Dissecting Selective Signatures and Candidate Genes in Grandparent Lines Subject to High Selection Pressure for Broiler Production and in a Local Russian Chicken Breed of Ushanka.

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.

Genome-Wide Association Study Revealed Putative SNPs and Candidate Genes Associated with Growth and Meat Traits in Japanese Quail.

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 F2 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.

Genotyping-by-Sequencing Strategy for Integrating Genomic Structure, Diversity and Performance of Various Japanese Quail (Coturnix japonica) Breeds.

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 indicating a lower selective pressure. Tuxedo and Texas White breeds showed the highest values of these indicators and genomic inbreeding suggesting a greater homozygosity. We revealed evidence for the integration of genomic and performance data, and our findings are applicable for elucidating the history of creation and genomic variability in quail breeds that, in turn, will be useful for future breeding improvement strategies.

Probiotics as an alternative to antibiotics in modulating the intestinal microbiota and performance of broiler chickens.

AIMS: Gut bacteria play an important role in poultry nutrition and the immune defense system. Changes in the intestinal microbiome affect the physiological state, metabolism, and innate immunity of poultry. The present study aimed to characterize age-related changes in the gastrointestinal tract microflora in broiler chickens, depending on supplementation of the diet with the in-feed antibiotic Stafac® 110 and a Bacillus subtilis strain-based probiotic. METHODS AND RESULTS: In this regard, a comprehensive analysis of the taxonomic structure of the microbial community in the gastrointestinal tract (GIT) of broiler chickens was carried out using a molecular genetic technique of the terminal-restriction fragment length polymorphism analysis and taking into account age dynamics and feeding treatment. A beneficial effect on the microbiological composition and body weight of broilers was observed when using the antibiotic and probiotic in compound feeds. Different bacterial communities were revealed in the duodenum and cecum, and their positive impact on broiler growth was established. The results obtained shed light on the formation of GIT microflora of broiler chickens during the growing period and its changes in response to the use of the antibiotic and the probiotic. CONCLUSIONS: We suggest that the implementation of the tested in-feed antibiotic and probiotic can be beneficial in regulating the intestinal microflora microbiological processes in the GIT and improving the feeding efficiency and productivity of broiler chickens.

Whole Genome Screening Procures a Holistic Hold of the Russian Chicken Gene Pool Heritage and Demographic History.

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 (WL), were used along with other breeds representing the Russian gene pool. The characteristics of the genetic diversity and phylogenetic relationships of the native breeds of chickens were represented in comparison with foreign breeds. It was established that the studied native breeds demonstrate their own genetic structure that distinguishes them from foreign breeds, and from each other. For example, we previously made an assumption on what could cause the differences between two RW populations, RW1 and RW2. From the data obtained here, it was verified that WL was additionally crossed to RW2, unlike RW1. Thus, inherently, RW1 is a purer population of this improved Russian breed. A significant contribution of the gene pool of native breeds to the global genetic diversity of chickens was shown. In general, based on the results of a multilateral survey of this sample of breeds, it can be concluded that phylogenetic relationships based on their genetic structure and variability robustly reflect the known, previously postulated and newly discovered patterns of evolution of native chickens. The results herein presented will aid selection and breeding work using this gene pool.

Selective footprints and genes relevant to cold adaptation and other phenotypic traits are unscrambled in the genomes of divergently selected chicken breeds.

BACKGROUND: The genomes of worldwide poultry breeds divergently selected for performance and other phenotypic traits may also be affected by, and formed due to, past and current admixture events. Adaptation to diverse environments, including acclimation to harsh climatic conditions, has also left selection footprints in breed genomes. RESULTS: Using the Chicken 50K_CobbCons SNP chip, we genotyped four divergently selected breeds: two aboriginal, cold tolerant Ushanka and Orloff Mille Fleur, one egg-type Russian White subjected to artificial selection for cold tolerance, and one meat-type White Cornish. Signals of selective sweeps were determined in the studied breeds using three methods: (1) assessment of runs of homozygosity islands, (2) FST based population differential analysis, and (3) haplotype differentiation analysis. Genomic regions of true selection signatures were identified by two or more methods or in two or more breeds. In these regions, we detected 540 prioritized candidate genes supplemented them with those that occurred in one breed using one statistic and were suggested in other studies. Amongst them, SOX5, ME3, ZNF536, WWP1, RIPK2, OSGIN2, DECR1, TPO, PPARGC1A, BDNF, MSTN, and beta-keratin genes can be especially mentioned as candidates for cold adaptation. Epigenetic factors may be involved in regulating some of these important genes (e.g., TPO and BDNF). CONCLUSION: Based on a genome-wide scan, our findings can help dissect the genetic architecture underlying various phenotypic traits in chicken breeds. These include genes representing the sine qua non for adaptation to harsh environments. Cold tolerance in acclimated chicken breeds may be developed following one of few specific gene expression mechanisms or more than one overlapping response known in cold-exposed individuals, and this warrants further investigation.

