Molecular epidemiology, phylogeny, and phylodynamics of CRF63_02A1, a recently originated HIV-1 circulating recombinant form spreading in Siberia

The HIV-1 epidemic in Russia is dominated by the former Soviet Union subtype A (A(FSU)) variant, but other genetic forms are circulating in the country. One is the recently described CRF63_02A1, derived from recombination between a CRF02_AG variant circulating in Central Asia and A(FSU), which has spread in the Novosibirsk region, Siberia. Here we phylogenetically analyze pol and env segments from 24 HIV-1 samples from the Novosibirsk region collected in 2013, with characterization of three new near full-length genome CRF63_02A1 sequences, and estimate the time of the most recent common ancestor (tMRCA) and the demographic growth of CRF63_02A1 using a Bayesian method. The analyses revealed that CRF63_02A1 is highly predominant in the Novosibirsk region (81.2% in pol sequences) and is transmitted both among injecting drug users and by heterosexual contact. Similarity searches with database sequences combined with phylogenetic analyses show that CRF63_02A1 is circulating in East Kazakhstan and the Eastern area of Russia bordering China. The analyses of near full-length genome sequences show that its mosaic structure is more complex than reported, with 18 breakpoints. The tMRCA of CRF63_02A1 was estimated around 2006, with exponential growth in 2008-2009 and subsequent stabilization. These results provide new insights into the molecular epidemiology, phylogeny, and phylodynamics of CRF63_02A1.We thank the personnel at the Genomic Unit of Instituto de Salud Carlos III, Majadahonda, Madrid, Spain, for technical assistance in sequencing, and Bonnie Mathieson, from the Office of AIDS Research, National Institutes of Health, Bethesda, Maryland for her support of this study. This work was funded by Office of AIDS Research, National Institutes of Health, through the training program “Molecular Epidemiology of HIV-1 in Eastern Europe and Its Significance for Vaccine Development.”S

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

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

Comparative analysis of molecular RFLP and SNP markers in assessing and understanding the genetic diversity of various chicken breeds

Monitoring the genetic diversity of small populations is important with respect to conserving rare and valuable chicken breeds, as well as discovery and innovation in germplasm research and application. Restriction fragment length polymorphisms (RFLPs), the molecular markers that underlie multilocus DNA fingerprinting (MLDF), have historically been employed for this purpose, but over the past two decades, there has been an irreversible shift toward high-throughput single-nucleotide polymorphisms (SNPs). In this study, we conducted a comparative analysis of archived MLDF results and new data from whole-genome SNP genotyping (SNPg) among 18 divergently selected breeds representing a large sample of the world gene pool. As a result, we obtained data that fit the general concept of the phylogenetic distribution of the studied breeds and compared them with RFLP and SNP markers. RFLPs were found to be useful markers for retrospective assessment of changes in the genetic architecture and variability underlying the phenotypic variation in chicken populations, especially when samples from previous generations used for MLDF are unavailable for SNPg. These results can facilitate further research necessary to assess the possibility of extrapolating previous MLDF results to study the long-term dynamics of genetic diversity in various small chicken germplasm populations over time. In general, the whole-genome characterization of populations and breeds by multiple SNP loci will further form the basis for the development and implementation of genomic selection with the aim of effective use of the genetic potential of the domestic gene pool in the poultry industry

Evolutionary subdivision of domestic chickens: implications for local breeds as assessed by phenotype and genotype in comparison to commercial and fancy breeds

To adjust breeding programs for local, commercial, and fancy breeds, and to implement molecular (marker-assisted) breeding, a proper comprehension of phenotypic and genotypic variation is a sine qua non for breeding progress in animal production. Here, we investigated an evolutionary subdivision of domestic chickens based on their phenotypic and genotypic variability using a wide sample of 49 different breeds/populations. These represent a significant proportion of the global chicken gene pool and all major purposes of breed use (according to their traditional classification model), with many of them being characterized by a synthetic genetic structure and notable admixture. We assessed their phenotypic variability in terms of body weight, body measurements, and egg production. From this, we proposed a phenotypic clustering model (PCM) including six evolutionary lineages of breed formation: egg-type, meat-type, dual purpose (egg-meat and meat-egg), game, fancy, and Bantam. Estimation of genotypic variability was carried out using the analysis of five SNPs, i.e., at the level of genomic variation at the NCAPG-LCORL locus. Based on these data, two generally similar genotypic clustering models (GCM1 and GCM2) were inferred that also had several overlaps with PCM. Further research for SNPs associated with economically important traits can be instrumental in marker-assisted breeding programs

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

[Genetic variation of the NCAPG-LCORL locus in chickens of local breeds based on SNP genotyping data] Генетическая изменчивость локуса NCAPG-LCORL у кур локальных пород на основе данных SNP-генотипирования

