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 Silkie chicken has been a model of melanoctye precursor and neural crest cell migration and proliferation in the developing embryo due to its extensive hyperpigmentation of dermal and connective tissues. Although previous studies have focused on the distribution and structure of the Silkie's pigment or the general mechanisms by which this phenotype presents itself, the causal genetic variants have not been identified. Classical breeding experiments have determined this trait to be controlled by 2 interacting genes, the sex-linked inhibitor of dermal melanin (Id) and autosomal fibromelanosis (Fm) genes. Genome-wide single nucleotide polymorphism (SNP)-trait association analysis was used to detect genomic regions showing significant association with these pigmentation genes in 2 chicken mapping populations designed to segregate independently for Id and Fm. The SNP showing the highest association with Id was located at 72.3 Mb on chromosome Z and 10.3-13.1 Mb on chromosome 20 showed the highest association with Fm. Prior to this study, the linkage group to which Fm belonged was unknown. Although the primary focus of this study was to identify loci contributing to dermal pigmentation in the Silkie chicken, loci associated with various other morphological traits segregating in these populations were also detected. A single SNP in a highly conserved cis-regulatory region of Sonic Hedgehog was significantly associated with polydactyly (Po). Genomic regions in association with silkie feathering or hookless (h), feathered legs (Pti), vulture hock (V), rose comb (R), and duplex comb (D) were also identified.

The chicken major histocompatibility complex (MHC) is commonly defined by serologic reactions of erythrocytes with antibodies specific to the highly polymorphic MHC class I (BF) and MHC class IV (BG) antigens. The microsatellite marker LEI0258 is known to be physically located within the MHC, between the BG and BF regions. DNA from various serologically defined MHC haplotypes was amplified by polymerase chain reaction with primers surrounding this marker. Twenty-six distinctive allele sizes were identified. Some serologically well-defined MHC haplotypes shared a common LEI0258 allele size but could be distinguished either by the addition of information from another nearby marker (MCW0371) or by small indels or single nucleotide polymorphism (SNP) differences between the alleles. The association between LEI0258 allele and serologically defined MHC haplotype was very consistent for the same haplotype from multiple sources. Sequence information for the region defined by LEI0258 was obtained for 51 different haplotypes. Two internal repeats whose lengths were 13 and 12 bp, respectively, are the primary basis for allelic variability. Allele size variation ranges from 182 to 552 bp. Four indels and five SNPs in the surrounding sequence provide additional means for distinguishing alleles. Typing with LEI0258 and MCW0371 will be useful in identifying MHC haplotypes in outbred populations of chickens particularly for the initial development of serological reagents.

Molecular genetic selection on individual genes is a promising method to genetically improve economically important traits in chickens. A resource population was developed to study the genetics of growth, body composition, skeletal integrity, and metabolism traits. Broiler sires were crossed to dams of 2 diverse, highly inbred lines (Leghorn and Fayoumi), and the F1 birds were intermated by dam line to produce broiler-Leghorn and broiler-Fayoumi F2 offspring. Growth, body composition, skeletal integrity, and hormonal and metabolic factors were measured in 713 F2 individuals. Insulin-like growth factor-I (IGF1) was selected for study as a biological and positional candidate gene. A single nucleotide polymorphism (SNP) was identified between the founder lines in the IGF1 promoter region, and a PCR-RFLP assay was developed. A mixed model was used to statistically analyze associations of IGF1-SNP1 with phenotypic traits. The IGF1-SNP1 had significant associations with most recorded traits, except metabolic traits. Strong interactions between the IGF1 gene and genetic background on growth traits in the 2 F2 populations suggest that genetic interaction is an important aspect for consideration before using the IGF1-SNP1 in marker-assisted selection programs. Several beneficial effects (improved growth, increased breast muscle weight, decreased abdominal fat, and enhanced skeletal integrity) associated with 1 allele indicate the presence of 1 or more loci near IGF1-SNP1 controlling biologically diverse and economically important traits in chickens.

