Genome-wide analysis reveals selection for important traits in domestic horse breeds.

Intense selective pressures applied over short evolutionary time have resulted in homogeneity within, but substantial variation among, horse breeds. Utilizing this population structure, 744 individuals from 33 breeds, and a 54,000 SNP genotyping array, breed-specific targets of selection were identified using an F(ST)-based statistic calculated in 500-kb windows across the genome. A 5.5-Mb region of ECA18, in which the myostatin (MSTN) gene was centered, contained the highest signature of selection in both the Paint and Quarter Horse. Gene sequencing and histological analysis of gluteal muscle biopsies showed a promoter variant and intronic SNP of MSTN were each significantly associated with higher Type 2B and lower Type 1 muscle fiber proportions in the Quarter Horse, demonstrating a functional consequence of selection at this locus. Signatures of selection on ECA23 in all gaited breeds in the sample led to the identification of a shared, 186-kb haplotype including two doublesex related mab transcription factor genes (DMRT2 and 3). The recent identification of a DMRT3 mutation within this haplotype, which appears necessary for the ability to perform alternative gaits, provides further evidence for selection at this locus. Finally, putative loci for the determination of size were identified in the draft breeds and the Miniature horse on ECA11, as well as when signatures of selection surrounding candidate genes at other loci were examined. This work provides further evidence of the importance of MSTN in racing breeds, provides strong evidence for selection upon gait and size, and illustrates the potential for population-based techniques to find genomic regions driving important phenotypes in the modern horse.

Multiple congenital ocular anomalies in Icelandic horses.

BACKGROUND: Multiple congenital ocular anomalies (MCOA) syndrome is a hereditary congenital eye defect that was first described in Silver colored Rocky Mountain horses. The mutation causing this disease is located within a defined chromosomal interval, which also contains the gene and mutation that is associated with the Silver coat color (PMEL17, exon 11). Horses that are homozygous for the disease-causing allele have multiple defects (MCOA-phenotype), whilst the heterozygous horses predominantly have cysts of the iris, ciliary body or retina (Cyst-phenotype). It has been argued that these ocular defects are caused by a recent mutation that is restricted to horses that are related to the Rocky Mountain Horse breed. For that reason we have examined another horse breed, the Icelandic horse, which is historically quite divergent from Rocky Mountain horses. RESULTS: We examined 24 Icelandic horses and established that the MCOA syndrome is present in this breed. Four of these horses were categorised as having the MCOA-phenotype and were genotyped as being homozygous for the PMEL17 mutation. The most common clinical signs included megaloglobus, iris stromal hypoplasia, abnormal pectinate ligaments, iridociliary cysts occasionally extending into the peripheral retina and cataracts. The cysts and pectinate ligament abnormalities were observed in the temporal quadrant of the eyes. Fourteen horses were heterozygous for the PMEL17 mutation and were characterized as having the Cyst-phenotype with cysts and occasionally curvilinear streaks in the peripheral retina. Three additional horses were genotyped as PMEL17 heterozygotes, but in these horses we were unable to detect cysts or other forms of anomalies.One eye of a severely vision-impaired 18 month-old stallion, homozygous for the PMEL17 mutation was examined by light microscopy. Redundant duplication of non-pigmented ciliary body epithelium, sometimes forming cysts bulging into the posterior chamber and localized areas of atrophy in the peripheral retina were seen. CONCLUSIONS: The MCOA syndrome is segregating with the PMEL17 mutation in the Icelandic Horse population. This needs to be taken into consideration in breeding decisions and highlights the fact that MCOA syndrome is present in a breed that are more ancient and not closely related to the Rocky Mountain Horse breed.

Effects of estrogens on sex differentiation in Japanese quail and chicken.

Estrogen production by the female avian embryo induces development of a female phenotype of the reproductive organs whereas the low estrogen concentration in the male embryo results in a male phenotype. Treatment of female embryos with exogenous estrogens disrupts Müllerian duct development resulting in malformations and impaired oviductal function. Exposure of male embryos to estrogens results in ovotestis formation and persisting Müllerian ducts in the embryos and testicular malformations, reduced semen production and partially developed oviducts in the adult bird. Furthermore, studies in Japanese quail show that the male copulatory behavior is impaired by embryonic estrogen treatment. Results from our experiments with selective agonists for ERalpha and ERbeta suggest that the effects of estrogens on the reproductive organs are mediated via activation of ERalpha. Abundant expression of ERalpha mRNA was shown in gonads and Müllerian ducts of early Japanese quail embryos. Both ERalpha and ERbeta transcripts were detected by real-time PCR in early embryo brains of Japanese quail indicating that both receptors may be involved in sex differentiation of the brain. However, in 9-day-old quail embryo brains in situ hybridization showed expression of ERbeta mRNA, but not of ERalpha mRNA, in the medial preoptic nucleus (POM) and the bed nucleus of the stria terminalis (BSTm), areas implicated in copulatory behavior of adult male quail. Furthermore, embryonic treatment with the selective ERalpha agonist propyl pyrazol triol (PPT) had no effect on the male copulatory behavior. These results suggest that ERbeta may be important for the effects of estrogens on brain differentiation.

