Large-scale genome-wide SNP analysis reveals the rugged (and ragged) landscape of global ancestry, phylogeny, and demographic history in chicken breeds. / å¤§è§„æ¨¡å ¨åŸºå› ç»„SNPåˆ†æžæ­ç¤ºäº†é¸¡å“ç§çš„å ¨çƒç¥–å ˆã€ç§ç¾¤å‘å±•å’Œç§ç¾¤åŽ†å²çš„å¤æ‚(å’Œå¤šæ ·)çš„é—ä¼ å›¾è°±.

The worldwide chicken gene pool encompasses a remarkable, but shrinking, number of divergently selected breeds of diverse origin. This study was a large-scale genome-wide analysis of the landscape of the complex molecular architecture, genetic variability, and detailed structure among 49 populations. These populations represent a significant sample of the world's chicken breeds from Europe (Russia, Czech Republic, France, Spain, UK, etc.), Asia (China), North America (USA), and Oceania (Australia). Based on the results of breed genotyping using the Illumina 60K single nucleotide polymorphism (SNP) chip, a bioinformatic analysis was carried out. This included the calculation of heterozygosity/homozygosity statistics, inbreeding coefficients, and effective population size. It also included assessment of linkage disequilibrium and construction of phylogenetic trees. Using multidimensional scaling, principal component analysis, and ADMIXTURE-assisted global ancestry analysis, we explored the genetic structure of populations and subpopulations in each breed. An overall 49-population phylogeny analysis was also performed, and a refined evolutionary model of chicken breed formation was proposed, which included egg, meat, dual-purpose types, and ambiguous breeds. Such a large-scale survey of genetic resources in poultry farming using modern genomic methods is of great interest both from the viewpoint of a general understanding of the genetics of the domestic chicken and for the further development of genomic technologies and approaches in poultry breeding. In general, whole genome SNP genotyping of promising chicken breeds from the worldwide gene pool will promote the further development of modern genomic science as applied to poultry.

Comparison of miR-106b, miR-191, and miR-30d expression dynamics in milk with regard to its composition in Holstein and Ayrshire cows.

OBJECTIVE: Milk composition varies considerably and depends on paratypical, genetic, and epigenetic factors. MiRNAs belong to the class of small non-coding RNAs; they are one of the key tools of epigenetic control because of their ability to regulate gene expression at the post-transcriptional level. We compared the relative expression levels of miR-106b, miR-191, and miR-30d in milk to demonstrate the relationship between the content of these miRNAs with protein and fat components of milk in Holstein and Ayrshire cattle. METHODS: Milk fat, protein, and casein contents were determined in the obtained samples, as well as the content of the main fatty acids (g/100 g milk), including: saturated acids, such as myristic (C14:0), palmitic (C16:0), and stearic (C18:0) acids; monounsaturated acids, including oleic (C18:1) acid; as well as long-, medium- and short-chain, polyunsaturated, and trans fatty acids. Real-time stem-loop one-tube reverse transcription polymerase chain reaction with TaqMan probes was used to measure the miRNA expression levels. RESULTS: The miRNA expression levels in milk samples were found to be decreased in the first two months in Holstein breed, and in the first four months in Ayrshire breed. Correlation analysis did not reveal any dependence between changes in the expression level of miRNA and milk fat content, but showed a multidirectional relationship with individual milk fatty acids. Positive associations between the expression levels of miR-106b and miR-30d and protein and casein content were found in the Ayrshire breed. Receiver operating characteristic curve analysis showed that miR-106b and miR-30d expression levels can cause changes in fatty acid and protein composition of milk in Ayrshire cows, whereas miR-106b expression level determines the fatty acid composition in Holsteins. CONCLUSION: The data obtained in this study showed that miR-106b, miR-191, and miR-30d expression levels in milk samples have peculiarities associated with breed affiliation and the lactation period.

Risk of Sperm Disorders and Impaired Fertility in Frozen-Thawed Bull Semen: A Genome-Wide Association Study.

