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Calypogeia is a genus of liverworts in the family Calypogeiaceae. The subject of this study was Calypogeia suecica. Samples of the liverwort Calypogeia suecica were collected from various places in southern Poland. A total of 25 samples were collected in 2021, and 25 samples were collected in 2022. Volatile organic compounds (VOCs) from liverworts were analyzed by gas chromatography–mass spectrometry (GC–MS). A total of 107 compounds were detected, of which 38 compounds were identified. The identified compounds were dominated by compounds from the sesquiterpene group (up to 34.77%) and sesquiterpenoids (up to 48.24%). The tested samples of Calypogeia suecica also contained compounds belonging the aromatic classification (up to 5.46%), aliphatic hydrocarbons (up to 1.66%), and small amounts of monoterpenes (up to 0.17%) and monoterpenoids (up to 0.30%). Due to the observed differences in the composition of VOCs, the tested plant material was divided into two groups, in accordance with genetic diversity. [ABSTRACT FROM AUTHOR]

The first report of African swine fever virus (ASFV) genotype II in Italy in 2022 marked the beginning of a significant invasion in at least eight Italian regions with different infection clusters. In this study, we used the multi-gene approach to investigate the epidemiological associations between ASFV strains causing cases and outbreaks in wild boar and pigs in Italy from January 2022 to the end of 2023. Our results confirm that all the tested ASFV-positive Italian samples belonged to genotype II and show high homology with genotype II ASFV sequences previously collected in Eurasian countries. Molecular characterization revealed the presence of four genetic groups in Italy. The majority of African swine fever (ASF) samples analyzed in the current study (72%) belonged to genetic group 3, which was the most representative in Europe. The results also provide evidence of the prevalence of genetic group 19 (15.9%). In addition, we identified new putative genetic groups, genetic group 25 (9.1%) and genetic group 26 (3.0%), which have never been described before. This is the first detailed report on the molecular characterization of more than 130 ASFV strains circulating in Italy. [ABSTRACT FROM AUTHOR]

As tilapia aquaculture expands globally, cold sensitivity remains a critical issue, leading to significant losses due to poor growth, disease susceptibility, and high mortality. This study evaluated the cold tolerance in fry of three tilapia varieties, incorporating a comprehensive analysis of 3240 specimens. The fry, segregated by variety into different tanks, were observed during summer to assess their performance. The study focused on two commercially prominent varieties, known for their rapid weight gain, and a third variety developed by the Federal University of Lavras, specifically bred for resilience to local climatic conditions. Following a 15-day acclimation period in experimental tanks, the fry were monitored for feeding to apparent satiety. Daily assessments included counting mortalities and measuring water temperature and dissolved oxygen levels. Survival data were analyzed using multivariate Cox regression, with survival curves derived via the Kaplan-Meier method. Lifespan predictions from these curves were compared using the log-rank test. Results indicated that older fry were more resilient to cold stress. Notably, the MGTUP variety, bred for local environmental adaptability, demonstrated superior cold tolerance. This variety also exhibited the lowest mortality rates across all age groups. These findings suggest that utilizing locally adapted tilapia varieties can significantly mitigate losses in aquaculture, especially in cold-prone regions.

Simple Summary: Maize is one of the major crops of the world for feed, food, and industrial uses. It originated in Central America and was first introduced into Europe at the end of the 15th century. Due to its adaptability, farmers and breeders across Europe have developed a wide diversity of local maize varieties with different characteristics over the past centuries. Many of these are conserved in genebanks' seed collections, but little is known about their specific characteristics. Here, we present results obtained by the European Evaluation Network for Maize, a private–public partnership with partners from nine countries aimed at promoting the valorization of maize genetic resources in breeding programs. The work describes the selection and the genetic and phenotypic evaluation of a collection of 626 maize landraces preserved in European genebanks, providing evidence for historic introductions and geographic adaptation. In a world where climate change, rising food prices, and other issues are affecting food security and the environment, the conservation and use of crop diversity is becoming increasingly important. The results of our study will facilitate the use of maize genetic resources in breeding for resilience to climate change, for sustainable agriculture, food security, and food quality. The ECPGR European Evaluation Network (EVA) for Maize involves genebanks, research institutions, and private breeding companies from nine countries focusing on the valorization of maize genetic resources across Europe. This study describes a diverse collection of 626 local landraces and traditional varieties of maize (Zea mays L.) from nine European genebanks, including criteria for selection of the collection and its genetic and phenotypic diversity. High-throughput pool genotyping grouped the landraces into nine genetic groups with a threshold of 0.6 admixture, while 277 accessions were designated admixed and likely to have resulted from previous breeding activities. The grouping correlated well with the geographic origins of the collection, also reflecting the various pathways of introduction of maize to Europe. Phenotypic evaluations of 588 accessions for flowering time and plant architecture in multilocation trials over three years confirmed the great diversity within the collection, although phenotypic clusters only partially correlated with the genetic grouping. The EVA approach promotes conservation of genetic resources and opens an opportunity to increase genetic variability for developing improved varieties and populations for farmers, with better adaptation to specific environments and greater tolerance to various stresses. As such, the EVA maize collection provides valuable sources of diversity for facing climate change due to the varieties' local adaptation. [ABSTRACT FROM AUTHOR]

