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Simple Summary: Quails are becoming increasingly popular for their meat and eggs, and thus, the productivity of laying hens, and how that can be predicted, is of growing interest to quail producers. Because of this, we wanted to find out whether we could predict the performance of laying hens (typically expressed as the number of eggs produced multiplied by the egg weight—the so-called total egg mass) simply by looking at certain growth traits (i.e., body weight, surface area, and volume), as well as the metabolic rate among eight Japanese quail breeds. To succeed in this analysis, we developed a novel method for calculating the volume and surface area of a quail body. As a result, we derived a new mathematical formula called the metabolic index, which included the measurements of body weight, surface area, and volume. We discovered that the total egg mass in quails can be judged from these growth parameters, particularly when we examined the slope angles of the trend lines in the graphs pertaining to these parameters. Abstract: The aim of the current study was to assess the female metabolic rate and test the hypothesis that there is a relationship between the egg productivity of Japanese quails from eight breeds and their morphometric, or growth, parameters. Parameters measured were body weight (B), volume (V), and surface area (S), as well as the metabolism level expressed by the ratio S/V. The collected egg performance traits were as follows: the number of eggs produced (N), the average egg weight (W), and the total egg mass (M) (i.e., N multiplied by W). To measure the S and V values, a novel technique was developed that takes into account the similarity of the quail’s body to an ellipsoid. An analysis of the relationships between productivity indicators allowed us to introduce a new index called the metabolic index, B·S/V, based on all three main growth parameters in quails. Using the values of this index, we were then able to judge indirectly the level of quai

The search for SNPs and candidate genes that determine the manifestation of major selected traits is one crucial objective for genomic selection aimed at increasing poultry production efficiency. Here, we report a genome-wide association study (GWAS) for traits characterizing meat performance in the domestic quail. A total of 146 males from an F 2 reference population resulting from crossing a fast (Japanese) and a slow (Texas White) growing breed were examined. Using the genotyping-by-sequencing technique, genomic data were obtained for 115,743 SNPs (92,618 SNPs after quality control) that were employed in this GWAS. The results identified significant SNPs associated with the following traits at 8 weeks of age: body weight (nine SNPs), daily body weight gain (eight SNPs), dressed weight (33 SNPs), and weights of breast (18 SNPs), thigh (eight SNPs), and drumstick (three SNPs). Also, 12 SNPs and five candidate genes (GNAL, DNAJC6, LEPR, SPAG9, and SLC27A4) shared associations with three or more traits. These findings are consistent with the understanding of the genetic complexity of body weight-related traits in quail. The identified SNPs and genes can be used in effective quail breeding as molecular genetic markers for growth and meat characteristics for the purpose of genetic improvement.

Breeding improvements and quantitative trait genetics are essential to the advancement of broiler production. The impact of artificial selection on genomic architecture and the genetic markers sought remains a key area of research. Here, we used whole-genome resequencing data to analyze the genomic architecture, diversity, and selective sweeps in Cornish White (CRW) and Plymouth Rock White (PRW) transboundary breeds selected for meat production and, comparatively, in an aboriginal Russian breed of Ushanka (USH). Reads were aligned to the reference genome bGalGal1.mat.broiler.GRCg7b and filtered to remove PCR duplicates and low-quality reads using BWA-MEM2 and bcftools software; 12,563,892 SNPs were produced for subsequent analyses. Compared to CRW and PRW, USH had a lower diversity and a higher genetic distinctiveness. Selective sweep regions and corresponding candidate genes were examined based on ZFST, hapFLK, and ROH assessment procedures. Twenty-seven prioritized chicken genes and the functional projection from human homologs suggest their importance for selection signals in the studied breeds. These genes have a functional relationship with such trait categories as body weight, muscles, fat metabolism and deposition, reproduction, etc., mainly aligned with the QTLs in the sweep regions. This information is pivotal for further executing genomic selection to enhance phenotypic traits.

After the domestication of goats around 10,000 years before the present (BP), humans transported goats far beyond the range of their wild ancestor, the bezoar goat. This brought domestic goats into contact with many wild goat species such as ibex and markhor, enabling introgression between domestic and wild goats. To investigate this, while shedding light on the taxonomic status of wild and domestic goats, we analysed genome-wide SNP data of 613 specimens from 14 taxonomic units, including Capra hircus, C. pyrenaica, C. ibex (from Switzerland, Austria, Germany and Slovenia), C. aegagrus aegagrus, C. a. cretica, C. h. dorcas, C. caucasica caucasica, C. c. severtzovi, C. c. cylindricornis, C. falconeri, C. sibirica sibirica, C. s. alaiana and C. nubiana, as well as Oreamnos americanus (mountain goat) as an outgroup. To trace gene flow between domestic and wild goats, we integrated genotype data of local goat breeds from the Alps as well as from countries such as Spain, Greece, Türkiye, Egypt, Sudan, Iran, Russia (Caucasus and Altai) and Pakistan. Our phylogenetic analyses displayed a clear separation between bezoar-type and ibex-type clades with wild goats from the Greek islands of Crete and Youra clustered within domestic goats, confirming their feral origin. Our analyses also revealed gene flow between the lineages of Caucasian tur and domestic goats that most likely occurred before or during early domestication. Within the clade of domestic goats, analyses inferred gene flow between African and Iberian goats. The detected events of introgression were consistent with previous reports and offered interesting insights into the historical relationships among domestic and wild goats., Deutscher Akademischer Austauschdienst http://dx.doi.org/10.13039/501100001655, Javna Agencija za Raziskovalno Dejavnost RS http://dx.doi.org/10.13039/501100004329, Ministry of Science and Higher Education of the Russian Federation http://dx.doi.org/10.13039/501100012190, Peer Reviewed