Revisiting Oxidative Stress and the Use of Organic Selenium in Dairy Cow Nutrition.

In commercial animals production, productive stress can negatively impact health status and subsequent productive and reproductive performance. A great body of evidence has demonstrated that as a consequence of productive stress, an overproduction of free radicals, disturbance of redox balance/signaling, and oxidative stress were observed. There is a range of antioxidants that can be supplied with animal feed to help build and maintain the antioxidant defense system of the body responsible for prevention of the damaging effects of free radicals and the toxic products of their metabolism. Among feed-derived antioxidants, selenium (Se) was shown to have a special place as an essential part of 25 selenoproteins identified in animals. There is a comprehensive body of research in monogastric species that clearly shows that Se bioavailability within the diet is very much dependent on the form of the element used. Organic Se, in the form of selenomethionine (SeMet), has been reported to be a much more effective Se source when compared with mineral forms such as sodium selenite or selenate. It has been proposed that one of the main advantages of organic Se in pig and poultry nutrition is the non-specific incorporation of SeMet into general body proteins, thus forming an endogenous Se reserve that can be utilized during periods of stress for additional synthesis of selenoproteins. Responses in ruminant species to supplementary Se tend to be much more variable than those reported in monogastric species, and much of this variability may be a consequence of the different fates of Se forms in the rumen following ingestion. It is likely that the reducing conditions found in the rumen are responsible for the markedly lower assimilation of inorganic forms of Se, thus predisposing selenite-fed animals to potential Se inadequacy that may in turn compromise animal health and production. A growing body of evidence demonstrates that organic Se has a number of benefits, particularly in dairy and beef animals; these include improved Se and antioxidant status and better Se transfer via the placenta, colostrum, and milk to the newborn. However, there is a paucity in the data concerning molecular mechanisms of SeMet assimilation, metabolism and selenoprotein synthesis regulation in ruminant animals, and as such, further investigation is required.

Antioxidant Defence Systems and Oxidative Stress in Poultry Biology: An Update.

Poultry in commercial settings are exposed to a range of stressors. A growing body of information clearly indicates that excess ROS/RNS production and oxidative stress are major detrimental consequences of the most common commercial stressors in poultry production. During evolution, antioxidant defence systems were developed in poultry to survive in an oxygenated atmosphere. They include a complex network of internally synthesised (e.g., antioxidant enzymes, (glutathione) GSH, (coenzyme Q) CoQ) and externally supplied (vitamin E, carotenoids, etc.) antioxidants. In fact, all antioxidants in the body work cooperatively as a team to maintain optimal redox balance in the cell/body. This balance is a key element in providing the necessary conditions for cell signalling, a vital process for regulation of the expression of various genes, stress adaptation and homeostasis maintenance in the body. Since ROS/RNS are considered to be important signalling molecules, their concentration is strictly regulated by the antioxidant defence network in conjunction with various transcription factors and vitagenes. In fact, activation of vitagenes via such transcription factors as Nrf2 leads to an additional synthesis of an array of protective molecules which can deal with increased ROS/RNS production. Therefore, it is a challenging task to develop a system of optimal antioxidant supplementation to help growing/productive birds maintain effective antioxidant defences and redox balance in the body. On the one hand, antioxidants, such as vitamin E, or minerals (e.g., Se, Mn, Cu and Zn) are a compulsory part of the commercial pre-mixes for poultry, and, in most cases, are adequate to meet the physiological requirements in these elements. On the other hand, due to the aforementioned commercially relevant stressors, there is a need for additional support for the antioxidant system in poultry. This new direction in improving antioxidant defences for poultry in stress conditions is related to an opportunity to activate a range of vitagenes (via Nrf2-related mechanisms: superoxide dismutase, SOD; heme oxygenase-1, HO-1; GSH and thioredoxin, or other mechanisms: Heat shock protein (HSP)/heat shock factor (HSP), sirtuins, etc.) to maximise internal AO protection and redox balance maintenance. Therefore, the development of vitagene-regulating nutritional supplements is on the agenda of many commercial companies worldwide.

Selenium in Poultry Nutrition: from Sodium Selenite to Organic Selenium Sources.

Selenium (Se) is an essential element in poultry nutrition and its bio-efficacy depends on its chemical form. A growing body of research proves that organic forms of Se, mainly selenomethionine (SeMet), in poultry diets have a range of important advantages over traditional sodium selenite. In fact, the organic Se concept considers SeMet as a storage form of Se in the chicken body. As chickens are not able to synthesize SeMet, its provision through diet is a key strategy to fight commercially relevant stresses. Indeed, in stress conditions, when increased selenoprotein expression requires additional Se, while its provision via feed usually decreases due to a reduction in feed consumption, Se reserves in the body (mainly in the muscles) could help maintain an effective antioxidant defense and prevent detrimental consequences of stresses. The poultry industry is looking for the most effective sources of organic Se for commercial use. In this review, advantages and disadvantages of main organic Se sources for poultry (Se-yeast, SeMet, and OH-SeMet) are analyzed, and future directions for the development of new Se sources are identified.

