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The transcriptional regulation of gene expression in higher organisms is essential for different cellular and biological processes. These processes are controlled by transcription factors and their combinatorial interplay, which are crucial for complex genetic programs and transcriptional machinery. The regulation of sex-biased gene expression plays a major role in phenotypic sexual dimorphism in many species, causing dimorphic gene expression patterns between two different sexes. The role of transcription factor (TF) in gene regulatory mechanisms so far has not been studied for sex determination and sex-associated colour patterning in zebrafish with respect to phenotypic sexual dimorphism. To address this open biological issue, we applied bioinformatics approaches for identifying the predicted TF pairs based on their binding sites for sex and colour genes in zebrafish. In this study, we identified 25 (e.g., STAT6-GATA4, JUN-GATA4, SOX9-JUN) and 14 (e.g., IRF-STAT6, SOX9-JUN, STAT6-GATA4) potentially cooperating TFs based on their binding patterns in promoter regions for sex determination and colour pattern genes in zebrafish, respectively. The comparison between identified TFs for sex and colour genes revealed several predicted TF pairs (e.g., STAT6-GATA4, JUN-SOX9) are common for both phenotypes, which may play a pivotal role in phenotypic sexual dimorphism in zebrafish.

Simple Summary The quality of chicken eggs is important for reasons of food safety and the consumers’ choice at the point of sale. Faba beans are a regionally produced alternative to soybeans, but they contain substances that could influence the egg quality. The aim of the present study was to test the influence of feeding faba beans on the egg quality of six different chicken genotypes including traditional breeds. The tested chicken genotypes were two local breeds, the Vorwerkhuhn and the Bresse Gauloise, as well as the commercial line White Rock and crossbreds thereof. The genotype had an influence on yolk weight, Haugh units, yolk and shell color, the frequency of inclusions in the eggs and the composition of the eggs. The feeding of faba beans influenced the yolk and shell color as well as Haugh units and shell portion. Egg traits were significantly influenced by the genotype. Abstract The quality of chicken eggs is an important criterion for food safety and the consumers’ choice at the point of sale. Several studies have shown that egg quality can be influenced by the chickens’ genotype and by the composition of the diet. The present study aimed to evaluate the effect of faba beans as a substitute for soybeans in the diet of chickens originating from traditional low-performance breeds in comparison with high-performing laying type hens and their crosses on egg quality parameters. Chickens of six different genotypes were fed either with a feed mix containing 20% faba beans with high or low vicin contents or, as a control, a feed mix containing soybeans. The genotypes studied were the local breeds Vorwerkhuhn and Bresse Gauloise, as well as commercial White Rock parent hens and their crosses. Yolk weight, Haugh units, yolk and shell color, the frequency of blood and meat spots and the composition of the eggs were significantly influenced by the genotype. The feeding of faba beans had an effect on yolk and shell color, Haugh units and shell portion, while there was no significant influence on the frequency of blood and meat spots.

Additional file 4. Relationships between observed heterozygosity and genetic distance to G. gallus for genes in the top 5% slope range.