Cryopreservation is a widely used method of semen conservation in animal breeding programs. This process, however, can have a detrimental effect on sperm quality, especially in terms of its morphology. The resultant sperm disorders raise the risk of reduced sperm fertilizing ability, which poses a serious threat to the long-term efficacy of livestock reproduction and breeding. Understanding the genetic factors underlying these effects is critical for maintaining sperm quality during cryopreservation, and for animal fertility in general. In this regard, we performed a genome-wide association study to identify genomic regions associated with various cryopreservation sperm abnormalities in Holstein cattle, using single nucleotide polymorphism (SNP) markers via a high-density genotyping assay. Our analysis revealed a significant association of specific SNPs and candidate genes with absence of acrosomes, damaged cell necks and tails, as well as wrinkled acrosomes and decreased motility of cryopreserved sperm. As a result, we identified candidate genes such as POU6F2, LPCAT4, DPYD, SLC39A12 and CACNB2, as well as microRNAs (bta-mir-137 and bta-mir-2420) that may play a critical role in sperm morphology and disorders. These findings provide crucial information on the molecular mechanisms underlying acrosome integrity, motility, head abnormalities and damaged cell necks and tails of sperm after cryopreservation. Further studies with larger sample sizes, genome-wide coverage and functional validation are needed to explore causal variants in more detail, thereby elucidating the mechanisms mediating these effects. Overall, our results contribute to the understanding of genetic architecture in cryopreserved semen quality and disorders in bulls, laying the foundation for improved animal reproduction and breeding.

Biologically Active Supplements Affecting Producer Microorganisms in Food Biotechnology: A Review.

Microorganisms, fermentation processes, and the resultant metabolic products are a key driving force in biotechnology and, in particular, in food biotechnology. The quantity and/or quality of final manufactured food products are directly related to the efficiency of the metabolic processes of producer microorganisms. Food BioTech companies are naturally interested in increasing the productivity of their biotechnological production lines. This could be achieved via either indirect or direct influence on the fundamental mechanisms governing biological processes occurring in microbial cells. This review considers an approach to improve the efficiency of producer microorganisms through the use of several types of substances or complexes affecting the metabolic processes of microbial producers that are of interest for food biotechnology, particularly fermented milk products. A classification of these supplements will be given, depending on their chemical nature (poly- and oligosaccharides; poly- and oligopeptides, individual amino acids; miscellaneous substances, including vitamins and other organic compounds, minerals, and multicomponent supplements), and the approved results of their application will be comprehensively surveyed.

Disentangling clustering configuration intricacies for divergently selected chicken breeds.

Divergently selected chicken breeds are of great interest not only from an economic point of view, but also in terms of sustaining diversity of the global poultry gene pool. In this regard, it is essential to evaluate the classification (clustering) of varied chicken breeds using methods and models based on phenotypic and genotypic breed differences. It is also important to implement new mathematical indicators and approaches. Accordingly, we set the objectives to test and improve clustering algorithms and models to discriminate between various chicken breeds. A representative portion of the global chicken gene pool including 39 different breeds was examined in terms of an integral performance index, i.e., specific egg mass yield relative to body weight of females. The generated dataset was evaluated within the traditional, phenotypic and genotypic classification/clustering models using the k-means method, inflection points clustering, and admixture analysis. The latter embraced SNP genotype datasets including a specific one focused on the performance-associated NCAPG-LCORL locus. The k-means and inflection points analyses showed certain discrepancies between the tested models/submodels and flaws in the produced cluster configurations. On the other hand, 11 core breeds were identified that were shared between the examined models and demonstrated more adequate clustering and admixture patterns. These findings will lay the foundation for future research to improve methods for clustering as well as genome- and phenome-wide association/mediation analyses.

Salmonidae Genome: Features, Evolutionary and Phylogenetic Characteristics.

