Genetic variability in local and imported germplasm chicken populations as revealed by analyzing runs of homozygosity

Simple Summary To maintain the uniqueness of conserved chicken populations of local and imported breeds is of great importance. In this study, we genotyped small populations belonging to 14 breeds and 7 crossbreds using an Illumina Chicken 60K SNP (Single Nucleotide Polymorphisms) BeadChip and looked for appropriate methods to characterize their purity/variability. It was not straightforward to identify crossbred individuals, and the best approach was based on calculating the length and number of homozygous regions, or runs of homozygosity (ROH), in the populations studied. The latter enabled most accurate identification of crossbreds and can be served as an effective tool in testing genome-wide purity of chicken breeds. Abstract Preserving breed uniqueness and purity is vitally important in developing conservation/breeding programs for a germplasm collection of rare and endangered chicken breeds. The present study was aimed at analyzing SNP genetic variability of 21 small local and imported purebred and F1 crossbred populations and identifying crossbreeding events via whole-genome evaluation of runs of homozygosity (ROH). The admixture models more efficiently reflected population structure, pinpointing crossbreeding events in the presence of ancestral populations but not in their absence. Multidimensional scaling and FST-based analyses did not discriminate properly between purebred populations and F1 crossbreds, especially when comparing related breeds. When applying the ROH-based approach, more and longer ROHs were revealed in purebred individuals/populations, suggesting this as an effective implement in genome-wide analysis of germplasm breed purity

Assessing the effects of rare alleles and linkage disequilibrium on estimates of genetic diversity in the chicken populations

Phenotypic diversity in poultry has been mainly driven by artificial selection and genetic drift. These led to the adaptation to the environment and the development of specific phenotypic traits of chickens in response to their economic use. This study evaluated genetic diversity within and between Russian breeds and populations using Illumina Chicken 60 K SNP iSelect BeadChip by analysing genetic differences between populations with Hudson's fixation index (FST statistic) and heterozygosity. We estimated the effect of rare alleles and linkage disequilibrium (LD) on these measurements. To assess the effect of LD on the genetic diversity population, we carried out the LD-based pruning (LD < 0.5 and LD < 0.1) for seven chicken populations combined (I) or separately (II). LD pruning was specific for different dataset groups. Because of the noticeably large sample size in the RussianWhite RG population, pruningwas substantial for Dataset I, and FST valueswere only positivewhen LD< 0.1 pruning was applied. For Dataset II, the LD pruning results were confirmed by examining heterozygosity and alleles' frequency distribution. LD between single nucleotide polymorphisms was consistent across the seven chicken populations, except the RussianWhite RG populationwith the smallest r2 values and the largest effective population size. Our findings suggest to study variability in each population LD pruning has to be carried separately not after merging to avoid bias in estimates

Risk of sperm disorders and impaired fertility in frozen–thawed bull semen: a genome-wide association study

Simple Summary This study tackles the genetic aspects of the risk of sperm damage and related impaired fertility when handling frozen–thawed bull semen for artificial insemination. To this end, we performed genomic association analysis to identify relevant genetic markers and candidate genes associated with various abnormalities in frozen–thawed Holstein cattle sperm. The results provide important insights into the molecular mechanisms underlying sperm morphology and abnormalities after cryopreservation. Further research is needed to explore causative genetic variants and implement these findings to improve animal reproduction and breeding. Abstract 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

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 NME8, OR2AP1 and 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

Selection-driven chicken phenome and phenomenon of pectoral angle variation across different chicken phenotypes

An appreciation of the synergy between genome and phenome of poultry breed is essential for a complete understanding of their biology. Phenotypic traits are shaped under the influence of artificial, production-oriented, selection that often acts contrary to that which would occur during natural selection. In this comparative study, we analysed the phenotypic diversity of 39 chicken breeds and populations that make up a significant part of the world gene pool. Grouping patterns of breeds found within the traditional, phenotypic models of their classification/clustering required in-depth analysis using sophisticated mathematical approaches. As a result of studying performance and conformation phenotypes, a phenomenon of previously underestimated variability in pectoral angle (PA) was revealed. Moreover, patterns of PA relationship with productive traits were analysed. We propose using PA measurement as a promising new auxiliary index for selecting hens and roosters of breeding flocks in egg production improvement programs

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 phenomewide association/mediation analyses

ИЗУЧЕНИЕ АПОПТОЗА В ЛИМФАТИЧЕСКИХ УЗЛАХ ЗОНЫ АБДОМИНАЛЬНОЙ ЛИМФОДИССЕКЦИИ ПОСЛЕ ИНТРАОПЕРАЦИОННОЙ ФОТОДИНАМИЧЕСКОЙ ТЕРАПИИ ПРИ ЗЛОКАЧЕСТВЕННЫХ НОВООБРАЗОВАНИЯХ ЖЕЛУДОЧНО-КИШЕЧНОГО ТРАКТА