Using SNP analysis, genomic variation of the NCAPG-LCORL locus in chickens of 49 gene pool breeds and crossbreds from the Genetic Collection of Rare and Endangered Chicken Breeds was analyzed. Genotyping was performed using an Illumina Chicken 60K SNP iSelect BeadChip. As a result of SNP scanning, five significant SNPs were identified in the NCAPG-LCORL region in all breeds and crossbreds of the analyzed groups of chickens for GGA4. Cluster analysis of admixture models revealed a subdivision of individuals according to their origin at K = 5. Chickens of the egg and meat types formed two separate clusters, which is consistent with the results of genotype frequencies. When analyzing genetic differentiation between groups of chickens with different utility types on the basis of pairwise FST values, significant differences (p < 0.05) were found for the group of egg-type chickens in comparison with meat-type (0.330), dual purpose (meat-egg, 0.178), game (0.225 ) and dual purpose (egg-meat, 0.237) chickens, as well as for meat-type relative to fancy chickens (0.153). The results showed that the compared groups differ genetically from each other, which is confirmed by the data on genotype frequencies. The population specificity of the linkage disequilibrium structure at the NCAPG-LCORL locus was revealed for 11 chicken breeds. В ходе исследования с помощью анализа однонуклеотидного полиморфизма (SNP) была проанализирована геномная изменчивость локуса NCAPG-LCORL у кур 49 генофондных пород и гибридных форм из «Генетической коллекции редких и исчезающих пород кур». Генотипирование проводили с помощью чипа Illumina Chicken 60K SNP iSelect BeadChip. В результате SNP-сканирования у всех пород и гибридов анализируемых групп кур на GGA4 в регионе, включающем NCAPG-LCORL, и в области рядом с этим регионом определено пять значимых SNPs, которые могут быть кандидатами для селекции с помощью маркеров (MAS). Кластерный анализ адмикс-моделей обнаружил разделение особей соответственно их происхождению при К=5. Куры яичного и мясного направления продуктивности сформировали два обособленных кластера, что согласуется с результатами частот генотипов. При анализе генетической дифференциации между группами кур различного направления продуктивности на основе попарных FST-значений отмечены достоверные различия (p < 0,05) для группы кур яичного направления продуктивности в сравнении с мясными (0,330), мясо-яичными (0,178), бойцовыми (0,225) и яично-мясными (0,237), а также для кур мясного направления продуктивности относительно декоративных (0,153). Результаты показали, что сравниваемые группы отличаются генетически друг от друга, что подтверждается данными о частотах генотипов. Выявлена популяционная специфичность структуры неравновесия по сцеплению (LD) по локусу NCAPG-LCORL для 11 пород кур

Phenological shifts of abiotic events, producers and consumers across a continent

Ongoing climate change can shift organism phenology in ways that vary depending on species, habitats and climate factors studied. To probe for large-scale patterns in associated phenological change, we use 70,709 observations from six decades of systematic monitoring across the former Union of Soviet Socialist Republics. Among 110 phenological events related to plants, birds, insects, amphibians and fungi, we find a mosaic of change, defying simple predictions of earlier springs, later autumns and stronger changes at higher latitudes and elevations. Site mean temperature emerged as a strong predictor of local phenology, but the magnitude and direction of change varied with trophic level and the relative timing of an event. Beyond temperature-associated variation, we uncover high variation among both sites and years, with some sites being characterized by disproportionately long seasons and others by short ones. Our findings emphasize concerns regarding ecosystem integrity and highlight the difficulty of predicting climate change outcomes. The authors use systematic monitoring across the former USSR to investigate phenological changes across taxa. The long-term mean temperature of a site emerged as a strong predictor of phenological change, with further imprints of trophic level, event timing, site, year and biotic interactions.Peer reviewe

Identification of Key Candidate Genes in Runs of Homozygosity of the Genome of Two Chicken Breeds, Associated with Cold Adaptation

It is well known that the chicken gene pools have high adaptive abilities, including adaptation to cold environments. This research aimed to study the genomic distribution of runs of homozygosity (ROH) in a population of Russian White (RW) chickens as a result of selection for adaptation to cold environments in the early postnatal period, to perform a structural annotation of the discovered breed-specific regions of the genome (compared to chickens of the Amroks breed) and to suggest key candidate genes associated with the adaptation of RW chickens to cold environments. Genotyping of individual samples was performed using Illumina Chicken 60K SNP BeadChip&reg; chips. The search for homozygous regions by individual chromosomes was carried out using the PLINK 1.9 program and the detectRuns R package. Twelve key genes on breed-specific ROH islands were identified. They may be considered as potential candidate genes associated with the high adaptive ability of chickens in cold environments in the early postnatal period. Genes associated with lipid metabolism (SOCS3, NDUFA4, TXNRD2, IGFBP 1, IGFBP 3), maintaining body temperature in cold environments (ADIPOQ, GCGR, TRPM2), non-shivering thermogenesis (RYR2, CAMK2G, STK25) and muscle development (METTL21C) are perspectives for further research. This study contributes to our understanding of the mechanisms of adaptation to cold environments in chickens and provides a molecular basis for selection work