A potential regulatory region near the EDN3 gene may control both harness racing performance and coat color variation in horses.

The Swedish-Norwegian Coldblooded trotter and the heavier North-Swedish draught horse both descend from the North-Swedish horse, but the Coldblooded trotters have been selected for racing performance while the North-Swedish draught horse is mainly used for agricultural and forestry work. By comparing the genomes of Coldblooded trotters, North-Swedish draught horses and Standardbreds for a large number of single-nucleotide polymorphisms (SNPs), the aim of the study was to identify genetic regions that may be under selection for racing performance. We hypothesized that the selection for racing performance, in combination with unauthorized crossbreeding of Coldblooded trotters and Standardbreds, has created regions in the genome where the Coldblooded trotters and Standardbreds are similar, but differ from the North-Swedish draught horse. A fixation index (Fst) analysis was performed and sliding window Delta Fst values were calculated across the three breeds. Five windows, where the average Fst between Coldblooded trotters and Standardbreds was low and the average Fst between Coldblooded trotters and North-Swedish draught horses was high, were selected for further investigation. Associations between the most highly ranked SNPs and harness racing performance were analyzed in 400 raced Coldblooded trotters with race records. One SNP showed a significant association with racing performance, with the CC genotype appearing to be negatively associated. The SNP identified was genotyped in 1915 horses of 18 different breeds. The frequency of the TT genotype was high in breeds typically used for racing and show jumping while the frequency of the CC genotype was high in most pony breeds and draught horses. The closest gene in this region was the Endothelin3 gene (EDN3), a gene mainly involved in melanocyte and enteric neuron development. Both functional genetic and physiological studies are needed to fully understand the possible impacts of the gene on racing performance.

Sex-dependent gene expression in early brain development of chicken embryos.

BACKGROUND: Differentiation of the brain during development leads to sexually dimorphic adult reproductive behavior and other neural sex dimorphisms. Genetic mechanisms independent of steroid hormones produced by the gonads have recently been suggested to partly explain these dimorphisms. RESULTS: Using cDNA microarrays and real-time PCR we found gene expression differences between the male and female embryonic brain (or whole head) that may be independent of morphological differentiation of the gonads. Genes located on the sex chromosomes (ZZ in males and ZW in females) were common among the differentially expressed genes, several of which (WPKCI-8, HINT, MHM non-coding RNA) have previously been implicated in avian sex determination. A majority of the identified genes were more highly expressed in males. Three of these genes (CDK7, CCNH and BTF2-P44) encode subunits of the transcription factor IIH complex, indicating a role for this complex in neuronal differentiation. CONCLUSION: In conclusion, this study provides novel insights into sexually dimorphic gene expression in the embryonic chicken brain and its possible involvement in sex differentiation of the nervous system in birds.

Effects of endocrine modulators on sexual differentiation and reproductive function in male Japanese quail.

A number of environmental contaminants have been shown to interfere with the endocrine system. Many of these compounds bind to estrogen receptors, thereby potentially disrupting estrogen-regulated functions. In this paper, we review some background data on avian sexual differentiation and present some of the results from our studies on effects of estrogenic chemicals administered during sexual differentiation in the Japanese quail. Initially, our goal was to elucidate whether a decreased male sexual behavior in quail is a suitable endpoint for studying long-term effects of exposure to estrogenic compounds during sexual differentiation in ovo. We thereafter tested some environmental pollutants, suspected to act via mimicking estrogens, using the test system developed. Results from our studies on the synthetic estrogens ethinylestradiol and diethylstilbestrol, as well as the environmental pollutants bisphenol A, tetrabromobisphenol A, and o,p'-DDT are reviewed in this paper. We conclude that the Japanese quail is well suited as an animal model for studying various long-term effects after embryonic exposure to estrogenic compounds. Depressed sexual behavior proved to be the most sensitive of the variables studied in males and we find this endpoint appropriate for studying effects of endocrine modulating chemicals in the adult quail following embryonic exposure.

Genetic diversity in the modern horse illustrated from genome-wide SNP data.

Horses were domesticated from the Eurasian steppes 5,000-6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds). This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity. F(ST) calculations, parsimony, and distance analysis demonstrated relationships among the breeds that largely reflect geographic origins and known breed histories. Low levels of population divergence were observed between breeds that are relatively early on in the process of breed development, and between those with high levels of within-breed diversity, whether due to large population size, ongoing outcrossing, or large within-breed phenotypic diversity. Populations with low within-breed diversity included those which have experienced population bottlenecks, have been under intense selective pressure, or are closed populations with long breed histories. These results provide new insights into the relationships among and the diversity within breeds of horses. In addition these results will facilitate future genome-wide association studies and investigations into genomic targets of selection.