Biscuit bran (BB) is a co-product with worldwide distribution, with Brazil as the second largest cookie producer in the world with 1,157,051 tons. We evaluate the impact of completely replacing corn with BB on the characteristics and morphometry of carcass of purebred and crossbred Morada Nova lambs using machine learning techniques as an auxiliary method. Twenty male lambs from two genetic groups (GG) were used: purebred red-coated Morada Nova (MNR) and crossbred MNR × white-coated Morada Nova (MNF1). Supervised and unsupervised machine learning techniques were used. No interaction (P > 0.05) was observed between diets (D) and genetic groups (GG) and no simple isolated effect was observed for carcass characteristics, qualitative-quantitative typification of the Longissimus dorsi muscle, weight of non-carcass components, weight and yield of commercial cuts and carcass morphometric measurements. The formation of two horizontal clusters was verified: (i) crossed lambs with corn and BB and (ii) purebred lambs fed corn and BB. Vertically, three clusters were formed based on carcass and meat characteristics of native lambs: (i) thermal insulation, body capacity, true yield, and commercial cuts; (ii) choice, performance, physical carcass traits, and palatability; and (iii) yield cuts and non-carcass components. The heatmap also allowed us to observe that pure MN lambs had a greater body capacity when fed BB, while those fed corn showed superiority in commercial cuts, true yields, and non-carcass components. Crossbred lambs, regardless of diet, showed a greater association of physical characteristics of the carcass, performance, palatability, and less noble cuts. Crossbred lambs, regardless of diet, showed a greater association of physical characteristics of the carcass, performance, palatability, and less noble cuts. BB can be considered an alternative energy source in total replacement of corn. Integrating of machine learning techniques is a useful statistical tool for studies with large numbers of variables, especially when it comes to analyzing complex data with multiple effects in the search for data patterns and insights in decision-making on the farm. [ABSTRACT FROM AUTHOR]

The Targhee breed is important to range sheep production in the Western United States. The objective of this research was to integrate industry sires participating in national genetic evaluation through the National Sheep Improvement Program (NSIP) into the U.S. Sheep Experiment Station (USSES) flock, where the breed originated, to benchmark sire performance. Estimated breeding values (EBV) of industry sires (n = 16) and USSES sires (n = 12) from the 2023 NSIP Targhee genetic evaluation differed (P < 0.05) only for the NSIP Number Born EBV. This difference, and small (nonsignificant) differences favoring industry sires for maternal weaning weight, yearling fiber diameter, and yearling staple length EBV also resulted in greater (P < 0.05) Western Range Index scores for industry sires. The performance of sires' direct progeny born 2016 to 2018 was compared for 17 traits. After data cleaning, there were 664 progeny (417 from industry sires and 247 from USSES sires) with 146 to 664 records per trait. Least squares means differed (P  < 0.05) for grease fleece weight, side fiber diameter, and britch fiber diameter in favor of the industry sires. Production traits were measured from the progeny and other retained descendants of both sire genetic groups from 2016 through 2022. After data cleaning, there was a range of 1,138 to 1,493 records per trait. A three-generation pedigree was constructed and the proportional assignment of each lamb to each genetic group (e.g. 0.5 industry, 0.5 USSES) was included in an augmented relationship matrix. A univariate animal model was fitted for each lamb trait and a repeated measures model for each of the three ewe traits was fitted to estimate variance components and predict breeding values. Genetic group solutions did not differ (P  > 0.05) for any of these traits but provided a means by which to compare the two groups. Establishment of a Targhee genetic reference flock at USSES has been initiated, which can be used to address issues of importance to the industry. [ABSTRACT FROM AUTHOR]

