Background: Bovine frontonasal dysplasias like arhinencephaly, synophthalmia, cyclopia and anophthalmia are sporadic congenital facial malformations. In this study, computed tomography, necropsy, histopathological examinations and whole genome sequencing on an Illumina NextSeq500 were performed to characterize a stillborn Limousin calf with frontonasal dysplasia. In order to identify private genetic and structural variants, we screened whole genome sequencing data of the affected calf and unaffected relatives including parents, a maternal and paternal halfsibling. Results: The stillborn calf exhibited severe craniofacial malformations. Nose and maxilla were absent, mandibles were upwardly curved and a median cleft palate was evident. Eyes, optic nerve and orbital cavities were not developed and the rudimentary orbita showed hypotelorism. A defect centrally in the front skull covered with a membrane extended into the intracranial cavity. Aprosencephaly affected telencephalic and diencephalic structures and cerebellum. In addition, a shortened tail was seen. Filtering whole genome sequencing data revealed a private frameshift variant within the candidate gene ZIC2 in the affected calf. This variant was heterozygous mutant in this case and homozygous wild type in parents, half-siblings and controls. Conclusions: We found a novel ZIC2 frameshift mutation in an aprosencephalic Limousin calf. The origin of this variant is most likely due to a de novo mutation in the germline of one parent or during very early embryonic development. To the authors’ best knowledge, this is the first identified mutation in cattle associated with bovine frontonasal dysplasia.

Modern horses represent heterogeneous populations specifically selected for appearance and performance. Genomic regions under high selective pressure show characteristic runs of homozygosity (ROH) which represent a low genetic diversity. This study aims at detecting the number and functional distribution of ROHs in different horse populations using next generation sequencing data. Next generation sequencing was performed for two Sorraia, one Dülmen Horse, one Arabian, one Saxon-Thuringian Heavy Warmblood, one Thoroughbred and four Hanoverian. After quality control reads were mapped to the reference genome EquCab2.70. ROH detection was performed using PLINK, version 1.07 for a trimmed dataset with 11,325,777 SNPs and a mean read depth of 12. Stretches with homozygous genotypes of >40 kb as well as >400 kb were defined as ROHs. SNPs within consensus ROHs were tested for neutrality. Functional classification was done for genes annotated within ROHs using PANTHER gene list analysis and functional variants were tested for their distribution among breed or non-breed groups. ROH detection was performed using whole genome sequences of ten horses of six populations representing various breed types and non-breed horses. In total, an average number of 3492 ROHs were detected in windows of a minimum of 50 consecutive homozygous SNPs and an average number of 292 ROHs in windows of 500 consecutive homozygous SNPs. Functional analyses of private ROHs in each horse revealed a high frequency of genes affecting cellular, metabolic, developmental, immune system and reproduction processes. In non-breed horses, 198 ROHs in 50-SNP windows and seven ROHs in 500-SNP windows showed an enrichment of genes involved in reproduction, embryonic development, energy metabolism, muscle and cardiac development whereas all seven breed horses revealed only three common ROHs in 50-SNP windows harboring the fertility-related gene YES1. In the Hanoverian, a total of 18 private ROHs could be shown to be located in the region of genes potentially involved in neurologic control, signaling, glycogen balance and reproduction. Comparative analysis of homozygous stretches common in all ten horses displayed three ROHs which were all located in the region of KITLG, the ligand of KIT known to be involved in melanogenesis, haematopoiesis and gametogenesis. The results of this study give a comprehensive insight into the frequency and number of ROHs in various horses and their potential influence on population diversity and selection pressures. Comparisons of breed and non-breed horses suggest a significant artificial as well as natural selection pressure on reproduction performance in all types of horse populations.

