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On October 25-26, 2019, a satellite meeting devoted to the preparation of a Chicken Genome Diversity Consortium was organised after the 11th European Symposium of Poultry Genetics in Prague. Researchers involved in chicken genomics from Europe, Africa and China, discussed the objectives of such a consortium with some presenting their data. However, the technical aspects of how to share and jointly analyse the data were not finalized, nor was the funding model for the cost of data storage and computation. In 2021, an opportunity arose with the call for projects of the SuperMUC computing cluster of the Leibniz-Rechenzentrum in Germany. A new consortium of scientists re-launched the discussion to establish a project with the aim to explore how the high-throughput genomics age can be harnessed to answer evolutionary questions surrounding the chicken. The FARMGENOMIC project (23826) was accepted for funding in autumn 2021, gathering around 20 members from 10 institutions in Europe, North America, and Africa. This newly formed Chicken Genomic Diversity consortium brings together members from a variety of disciplines, including genomics, palaeogenetics, animal breeding, immunology, organismal biology, evolutionary biology, and archaeology. Central to the consortium are the concepts of inclusivity and openness – all data are to be made available to all members of the consortium, and later distributed to the wider community, and collaborations between groups are fostered and actively encouraged. It is hoped this state-of-the-art resource, curated in-house by bioinformaticians, will enable the community to answer previously intractable questions in chicken evolution.

Vitamin D3 has an integral part in calcium and phosphorus homoeostasis, which in turn plays a key role in egg production of hens. The present study aimed to investigate whether an additional vitamin D3 supplementation improves the laying performance and egg quality of hens according to their genetic potential. For this purpose, four layer lines (low performing: R11 and L68; high performing: WLA and BLA) supplemented either with 300 or 3000 IU vitamin D3 per kg feed were compared concerning serum 25-hydroxyvitamin D3 (25-OHD3), calcium, phosphorus and alkaline phosphatase (ALP), laying performance and egg quality. The higher supplementation of vitamin D3 increased 25-OHD3 serum concentrations in all genotypes, except for R11 and WLA hens in week 49, and also elevated vitamin D3 and 25-OHD3 content in the egg yolk (p < 0.05). In week 29, 3000 IU vitamin D3 decreased pooled least squares means (LSMeans) of serum calcium concentrations considering all genotypes and increased the ALP concentrations in BLA hens (p < 0.05). Considering the whole experimental period daily egg mass of R11 hens was increased by an additional vitamin D3 supplementation (p < 0.001). Regarding all genotypes and the whole experimental period the pooled LSMeans of breaking strength of eggs from hens fed 3000 IU vitamin D3 were higher than those of hens fed 300 IU (p = 0.044). In conclusion, present results give evidence that the higher vitamin D3 supplementation might have genotype-dependently beneficial effects on calcium and phosphorus homoeostasis of hens, which might improve feed efficiency in the early laying period and promote the persistence of the laying period irrespectively of genotype. The increase of serum 25-OHD3 by the higher vitamin D supplementation supported the higher transfer of vitamin D in the egg yolk and improved genotype-dependently the breaking strength of the eggshell.

Additional file 1. Supplementary results, tables and figures.

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.

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

Additional file 2: Supplementary File 2. Supplementary Methods.

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.

The current practices of the poultry industry have raised concerns among consumers. Among these is the culling of day-old male chicks of laying hybrids, a suitable alternative for this could be the use of dual-purpose breeds where both sexes are used. Another practice that causes concern is the import of large quantities of soybeans for feedstuff production. Substitutes for these soybean-based products are regional protein crops, such as faba beans (Vicia faba L., FBs). The objective of this study was to test the suitability of FB as a locally produced soybean meal replacement for two local dual-purpose chicken breeds and one high-performing layer line. The breast and leg meat of male Bresse Gauloise (BG), Vorwerkhuhn (VH), and White Rock (WR) animals was evaluated for different meat quality parameters: pH, color, water holding capacity, and tenderness. Sensory properties of the samples were evaluated by a trained panel with a conventional descriptive analysis. Results show different effects of FB diets on meat quality parameters in the different breeds. The attributes mostly affected by the diet are related to aroma, flavor, and texture, particularly in VH and WR. Overall, faba beans appear to be an acceptable dietary protein source for rearing these breeds for meat production.