Expression of estrogen receptor-alpha and -beta mRNA in the brain of Japanese quail embryos.

The present study was conducted to investigate the mRNA expression of the two estrogen receptor (ER) subtypes ERalpha and ERbeta in the brain of Japanese quail embryos. We found expression of both ERalpha and ERbeta mRNA in homogenate of whole head from 6-day-old embryos, and in brain homogenate from 9- and 12-day-old embryos using real-time PCR. In 9- and 12-day-old embryos the ERalpha expression was higher in females than in males. We used in situ hybridization to examine the localization of the ERs in sections from male and female brains on day 9 and day 17 of incubation. On day 9, ERbeta mRNA was detected in the developing medial preoptic nucleus (POM), in the medial part of the bed nucleus of the striae terminalis (BSTm), and in the tuberal region of the hypothalamus. ERalpha signal could not be detected in the POM, the BSTm or the tuberal region in 9-day-old embryos. In 17-day-old embryos, ERbeta was highly expressed in the preoptic area, the nucleus Taeniae of the Amygdala (TnA) and the BSTm. Expression of ERalpha mRNA was detected in parts of the preoptic area and in the telencephalic TnA. No ERalpha expression was found in the BSTm, an area known to be sexually dimorphic in adults. The high embryonic expression of ERbeta in brain areas linked to sexual behavior indicates that ERbeta plays a role in sexual differentiation of the Japanese quail brain.

Localization of estrogen receptor-alpha and -betamRNA in brain areas controlling sexual behavior in Japanese quail.

Two estrogen receptors (ERs), denoted ERalpha and ERbeta, have been identified in humans and various animal species, including the Japanese quail. Estrogens play a key role in sexual differentiation and in activation of sexual behavior in Japanese quail. The distribution of ERalpha in the brain of male and female adult quail has previously been studied using immunohistochemistry, whereas in situ hybridization has been employed to study the distribution of ERbeta mRNA in males only. In this article, we used in situ hybridization to study the distribution of mRNAs for both ERalpha and ERbeta in brain areas controlling sexual behavior of Japanese quail. Our results show that both ERalpha mRNA and ERbeta mRNA are localized in areas important for sexual behavior, such as the preoptic area and associated limbic areas, in both males and females. Moreover, we found differences in distribution of mRNA for the two receptors in these areas. The results of this article support previously reported data and provide novel data on localization of ER mRNAs in adult quail brain of both sexes.

Embryonic co-exposure to methoxychlor and Clophen A50 alters sexual behavior in adult male quail.

Embryonic exposure to estrogens and estrogenic pollutants is known to demasculinize sexual behavior in adult male Japanese quail. In the present study, we administered the insecticide methoxychlor to quail eggs at a dose of 150 microg/g egg and then studied sexual behavior and other reproductive variables in adult males. In a second experiment we administered the same dose of methoxychlor together with 10 microg/g egg of the commercial polychlorinated biphenyl (PCB) mixture Clophen A50 (CA50) and also CA50 alone. Neither methoxychlor nor CA50 had any significant effects by themselves, but when they were administered together a significant reduction in male sexual behavior was observed. It seems likely that induction of biotransformation enzymes in the embryos by CA50 resulted in increased conversion of methoxychlor to the more estrogenic metabolite 2,2-bis(p-hydroxyphenyl)-1,1,1-trichloroethane (HPTE).

Effects of endocrine modulators on sex differentiation in birds.

This mini-review focuses on sexual differentiation of the reproductive organs and the brain in birds and the effects of endocrine modulators on these processes. Sex determination in birds is genetically controlled, but the genetic events implicated are largely unknown. Female birds have one Z and one W sex chromosome, while males have two Z sex chromosomes. It is not clear whether it is the presence of the W chromosome in females, the double dose of the Z chromosome in males vis-à-vis females, or both of these characteristics that are crucial for the determination of sex in birds. Oestradiol directs sexual differentiation in birds during critical periods of development. Consequently, exogenous compounds that interfere with the endogenous oestrogen balance can disrupt sexual differentiation of the reproductive organs and the brain. Therefore, sexual differentiation in birds provides a good model for studying the effects of endocrine modulators at various biological levels from gene expression to behaviour. Some compounds known to be present in the environment can alter endocrine function and have adverse effects when administered during development, resulting in alterations in gonads, accessory sexual organs, and behaviour. Data reviewed in this paper are mostly from laboratory studies on endocrine modulators with oestrogenic activity, whereas evidence for adverse effects of pollutants on sexual differentiation in avian wildlife is scarce.