Body size is an important characteristic for horses of various breeds and essential for the classification of ponies concerning the limit value of 148 cm (58.27 inches) height at the withers. Genome-wide association analyses revealed the highest associated quantitative trait locus for height at the withers on horse chromosome (ECA) 3 upstream of the candidate gene LCORL. Using 214 Hanoverian horses genotyped on the Illumina equine SNP50 BeadChip and 42 different horse breeds across all size ranges, we confirmed the highly associated single nucleotide polymorphism BIEC2-808543 (−log₁₀P = 8.3) and the adjacent gene LCORL as the most promising candidate for body size. We investigated the relative expression levels of LCORL and its two neighbouring genes NCAPG and DCAF16 using quantitative real-time PCR (RT-qPCR). We could demonstrate a significant association of the relative LCORL expression levels with the size of the horses and the BIEC2-808543 genotypes within and across horse breeds. In heterozygous C/T-horses expression levels of LCORL were significantly decreased by 40% and in homozygous C/C-horses by 56% relative to the smaller T/T-horses. Bioinformatic analyses indicated that this SNP T>C mutation is disrupting a putative binding site of the transcription factor TFIID which is important for the transcription process of genes involved in skeletal bone development. Thus, our findings suggest that expression levels of LCORL play a key role for body size within and across horse breeds and regulation of the expression of LCORL is associated with genetic variants of BIEC2-808543. This is the first functional study for a body size regulating polymorphism in horses and a further step to unravel the mechanisms for understanding the genetic regulation of body size in horses.

The effects of 3 different furnished cage systems (Aviplus, Eurovent 625a, Eurovent 625A) on 2 different laying hen strains [Lohmann Selected Leghorn (LSL), Lohmann Brown (LB)] were examined for the traits of production, egg quality, bone strength, claw length, and keel bone status. Two trials were carried out in which all hens received identical feeding and management. In brown hens, the traits egg production per average hen housed, cracked eggs, feed conversion, egg weight, and humerus breaking strength were significantly higher than in white hens. Furthermore, the claws of the brown hens were shorter than those of white hens. There were more dirty eggs, higher shell density, and fewer keel bone deformities in white hens than in brown hens. In the Aviplus system, egg production per average hen housed was higher than in the other systems, whereas shell thickness and density were lower. Humerus strength was also higher in the Aviplus than in the Eurovent 625a system, whereas there was no significant difference in tibia strength among the 3 systems. The shortest claws were found in the Aviplus system, and the fewest keel bone deformities occurred in the Eurovent 625a system. The study showed that the high standards of conventional cages for production and egg quality were met in furnished cages and that bone strength was significantly greater than in conventional cages. Claw shortening devices in furnished cages seemed satisfactory, because claws were generally short. However, the occurrence of keel bone deformities due to the intensive use of perches seemed to be a problem of furnished cages.

A data set constituting a total of 310,109 Hanoverian warmblood horses was analyzed to ascertain the genetic variability, coefficients of inbreeding, and gene contributions of foreign populations. The reference population contained all Hanoverian horses born from 1980 to 2000. In addition, Hanoverian stallions born from 1980 to 1995 and Hanoverian breeding mares from the birth years 1980 to 1995 with registered foals were analyzed for the same genetic parameters. The average complete generation equivalent was approximately 8.43 for the reference population. The mean coefficient of inbreeding was 1.33, 1.19, and 1.29% for the reference population, stallions, and breeding mares, respectively. The effective number of founders was largest in stallions (364.3) and smallest in the reference population (244.9). The ratio between the effective number of founders and the effective number of ancestors was 3.15 for the reference population, 3.25 for the stallions, and 3.06 for the breeding mares. The effective population size in the Hanoverian warmblood reference population was 372.34. English Thoroughbreds contributed nearly 35% of the genes to the Hanoverian reference population and even slightly greater contributions (39%) to the stallions. Trakehner and Arab horses contributed approximately 8 and 2.7%, respectively, to the Hanoverian gene pool. The most important male ancestors were Aldermann I from the A/E line, Fling from the F/W line, and Absatz from the Trakehner line, whereas the breeding mare Costane had the greatest contribution to the reference population, stallions, and breeding mares. From 1996 onward, the stallions Weltmeyer and Donnerhall had the largest genetic impact on the Hanoverian horse population.

(2005). Keeping laying hens in furnished cages and an aviary housing system enhances their bone stability. British Poultry Science: Vol. 46, No. 5, pp. 536-544.