The method of DNA-electrophoresis was used to study apoptosis in the lymph nodes of the abdominal lymphodissection zone after local intraoperative photodynamic therapy (PDT) for the gastrointestinal cancers. Apoptosis (apoptotic ladder) was determined in the four cell populations of lymph nodes:– in the lymph nodes with metastases that have not been irradiated;– in the irradiated during PDT lymph nodes with metastases;– in the lymph nodes without metastases that have not been irradiated;– in the irradiated during PDT lymph nodes without metastases.The implementation of this study was possible due to intraoperative division of lymph nodes into two parts, one of which was removed while another one intentionally wasn’t removed and was irradiated (in human). It was also removed 60-90 minutes after PDT treatment and examined for apoptosis. As a result, it was found that apoptosis is detected in the irradiated during PDT lymph nodes with metastases. The obtained results show the fact that in the lymph nodes of the abdominal lymphodissection zone tumor cells selectively die by apoptosis as a result of the local intraoperative photodynamic therapy (PDT) for the gastrointestinal cancers while in non-malignant cells apoptosis doesn’t occur after PDT (p &lt;0.01). Thus, the obtained clinical and experimental data made it possible to evaluate the target PDT effect and confirm the safety of the photodynamic effect on healthy tissues of the lymphoid system located in the irradiation zone.Методом ДНК-электрофореза исследован апоптоз в лимфоузлах после интраоперационной фотодинамической терапии (ФДТ) зоны абдоминальной лимфодиссекции при злокачественных новообразованиях желудочно-кишечного тракта. Апоптоз («апоптотическую лестницу») определяли в четырех клеточных популяциях лимфоузлов:– в лимфоузлах с метастазами, не подвергавшихся ФДТ;– в тех же лимфоузлах с метастазами после ФДТ;– в лимфоузлах без метастазов, не подвергавшихся ФДТ;– в тех же лимфоузлах без метастазов после ФДТ. Дизайн исследования включал интраоперационное разделение лимфоузлов на две части, одна из которых была сразу удалена и не подвергалась воздействию ФДТ, а вторая оставалась неудаленной и подвергалась ФДТ, затем через 60–90 мин после сеанса ФДТ также была удалена и исследована на апоптоз. В результате оказалось, что апоптоз обнаруживается только в лимфоузлах с метастазами, облучённых во время ФДТ. Полученные результаты указывают на тот факт, что в лимфоузлах зоны абдоминальной лимфодиссекции в результате местной интраоперационной ФДТ при злокачественных новообразованиях желудочно-кишечного тракта злокачественные клетки избирательно гибнут путём апоптоза, а незлокачественные клетки при этом в апоптоз не вступают (р&lt;0,01). Таким образом, полученные клинические данные позволили оценить таргетный эффект ФДТ и подтвердить безопасность фотодинамического воздействия на здоровые ткани лимфоидной системы, находящихся в зоне облучения

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

APOPTOSIS IN THE LYMPH NODES OF THE ABDOMINAL LYMPHODISSECTION ZONE AFTER LOCAL INTRAOPERATIVE PHOTODYNAMIC THERAPY OF GASTROINTESTINAL CANCERS

The method of DNA-electrophoresis was used to study apoptosis in the lymph nodes of the abdominal lymphodissection zone after local intraoperative photodynamic therapy (PDT) for the gastrointestinal cancers. Apoptosis (apoptotic ladder) was determined in the four cell populations of lymph nodes:– in the lymph nodes with metastases that have not been irradiated;– in the irradiated during PDT lymph nodes with metastases;– in the lymph nodes without metastases that have not been irradiated;– in the irradiated during PDT lymph nodes without metastases.The implementation of this study was possible due to intraoperative division of lymph nodes into two parts, one of which was removed while another one intentionally wasn’t removed and was irradiated (in human). It was also removed 60-90 minutes after PDT treatment and examined for apoptosis. As a result, it was found that apoptosis is detected in the irradiated during PDT lymph nodes with metastases. The obtained results show the fact that in the lymph nodes of the abdominal lymphodissection zone tumor cells selectively die by apoptosis as a result of the local intraoperative photodynamic therapy (PDT) for the gastrointestinal cancers while in non-malignant cells apoptosis doesn’t occur after PDT (p &lt;0.01). Thus, the obtained clinical and experimental data made it possible to evaluate the target PDT effect and confirm the safety of the photodynamic effect on healthy tissues of the lymphoid system located in the irradiation zone

Novel Highly Efficient Green and Reusable Cu(II)/Chitosan-Based Catalysts for the Sonogashira, Buchwald, Aldol, and Dipolar Cycloaddition Reactions

In this study, new Cu(II)/chitosan-based systems were designed via (i) the treatment of chitosan with sodium sulfate (1a) or sodium acetate (1b); (ii) the coating of 1a or 2a with a sodium hyaluronate layer (2a and 2b, correspondingly); (iii) the treatment of a cholesterol–chitosan conjugate with sodium sulfate (3a) or sodium acetate (3b); and (iv) the succination of 1a and 1b to afford 4a and 4b or the succination of 2a and 2b to yield 5a and 5b. The catalytic properties of the elaborated systems in various organic transformations were evaluated. The use of copper sulfate as the source of Cu2+ ions results in the formation of nanoparticles, while the use of copper acetate leads to the generation of conventional coarse-grained powder. Cholesterol-containing systems have proven to be highly efficient catalysts for the cross-coupling reactions of different types (e.g., Sonogashira, Buchwald–Hartwig, and Chan–Lam types); succinated systems coated with a layer of hyaluronic acid are promising catalysts for the aldol reaction; systems containing inorganic copper(II) salt nanoparticles are capable of catalyzing the nitrile-oxide-to-nitrile 1,3-dipolar cycloaddition. The elaborated catalytic systems efficiently catalyze the aforementioned reactions in the greenest solvent available, i.e., water, and the processes could be conducted in air. The studied catalytic reactions proceed selectively, and the isolation of the product does not require column chromatography. The product is separated from the catalyst by simple filtration or centrifugation