Abstract The objective of this work was to compare nitrous oxide (N2O) emissions from urine and manure of Nellore and crossbred (Nellore x Angus) cattle finished in feedlot. Twenty Nellore and 20 crossbred bulls were fed a diet consisting of 75% concentrate and 25% roughage. Excreta were applied to the pens after 43 days of confinement, when N2O monitoring started through static chambers. The data were subjected to the analysis of variance, and averages were compared by Tukey’s test. The N2O fluxes from urine and manure were similar among the breeds, with important peaks after rain events. The cumulative emissions of N2O from urine per kilogram of body weight gain (BWG) and the total emissions from manure per kilogram of BWG were 22.7% and 24.4% higher in Nellore cattle. There is no breed effect on N2O flux and cumulative emissions by excreta from confined beef cattle; however, the crossbreed emits less per kilogram of BWG. There is a high correlation between rainfall volume and the N2O emissions of the next day, which indicates a period between rain occurrence and the increase in N2O emission.

Introduction. Genetic diversity, registration, and traceability of cacao planting material are the essential tripod to support its sustainable cultivation. In Nicaragua, cocoa planting material is mostly obtained from seeds, which leads to great variability in yield, bean quality, and tolerance to pests and diseases. Farmers, technical staff, development projects, and investors depend on a limited supply of elite trees as a reliable source of genetic material to support new cacao fronts and meet market quality standards. Therefore, the development of a national genetic improvement program and a planting material traceability system in Nicaragua are necessary to improve the sustainability of cacao cultivation. Objective. To evaluate the genetic resources on farms and provide information for future breeding programs, as well as to lay foundation for a national traceability and certification system. Materials and methods. Fourty-nine elite trees selected by farmers in the main producing regions in Nicaragua between 2018 and 2020 were sampled. Ninety-three SNP markers were used to characterize them and resolve their genetic origins. Results. The evaluated cacao trees had a narrow genetic background, mainly composed of hybrids with Amelonado (36 %), Criollo (17 %) and Iquitos (15 %) origins. A set of trees with high genetic diversity that could be incorporated into a selection and breeding program was identified. Conclusion. Fingerprinting with SNP markers was a useful tool for evaluating the genetic links of cultivated cacao and can be used for varietal identity test at the farm level. The study provided the basis for developing both a breeding program and a traceability system of cacao planting material in Nicaragua.

IntroductionAfrican swine fever (ASF) is a contagious viral disease of pigs and wild boar that poses a major threat to the global swine industry. The genotype II African swine fever virus (ASFV) entered the European Union (EU) in 2014 and since then fourteen countries have been affected, Italy and North Macedonia being the last in 2022. While whole genome sequencing remains the gold standard for the identification of new genetic markers, sequencing of multiple loci with significant variations could be used as a rapid and cost-effective alternative to track outbreaks and study disease evolution in endemic areas.Materials and methodsTo further our understanding of the epidemiology and spread of ASFV in Europe, 382 isolates collected during 2007 to 2022 were sequenced. The study was initially performed by sequencing the central variable region (CVR), the intergenic region (IGR) between the I73R and I329L genes and the O174L and K145R genes. For further discrimination, two new PCRs were designed to amplify the IGR between the 9R and 10R genes of the multigene family 505 (MGF505) and the IGR between the I329L and I215L genes. The sequences obtained were compared with genotype II isolates from Europe and Asia.ResultsThe combination of the results obtained by sequencing these variable regions allowed to differentiate the European II-ASFV genotypes into 24 different groups. In addition, the SNP identified in the IGR I329L-I215L region, not previously described, grouped the viruses from North Macedonia that caused the 2022 outbreaks with viruses from Romania, Bulgaria, Serbia and Greece, differentiating from other genotype II isolates present in Europe and Asia. Furthermore, tandem repeat sequence (TRS) within the 9R-10R genes of the multigene family 505 (MGF505) revealed eight different variants circulating.DiscussionThese findings describe a new multi-gene approach sequencing method that can be used in routine genotyping to determine the origin of new introductions in ASF-free areas and track infection dynamics in endemic areas.