Additional file 2: Figure S1. Observed heterozygosity vs. Reynolds’ genetic distance to the Gallus gallus estimated from 1000 SNP samples in 100 replicates. The dashed lines represent the 100 sample sets and the gray area shows the 95% confidence interval. Figure S2. Relationship between the observed heterozygosity and genetic differentiation ( $${F}_{\mathrm{ST}})$$ F ST ) from G. gallus (left), and the relationship between $${F}_{\mathrm{ST}}$$ F ST and Reynolds’ genetic distance to G. gallus (right). The regression lines of the relationships are drawn in red. The R2 is equal to 0.885 and 0.988, for the left and right figures, respectively. Different breed categories are denoted in different colors and/or shapes. Figure S3. Comparison of the relationship between the genetic distance to G. gallus and the observed heterozygosity estimated from the non-synonymous class vs. 100 random samples of the same number of SNPs as the non-synonymous class from the overall SNPs. The black dotted lines represent estimations with the overall SNPs, the red solid line represents the non-synonymous SNPs. The shaded areas represent the 95% confidence intervals of the regression lines. The mean R2 of the 100 samples is 0.880 and the mean slope is − 0.708. Figure S4. Comparison of the relationship between the genetic distances to G. gallus and the observed heterozygosity estimated from intronic SNPs vs. the overall set. The black dashed lines represent estimations with the 100 replicates of 1000 randomly samples SNPs from the intronic SNPs and the red solid line represents overall SNPs. The 95% confidence intervals are shaded in gray. The mean R2 and slope of the 100 samples are 0.880 and − 0.711, respectively. Figure S5. Comparison of the relationship between the genetic distance to G. gallus and the observed heterozygosity estimated from intergenic SNPs vs. the overall set. The black dashed lines represent estimations with the 100 replicates of 1000 randomly sampled SNPs from the intergenic SNPs and the red solid line represents overall SNPs. The 95% confidence intervals are shaded in gray. The mean R2 and slope of the 100 samples are 0.878 and − 0.701, respectively.

Das hier beschriebene Verbundvorhaben umfasst folgende Teilprojekte: FKZ 15NA023, FKZ 15NA085, FKZ 15NA086 und FKZ 15NA087. Ziel des Projektes war die Bestimmung von Prävalenzen von Schwanzbeißmerkmalen sowie deren ge-netischer Hintergrund zur Entwicklung von Zuchtstrategien gegen Schwanzbeißen. Schwanzboniturdaten von ca. 1750 unkupierten Tieren von der LSZ und 18,600 kupierten Tieren aus Bayern wurden berücksichtigt. Auch lagen Daten von ca. 26000 Tieren hinsichtlich Opfer-/Täter-Status sowie Verhaltensnoten und Leistungsdaten von BHZP vor. Die höchsten Prävalenzen wurden bei den unkupierten Schweinen beobachtet, und zwar am Ende der Aufzucht: 31% Nekrose, 41% Längenverluste (62% gegen Mastende), 9,5% DBH, 3% Blutung und 3,1% Schwellung. Auch in Bayern wurden die höchsten Prävalenzen am Ende der Aufzucht beobachtet mit 14% DBH und 1,6% Blutung. Inzidenzen von Nekrose und Längenverlusten lagen unter 1%. Bei Saug-ferkeln wurden Akren-Nekrosen an den Klauen (60%), Zitzen (12%), Kronsaum (3%) und Vulva (3%) beobachtet. Die Heritabilitätsschätzwerte für Schwanzverletzungsmerkmale und Schwanzbeißen variierten von 0 bis 0,22; die Heritabilität von Klauennekrose war 0,36. Höhere Prävalenzen von Opfern bzw. Tätern wurden bei Mutterrassen beobachtet: Bezogen auf die Anzahl Tiere lag die Prävalenz von Opfern bei DE und DL bei 5%-6%; bei PI und DU war sie

Additional file 2: Supplementary File 2. Supplementary Methods.

Additional file 14: Table S1. Quantiles of theoretical imputation accuracies (DR2) by reference set.

Pan-genomic open reading frames (ORFs) potentially carry protein-coding gene or coding variant information in a population. In this study, we suggest that pan-genomic ORFs are promising to be utilized in estimation of heritability and genomic prediction. A Saccharomyces cerevisiae dataset with whole-genome SNPs, pan-genomic ORFs, and the copy numbers of those ORFs is used to test the effectiveness of ORF data as a predictor in three prediction models for 35 traits. Our results show that the ORF-based heritability can capture more genetic effects than SNP-based heritability for all traits. Compared to SNP-based genomic prediction (GBLUP), pan-genomic ORF-based genomic prediction (OBLUP) is distinctly more accurate for all traits, and the predictive abilities on average are more than doubled across all traits. For four traits, the copy number of ORF-based prediction(CBLUP) is more accurate than OBLUP. When using different numbers of isolates in training sets in ORF-based prediction, the predictive abilities for all traits increased as more isolates are added in the training sets, suggesting that with very large training sets the prediction accuracy will be in the range of the square root of the heritability. We conclude that pan-genomic ORFs have the potential to be a supplement of single nucleotide polymorphisms in estimation of heritability and genomic prediction., Author summary The properties of single nucleotide polymorphisms (SNPs) as a main source of genetic variability for estimation of heritability and genomic prediction have been widely studied over the past years. This data type remarkably accelerated the development of medical diagnosis in human genetics and prediction of breeding values in livestock and crop breeding field. However, due to the inherent pitfalls of SNP-based prediction, e.g. imperfect LD between markers and causal variants, seeking new genomic datasets of causal variants has become imperative. Our study point out some of the superiorities of pan-genomic open reading frames as independent variables in estimation of heritability and genomic prediction.

