM), is a defining characteristic of the Silkie chicken breed, which originates in China. Chickens very similar to the Silkie have been described in ancient Chinese texts on traditional medicine, illustrating how unique phenotypes in domesticated animals are incorporated into human culture and tradition that persists to this day. The presence of the same rearrangement in other FM chicken breeds found around the world highlights both the causality of this mutation as well as how humans serve to spread genetic variation linked to novel traits in domestic animals.

To understand the genetic mechanisms leading to phenotypic differentiation, it is important to identify genomic regions under selection. We scanned the genome of two chicken lines from a single trait selection experiment, where 50 generations of selection have resulted in a 9-fold difference in body weight. Analyses of nearly 60,000 SNP markers showed that the effects of selection on the genome are dramatic. The lines were fixed for alternative alleles in more than 50 regions as a result of selection. Another 10 regions displayed strong evidence for ongoing differentiation during the last 10 generations. Many more regions across the genome showed large differences in allele frequency between the lines, indicating that the phenotypic evolution in the lines in 50 generations is the result of an exploitation of standing genetic variation at 100s of loci across the genome. Evolution is the process of change in response to selection. Typically, this results in more or less obvious changes to the appearance and physical properties—the phenotype—of an organism. However, these changes reflect underlying changes to the genome of that organism—the genotype. We examine the genomes of two lines of chickens that share a very recent ancestry but have been subjected to 50 generations of selection for high or low body weight, respectively. The effect of selection on the phenotype was dramatic, where on average high line birds are nine times heavier than low line ones. The effect on the genotype was equally dramatic, with a large number of changes distributed all across the genome. We observed more than 100 regions where different genetic variants were established in the two lines of chickens, which is considerable given the number of generations involved.

Background: Thousands of years of natural and artificial selection have resulted in indigenous cattle breeds that are well-adapted to the environmental challenges of their local habitat and thereby are considered as valuable genetic resources. Understanding the genetic background of such adaptation processes can help us design effective breeding objectives to preserve local breeds and improve commercial cattle. To identify regions under putative selection, GGP HD 150 K single nucleotide polymorphism (SNP) arrays were used to genotype 106 individuals representing five Swedish breeds i.e. native to different regions and covering areas with a subarctic cold climate in the north and mountainous west, to those with a continental climate in the more densely populated south regions. Results: Five statistics were incorporated within a framework, known as de-correlated composite of multiple signals (DCMS) to detect signatures of selection. The obtained p -values were adjusted for multiple testing (FDR < 5%), and significant genomic regions were identified. Annotation of genes in these regions revealed various verified and novel candidate genes that are associated with a diverse range of traits, including e.g. high altitude adaptation and response to hypoxia ( DCAF8 , PPP1R12A , SLC16A3 , UCP2 , UCP3 , TIGAR ), cold acclimation ( AQP3 , AQP7 , HSPB8 ), body size and stature ( PLAG1 , KCNA6 , NDUFA9 , AKAP3 , C5H12orf4 , RAD51AP1 , FGF6 , TIGAR , CCND2 , CSMD3 ), resistance to disease and bacterial infection ( CHI3L2 , GBP6 , PPFIBP1 , REP15 , CYP4F2 , TIGD2 , PYURF , SLC10A2 , FCHSD2 , ARHGEF17 , RELT , PRDM2 , KDM5B ), reproduction ( PPP1R12A , Z FP36L2 , CSPP1 ), milk yield and components ( NPC1L1 , NUDCD3 , ACSS1 , FCHSD2 ), growth and feed efficiency ( TMEM68 , TGS1 , LYN , XKR 4 , FOXA2 , GBP2 , GBP5 , FGD6 ), and polled phenotype ( URB1 , EVA1C ). Conclusions: We identified genomic regions that may provide background knowledge to understand the mechanisms that are involved in economic traits and adaptation to cold climate in cattle. Incorporating p -values of different statistics in a single DCMS framework may help select and prioritize candidate genes for further analyses.

This study aimed at investigating the genetic diversity, relationship and population structure of 110 local Swedish chickens derived from five breeds (Gotlandshöna, Hedemorahöna, Öländsk dvärghöna, Skånsk blommehöna, and Bohuslän- Dals svarthöna, in the rest of the paper the shorter name Svarthöna is used) using 24 microsatellite markers. In total, one hundred thirteen alleles were detected in all populations, with a mean of 4.7 alleles per locus. For the five chicken breeds, the observed and expected heterozygosity ranged from 0.225 to 0.408 and from 0.231 to 0.515, with the lowest scores for the Svarthöna and the highest scores for the Skånsk blommehöna breeds, respectively. Similarly, the average within breed molecular kinship varied from 0.496 to 0.745, showing high coancestry, with Skånsk blommehöna having the lowest and Svarthöna the highest coancestry. Furthermore, all breeds showed significant deviations from Hardy-Weinberg expectations. Across the five breeds, the global heterozygosity deficit (F_IT) was 0.545, population differentiation index (F_ST) was 0.440, and the global inbreeding of individuals within breed (F_IS) was 0.187. The phylogenetic relationships of chickens were examined using neighbor-joining trees constructed at the level of breeds and individual samples. The neighbor-joining tree constructed at breed level revealed two main clusters, with Hedemorahöna and Öländsk dvärghöna breeds in one cluster, and Gotlandshöna and Svarthöna breeds in the second cluster leaving the Skånsk blommehöna in the middle. Based on the results of the STRUCTURE analysis, the most likely number of clustering of the five breeds was at K = 4, with Hedemorahöna, Gotlandshöna and Svarthöna breeds forming their own distinct clusters, while Öländsk dvärghöna and Skånsk blommehöna breeds clustered together. Losses in the overall genetic diversity of local Swedish chickens due to breeds extinction varied from -1.46% to -6.723%. The results of the current study can be used as baseline genetic information for genetic conservation program, for instance, to control inbreeding and to implement further genetic studies in local Swedish chickens.

DNA methylation in CpGs dinucleotides is associated with high mutability and disappearance of CpG sites during evolution. Although the high mutability of CpGs is thought to be relevant for vertebrate evolution, very little is known on the role of CpG-related mutations in the genomic diversification of vertebrates. Our study analysed genetic differences in chickens, between Red Junglefowl (RJF; the living closest relative to the ancestor of domesticated chickens) and domesticated breeds, to identify genomic dynamics that have occurred during the process of their domestication, focusing particularly on CpG-related mutations. Single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) between RJF and these domesticated breeds were assessed in a reduced fraction of their genome. Additionally, DNA methylation in the same fraction of the genome was measured in the sperm of RJF individuals to identify possible correlations with the mutations found between RJF and the domesticated breeds. Our study shows that although the vast majority of CpG-related mutations found relate to CNVs, CpGs disproportionally associate to SNPs in comparison to CNVs, where they are indeed substantially under-represented. Moreover, CpGs seem to be hotspots of mutations related to speciation. We suggest that, on the one hand, CpG-related mutations in CNV regions would promote genomic ‘flexibility’ in evolution, i.e., the ability of the genome to expand its functional possibilities; on the other hand, CpG-related mutations in SNPs would relate to genomic ‘specificity’ in evolution, thus, representing mutations that would associate with phenotypic traits relevant for speciation.