Antioxidant systems in chick embryo development. Part 1. Vitamin E, carotenoids and selenium.

Chick viability is known to be an important factor determining profitability of the poultry industry. Chick embryo tissues contain a high proportion of highly polyunsaturated fatty acids in the lipid fraction and therefore need antioxidant defence. The antioxidant system of the developing embryo and newly hatched chick includes the antioxidant enzymes (superoxide dismutase, glutathione peroxidase, catalase), water-soluble antioxidants (ascorbic acid, taurine, carnitine, glutathione, etc.), fat-soluble antioxidants (vitamin E, carotenoids, coenzyme Q) as well as selenium (Se). In fact, the high levels of endogenous antioxidants within the egg and embryonic tissues can clearly serve as a major adaptive mechanism for the protection of the tissue during the oxidative stress experienced at hatching. It has been shown that among different nutrients in the maternal diet which could significantly affect chick embryo development and their viability in the early posthatch life, natural antioxidants have been suggested to play a central role. Our data indicate that increased supplementation of the maternal diet can substantially increase concentrations of vitamin E, carotenoids (especially canthaxanthin) and Se in developing chick tissues and significantly decrease susceptibility to lipid peroxidation being effective nutritional tools to deal with various commercial stresses in poultry production.

Selenium in pig nutrition and reproduction: boars and semen quality-a review.

Selenium plays an important role in boar nutrition via participating in selenoprotein synthesis. It seems likely that selenoproteins are central for antioxidant system regulation in the body. Se-dependent enzyme glutathione peroxidase (GSH-Px) is the most studied selenoprotein in swine production. However, roles of other selenoproteins in boar semen production and maintenance of semen quality also need to be studied. Boar semen is characterised by a high proportion of easily oxidized long chain polyunsaturated fatty acids and requires an effective antioxidant defense. The requirement of swine for selenium varies depending on many environmental and other conditions and, in general, is considered to be 0.15 to 0.30 mg/kg feed. It seems likely that reproducing sows and boars are especially sensitive to Se deficiency, and meeting their requirements is an important challenge for pig nutritionists. In fact, in many countries there are legal limits as to how much Se may be included into the diet and this restricts flexibility in terms of addressing the Se needs of the developing and reproducing swine. The analysis of data of various boar trials with different Se sources indicates that in some cases when background Se levels were low, there were advantages of Se dietary supplementation. It is necessary to take into account that only an optimal Se status of animals is associated with the best antioxidant protection and could have positive effects on boar semen production and its quality. However, in many cases, background Se levels were not determined and therefore, it is difficult to judge if the basic diets were deficient in Se. It can also be suggested that, because of higher efficacy of assimilation from the diet, and possibilities of building Se reserves in the body, organic selenium in the form of selenomethionine (SeMet) provided by a range of products, including Se-Yeast and SeMet preparations is an important source of Se to better meet the needs of modern pig genotypes in commercial conditions of intensive pig production.

Producing selenium-enriched eggs and meat to improve the selenium status of the general population.

The role of selenium (Se) in human health and diseases has been discussed in detail in several recent reviews, with the main conclusion being that selenium deficiency is recognised as a global problem which urgently needs resolution. Since selenium content in plant-based food depends on its availability from soil, the level of this element in food and feeds varies among regions. In general, eggs and meat are considered to be good sources of selenium in human diet. When considering ways to improve human selenium intake, there are several potential options. These include direct supplementation, soil fertilisation and supplementation of food staples such as flour, and production of functional foods. Analysing recent publications related to functional food production, it is evident that selenium-enriched eggs can be used as an important delivery system of this trace mineral for humans. In particular, developments and commercialisation of organic forms of selenium have initiated a new era in the availability of selenium-enriched products. It has been shown that egg selenium content can easily be manipulated to give increased levels, especially when organic selenium is included in hens' diet at levels that provide 0.3-0.5 mg/kg selenium in the feed. As a result, technology for the production of eggs delivering approximately 50% (30-35 microg) of the human selenium RDA have been developed and successfully tested. Currently companies all over the world market selenium-enriched eggs including the UK, Ireland, Mexico, Columbia, Malaysia, Thailand, Australia, Turkey, Russia and the Ukraine. Prices for enriched eggs vary from country to country, typically being similar to free-range eggs. Selenium-enriched chicken, pork and beef can also be produced when using organic selenium in the diet of poultry and farm animals. The scientific, technological and other advantages and limitations of producing designer/modified eggs as functional foods are discussed in this review.