Broiler breeder pullets were divided into two groups at 21 wk of age. One group was given free access to feed (ad libitum) and the other fed a limited amount of feed (restricted). At 22 wk, all birds were photostimulated and maintained throughout an egg-laying cycle ending at 36 wk. Samples of liver and abdominal fat pad were collected just before photostimulation (prelight), after photostimulation at first egg and at peak egg production (plateau). Hepatic expression of sterol regulatory element binding protein-1, ATP-citrate lyase, fatty acid synthase, malic enzyme, acetyl-CoA carboxylase and stearoyl-CoA (Delta9) desaturase 1 genes in ad libitum birds declined from their highest levels just before photostimulation as the birds came into and maintained egg production. In contrast, the restricted birds had significant (P < 0.05) increases in the expression of these genes after photostimulation at first egg with a subsequent decline as they reached peak egg production. Hepatic expression of fatty acid binding protein, VLDL apolipoprotein (apoVLDL-II) and apoB genes increased significantly (P < 0.05) in both ad libitum and restricted breeders after photostimulation, whereas apoA1 gene expression declined during this time. Abdominal fat pad weights were significantly (P < 0.05) higher in the ad libitum compared with restricted birds after photostimulation. Lipoprotein lipase in this tissue showed a pattern of expression similar to that observed for the hepatic lipogenic enzyme genes. In conclusion, feed restriction during the pullet-to-breeder transition period significantly (P < 0.05) altered hepatic lipogenic gene expression in broiler breeders.

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Leptin, the polypeptide hormone encoded by the obese gene, is secreted by adipose tissue and has been shown to induce satiety and increase energy expenditure in mammals. In this study, we confirmed the presence of a leptin homolog in liver and adipose tissues of broiler chickens. Leptin expression was also detected in chicken embryonic liver and yolk sac. The effects of hormone treatment on leptin expression in chickens were also investigated. Leptin expression in the liver is increased by insulin and dexamethasone and decreased by glucagon and estrogen. There was no induction of leptin expression in adipose tissue by any treatment, whereas only estrogen decreased adipose expression. The differential effect on liver and adipose tissue suggests that adipocytes in chickens may be expressing leptin at a maximal rate or that its mechanism of expression regulation differs from liver. The localization of leptin expression and tissue-specific effects of hormone treatments on leptin expression observed in chickens may indicate a relationship between leptin and avian lipid metabolism.

The majority of pregnancy loss in cattle occurs between Days 8 and 16 of gestation, coincident with the initiation of conceptus elongation and the onset of maternal recognition of pregnancy. Differences in conceptus length on the same day of gestation may be related to an inherent lack of developmental competency or may simply be a consequence of asynchrony with the maternal environment. The objective of this work was to characterize differential patterns of mRNA expression between short and long bovine conceptuses recovered on Day 15 of gestation. Embryos were produced from super-ovulated Holstein donor cows, and groups of Grade-1 and Grade-3 compact morulas were transferred into recipient heifers at Day 6.5 of their cycle. Conceptuses were recovered at Day 15 of gestation, and measured to assess overall length and area. Total RNA was extracted and analyzed on individual GeneChip Bovine Genome Arrays (Affymetrix, Santa Clara, CA). Gene expression was compared between conceptuses derived from the transfer of Grade-1 versus Grade-3 embryos; no differences were identified in the profiles of Day-15 conceptuses of these different embryo grades. When gene expression was compared between conceptuses classified as either short (mean length of 4.2 ± 0.1 mm [standard error]) or long (24.7 ± 1.9 mm) upon recovery at Day 15 of gestation, a total of 348 genes were differentially expressed. Of these, 221 genes were up-regulated and 127 were down-regulated in long compared to short conceptuses. In summary, differences in gene expression were identified between conceptuses recovered on Day 15 of gestation, based on their length. These data may be used to identify genes and cellular pathways involved in enhanced conceptus elongation that could serve as markers of successful pregnancy. Mol. Reprod. Dev. 83: 424-441, 2016. © 2016 Wiley Periodicals, Inc.