The salmon family is one of the most iconic and economically important fish families, primarily possessing meat of excellent taste as well as irreplaceable nutritional and biological value. One of the most common and, therefore, highly significant members of this family, the Atlantic salmon (Salmo salar L.), was not without reason one of the first fish species for which a high-quality reference genome assembly was produced and published. Genomic advancements are becoming increasingly essential in both the genetic enhancement of farmed salmon and the conservation of wild salmon stocks. The salmon genome has also played a significant role in influencing our comprehension of the evolutionary and functional ramifications of the ancestral whole-genome duplication event shared by all Salmonidae species. Here we provide an overview of the current state of research on the genomics and phylogeny of the various most studied subfamilies, genera, and individual salmonid species, focusing on those studies that aim to advance our understanding of salmonid ecology, physiology, and evolution, particularly for the purpose of improving aquaculture production. This review should make potential researchers pay attention to the current state of research on the salmonid genome, which should potentially attract interest in this important problem, and hence the application of new technologies (such as genome editing) in uncovering the genetic and evolutionary features of salmoniforms that underlie functional variation in traits of commercial and scientific importance.

Genome-wide association study for frozen-thawed sperm motility in stallions across various horse breeds.

OBJECTIVE: The semen quality of stallions including sperm motility is an important target of selection as it has a high level of individual variability. However, effects of the molecular architecture of the genome on the mechanisms of sperm formation and their preservation after thawing have been poorly investigated. Here, we conducted a genome-wide association study (GWAS) for the sperm motility of cryopreserved semen in stallions of various breeds. METHODS: Semen samples were collected from the stallions of 23 horse breeds. The following semen characteristics were examined: progressive motility (PM), progressive motility after freezing (FPM), and the difference between PM and FPM. The respective DNA samples from these stallions were genotyped using Axiom Equine Genotyping Array. RESULTS: We performed a GWAS search for single nucleotide polymorphism (SNP) markers and potential genes related to motility properties of frozen-thawed semen in the stallions of various breeds. As a result of the GWAS analysis, two SNP markers, rs1141327473 and rs1149048772, were identified that were associated with preservation of the frozen-thawed stallion sperm motility, the relevant putative candidate genes being NME/NM23 family member 8 (NME8), olfactory receptor family 2 subfamily AP member 1 (OR2AP1), and olfactory receptor family 6 subfamily C member 4 (OR6C4). Potential implications of effects of these genes on sperm motility are herein discussed. CONCLUSION: The GWAS results enabled us to localize novel SNPs and candidate genes for sperm motility in stallions. Implications of the study for horse breeding and genetics are a better understanding of genomic regions and candidate genes underlying stallion sperm quality, and improvement in horse reproduction and breeding techniques. The identified markers and genes for sperm cryotolerance and the respective genomic regions are promising candidates for further studying the biological processes in the formation and function of the stallion reproductive system.

The Role of microRNAs in the Mammary Gland Development, Health, and Function of Cattle, Goats, and Sheep.

Milk is an integral and therefore complex structural element of mammalian nutrition. Therefore, it is simple to conclude that lactation, the process of producing milk, is as complex as the mammary gland, the organ responsible for this biochemical activity. Nutrition, genetics, epigenetics, disease pathogens, climatic conditions, and other environmental variables all impact breast productivity. In the last decade, the number of studies devoted to epigenetics has increased dramatically. Reports are increasingly describing the direct participation of microRNAs (miRNAs), small noncoding RNAs that regulate gene expression post-transcriptionally, in the regulation of mammary gland development and function. This paper presents a summary of the current state of knowledge about the roles of miRNAs in mammary gland development, health, and functions, particularly during lactation. The significance of miRNAs in signaling pathways, cellular proliferation, and the lipid metabolism in agricultural ruminants, which are crucial in light of their role in the nutrition of humans as consumers of dairy products, is discussed.

Novel non-toxic high efficient antibacterial azido chitosan derivatives with potential application in food coatings.