Poultry production is raising concerns within the public regarding the practice of culling day-old chicks and the importation of soy from overseas for feedstuff. Therefore, an alternative approach to poultry production was tested. In two consecutive experiments, two traditional chicken breeds, Vorwerkhuhn and Bresse Gauloise, and White Rock as a commercial layer genotype as well as crossbreds thereof were fed diets containing either 20% vicin-rich or vicin-poor faba beans, though addressing both subjects of debate. Hen performance traits and bone stability were recorded. All parameters were considerably influenced by the genotype with White Rock showing the significantly highest (p &lt, 0.05) laying performance (99.4% peak production) and mean egg weights (56.6 g) of the purebreds, but the lowest bone breaking strength (tibiotarsus 197.2 N, humerus 230.2 N). Regarding crossbreds, the Bresse Gauloise &times, White Rock cross performed best (peak production 98.1%, mean egg weight 58.0 g). However, only limited dietary effects were found as only the feeding of 20% vicin-rich faba beans led to a significant reduction of egg weights of at most 1.1 g (p &lt, 0.05) and to a significant reduction of the shell stability in the crossbred genotypes. In terms of dual-purpose usage, crossing of Bresse Gauloise with White Rock seems to be the most promising variant studied here.

The faba bean (Vicia faba L.) is a native protein crop and considered a promising alternative to soybeans. Due to its anti-nutritive substances such as vicin and convicin (VC) its use in animal nutrition has been restricted. In the present study, two consecutive experiments were conducted to analyse the effects of feeding 20% faba beans, which differ in their VC content on fattening performance and slaughter traits of different chicken genotypes. In a first trial, purebred male chickens of the local breeds Bresse Gauloise and Vorwerkhuhn as well as of a high-performance White Rock line were tested. In a second trial, crossbreds of them were evaluated: Vorwerkhuhn x Bresse Gauloise, Vorwerkhuhn x White Rock, Bresse Gauloise x White Rock. Daily weight gain and feed intake were recorded until slaughter at approximately 2100 g. At slaughter the final live weight, carcass yield and the weights of the valuable parts (breasts and legs) were measured. For the genotypes studied, no adverse or undesirable effects of both VC&minus, rich and VC&minus, poor faba beans in the feedstuff were detected regarding body weight development, carcass quality, and fattening parameters. Furthermore, there was no indication that the birds&rsquo, health was impaired.

Additional file 12. Brazilian geographical regions of the four cattle breeds sampled in the study (Adapted from https://pt.wikipedia.org/wiki/Ficheiro:Brazil_Labelled_Map.svg ).

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Additional file 1:Supplementary tables. Table S1. Genomic regions associated with extreme |iHS| values. |iHS| values averaged over non-overlapping windows of each 500 kb. Table S2. Genomic regions associated with extreme FST values (P < 2.5%). FST values averaged over non-overlapping windows of each 500 kb. (DOC 388 KB)

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Additional file 4. Analysis of Molecular Variance results.

Additional file of Application of site and haplotype-frequency based approaches for detecting selection signatures in cattle

Additional file 2:Figure S1. Distribution of |iHS| values across the genome of beef breeds. Dashed lines display the threshold level of 0.05. (DOC 138 KB)

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