Simple Summary: Artificial selection has been applied to domesticated birds for many decades. More recently, this selection has made use of so-called single-nucleotide polymorphism (SNP) markers—simple variants in a DNA sequence. These SNPs can be used for whole-genome screening to detect the unique traces of areas of the genome that are subject to selection. Doing this may help to shed light on the evolutionary and family history (phylogeny) of domestic Japanese quails of different breeds and utility types (e.g., egg, meat or dual-purpose breeds). In this study, 99 birds were used, representing eight breeds (11% of the world’s quail gene pool) and various purposes of use to gather genetic (whole-genome) data in the first-ever analysis of its kind performed on domestic quails. We thereby uncovered evolutionary relationships and points of divergence of individual quail breeds, gleaning important insights into the genetic diversity of domestic quail breeds and their future breeding potential. Abstract: Traces of long-term artificial selection can be detected in genomes of domesticated birds via whole-genome screening using single-nucleotide polymorphism (SNP) markers. This study thus examined putative genomic regions under selection that are relevant to the development history, divergence and phylogeny among Japanese quails of various breeds and utility types. We sampled 99 birds from eight breeds (11% of the global gene pool) of egg (Japanese, English White, English Black, Tuxedo and Manchurian Golden), meat (Texas White and Pharaoh) and dual-purpose (Estonian) types. The genotyping-by-sequencing analysis was performed for the first time in domestic quails, providing 62,935 SNPs. Using principal component analysis, Neighbor-Net and Admixture algorithms, the studied breeds were characterized according to their genomic architecture, ancestry and direction of selective breeding. Japanese and Pharaoh breeds had the smallest number and length of homozygous segments indica

Domesticated animals play a significant role in local, national, and international agricultural output as well as in daily human life and culture. Additionally, they make up a sizeable portion of the biodiversity of the planet, which is essential for producing food and other animal products for human consumption. The present Frontiers in Genetics Research Topic (Figure 1) is devoted to various issues pertinent diversity of farm animals. The latter is at serious risk today, which could result in a reduction in the resources available to produce breed-specific food products and other necessities of everyday living. Importantly, genetic diversity is necessary for future animal breeding to be flexible enough to adapt livestock populations to changing customer demands and climatic conditions. Continued efforts are required to protect biodiversity, stop the loss of animal breeds, and maintain genetic diversity and develop strategies to use resource population in regional (niche) production systems.

Domesticated animals (including poultry) represent both an integral part of global, regional, and small-scale agricultural production, as well as a common element of human everyday life and culture. They also constitute a significant part of the world's biodiversity, on which humanity's supply of food and other animal products depends. In the modern world, there is a high risk of loss of the diversity of farm animals, which can entail a narrowing of resources for production of food and other items of daily life. Furthermore, the flexibility of future animal breeding to adapt livestock populations to climate change and changing consumer demands requires genetic diversity. Efforts must continue to conserve biodiversity and prevent decline in the number of available animal breeds and size of existing populations. To have all the necessary information about the conserved breeds and populations, it is necessary to assess them as comprehensively as possible in terms of phenotypic characteristics, genetic diversity, and genomic features associated with performance of animals, their adaptation to local conditions, and resistance to diseases. Introducing this Research Topic, we aim to present a series of research articles and reviews that would elucidate traditional approaches, coupled with genotypic/genomic data, and recent advances in conservation and investigation of domestic animal diversity. To contribute to this Research Topic, we invite researchers and breeders who have in their instrumental arsenal traditional techniques and approaches in combination with state-of-the-art genetic and genomic methods that enable the evaluation of breeds by comprehensive phenotyping and studying effectively genetic diversity of breeds using suitable polymorphic markers or genome-wide SNP genotyping. Herewith, we see a lot of benefit of papers combining or comparing traditional and genomic measures and will encourage papers preferably with genotype/genomic content. We also aim to collec

Simple Summary: A collection of native farm animal breeds can be considered as a gene pool and a national heritage. Long-term artificial selection in domesticated animals has certain effects on their genomes, which can be investigated using genome-wide screens for DNA sequence variation, that is, so-called single nucleotide polymorphism (SNP) screens. Here, we looked at the genomes of 19 Russian chicken gene pool breeds, both native and imported, evaluating the contrasting egg, meat and dual-purpose types. Based on genetic diversity statistics, we identified differences between the breeds using many DNA markers (SNPs) that may represent genomic regions that are being selected for, either within a specific breed or shared between breeds. Our research will be helpful for further understanding the genomic diversity and demographic history of Russian domestic chickens. This would be essential for their successful breeding. Abstract: A study for genomic variation that may reflect putative selective signaling and be associated with economically important traits is instrumental for obtaining information about demographic and selection history in domestic animal species and populations. A rich variety of the Russian chicken gene pool breeds warrants a further detailed study. Specifically, their genomic features can derive implications from their genome architecture and selective footprints for their subsequent breeding and practical efficient exploitation. In the present work, whole genome genotyping of 19 chicken breeds (20 populations with up to 71 samples each) was performed using the Chicken 50 K BeadChip DNA chip. The studied breed sample included six native Russian breeds of chickens developed in the 17th–19th centuries, as well as eight Russian chicken breeds, including the Russian White (RW), created in the 20th century on the basis of improving local chickens using breeds of foreign selection. Five specialized foreign breeds of chickens, including the White Leghorn