In this work, we developed a simple method for the preparation of N-(3-azido-2-hydroxypropyl)chitosan. We compared the antibacterial activity of N-(3-azido-2-hydroxypropyl)chitosans and previously synthesized N-(2-azidoethyl)chitosans. N-(3-azido-2-hydroxypropyl)chitosans possess higher antibacterial effect which is comparable with that of ampicillin and gentamicin. The effect is due to azido pharmacophore -CH2-CH(OH)-CH2-N3 (for N-(3-azido-2-hydroxypropyl)chitosan) or -CH2-CH2-N3 (for N-(2-azidoethyl)chitosan) introduced in chitosan chain, since the corresponding organic azides NH2-CH2-CH2-N3 and NH2-CH2-CH2-N3 are characterized by high antibacterial activity. However, high antibacterial organic azides NH2-CH2-CH2-N3 and NH2-CH2-CH2-N3 are characterized by high toxicity. Their conjugation to the chitosan chain saves their antibacterial effect, but strongly diminishes their toxicity, and the toxicity of the resulting derivatives is comparable with that of the starting chitosan. These findings are of interest to food science, since novel effective food coatings can be developed on basis of prepared derivatives.

Ultrasound-assisted Cu(I)-catalyzed azide-alkyne click cycloaddition as polymer-analogous transformation in chitosan chemistry. High antibacterial and transfection activity of novel triazol betaine chitosan derivatives and their nanoparticles.

In this work, we involved ultrasound-assisted click CuAAC in chitosan chemistry. Ultrasound-mediated CuAAC between propargylic ester of betaine and azido chitosan derivative proceeds fast in water under aerobic conditions and gives rise novel water-soluble triazole betaine chitosan derivatives. Using ionic gelation technique, we prepared and characterized nanoparticles from the synthesized chitosan derivatives. We studied antibacterial and transfection activity of the novel chitosan derivatives and their nanoparticles. The nanoparticles with size ca. 100 nm and ζ-potential ca. +65 mV proved to possess outstanding antibacterial activity, which is much more than that of the triazole betaine derivatives in their native form, and it is equal to the activity of ampicillin and gentamicin. Opposite, triazole betaine chitosan derivatives in their native form are characterized by remarkable transfection activity as compared with their nanoparticles. The most active triazole betaine chitosan derivatives are derivatives of moderate molecular weight with moderate degree of substitution. Their transfection activity is extremely high for chitosan species and it is comparable (values of the same order) with activity of Lipofectin - commercially available gene delivery vector.

Natural polysaccharide-based smart (temperature sensing) and active (antibacterial, antioxidant and photoprotective) nanoparticles with potential application in biocompatible food coatings.

Smart and active nanoparticles are of increasing interest in food films and coatings application. In the current study, we purpose novel nanoparticles NPs-4(1:5) and NPs-4(1:5.5), which possess simultaneously both smart (temperature sensitive) and active (antibacterial, light absorbing and antioxidant) properties. The obtained nanoparticles are based on PEG/MC core with anthocyanidin and sodium acetate, and chitosan/gallotannin-based shell. The nanoparticles have hydrodynamic diameter ca. 450 nm and are positively charged (ζ-potential is 21 mV for NPs-4(1:5) and +23 mV for NPs-4(1:5.5). NPs-4(1:5) and NPs-4(1:5.5) are thermochromic and turn from colorless to purple at ca. 20 °C 0 °C respectively. The nanoparticles possess antibacterial activity much more than the starting chitosan (MIC, µg/mL, E. coli: 1.35 (NPs-4(1:5)), 1.18 (NPs-4(1:5.5)) and 10.12 (chitosan); S. aureus: 1.14 (NPs-4(1:5)), 1.10 (NPs-4(1:5.5)) and 6.20 (chitosan)). The nanoparticles efficiently absorb ultraviolet light, have high antioxidant effect (0.051 trolox equivalents), are non-toxic and fully composed of substances approved for use in the food industry.