Simple Summary: The importance of the coat color in horses has been present since their domestication. The interactive effect of coat color-determinant genes on other traits, such as behavior, makes it a factor of importance in horse selection, as it determines the way the horse perceives and reacts to its environment. Eye temperature at rest (ETR) assessed with infrared thermography was used as a suitable non-invasive tool to assess basal reactivity. The aim of this study was to evaluate the influence of coat color on basal reactivity assessed with infrared thermography, determine their relationship with the results obtained in show jumping competitions, and to estimate the genetic parameters for ETR to test its suitability for genetic selection. Our results indicated differences in ETR due to six different factors. We also discovered a positive correlation with ranking in show jumping, indicating that less reactive horses were more likely to achieve better rankings. The genetic results indicated that part of the variability present in the basal reactivity due to coat color has an environmental origin. The heritability values indicate that ETR has a suitable genetic basis to be used in the breeding program to select for basal reactivity due to coat color. Horses have been valued for their diversity of coat color since prehistoric times. In particular, the pleiotropic effect that coat color genes have on behavior determines the way the horse perceives and reacts to its environment. The primary aim of this study was to evaluate the influence of coat color on basal reactivity assessed with infrared thermography as eye temperature at rest (ETR), determine their relation with the results obtained by these horses in Show Jumping competitions and to estimate the genetic parameters for this variable to test its suitability for genetic selection. A General Linear Model (GLM) and Duncan post-hoc analysis indicated differences in ETR due to coat color, sex, age, location, and breed-group factors. A Spearman's rank correlation of 0.11 (p < 0.05) was found with ranking, indicating that less reactive horses were more likely to achieve better rankings. Heritability values ranged from 0.17 to 0.22 and were computed with a model with genetic groups and a model with residual variance heterogeneity. Breeding values were higher with the last genetic model, thus demonstrating the pleiotropic effect of coat color. These results indicate that ETR has a suitable genetic basis to be used in the breeding program to select for basal reactivity due to coat color. [ABSTRACT FROM AUTHOR]

Western Iberia Early Neolithic has been described as an ultimate and very altered form of the Mediterranean Neolithisation process. Despite its Atlantic position, this territory – corresponding mainly to Central/Southern Portugal – is, in its physical and cultural geography, a Mediterranean landscape deeply connected to a historical process arriving from beyond the Strait of Gibraltar. The presence of cardial pottery led archaeologists to ascribe Portuguese Early Neolithic to a Mediterranean impressed Pottery cultural area, and according to demic diffusion models, small pioneer groups carrying the Neolithic package originated there. Recently, the archaeological record for the Western Mediterranean Neolithisation is becoming more complex and longer lasting cardial dominance over the seas has been disputed. Previous Neolithic groups seafaring the Mediterranean coasts with Impressa style pottery could have reached Iberian Peninsula by 5600–5400 cal BC, proving that by the mid-sixth millennium, different cultural entities were moving in the Western Mediterranean regardless of their genetic features. The main goal of this study is to disclose this cultural diversity in Western Iberia using a robust chronological database and debating how different proxies, like pottery styles and ancient DNA (aDNA), reveal it in Western Iberia. While recognising the Mediterranean input to Western Iberia groups, mapping the variability and the significance of different decoration techniques, such as cardial, false acacia leaf, impressed stripes, and using the aDNA to identify continuities/changes in ancient populations are here as tools to understand when, who, and how new kids came to the block. To do so, different disciplinary boundaries are crossed, and some transdisciplinary critical aspects are also commented.

Single-step genomic BLUP (ssGBLUP) model for routine genomic prediction of breeding values is developed intensively for many dairy cattle populations. Compatibility between the genomic (G) and the pedigree (A) relationship matrices remains an important challenge required in ssGBLUP. The compatibility relates to the amount of missing pedigree information. There are two prevailing approaches to account for the incomplete pedigree information: unknown parent groups (UPG) and metafounders (MF). unknown parent groups have been used routinely in pedigree-based evaluations to account for the differences in genetic level between groups of animals with missing parents. The MF approach is an extension of the UPG approach. The MF approach defines MF which are related pseudo-individuals. The MF approach needs a Γ matrix of the size number of MF to describe relationships between MF. The UPG and MF can be the same. However, the challenge in the MF approach is the estimation of Γ having many MF, typically needed in dairy cattle. In our study, we present an approach to fit the same amount of MF as UPG in ssGBLUP with Woodbury matrix identity (ssGTBLUP). We used 305-day milk, protein, and fat yield data from the DFS (Denmark, Finland, Sweden) Red Dairy cattle population. The pedigree had more than 6 million animals of which 207,475 were genotyped. We constructed the preliminary gamma matrix (Γpre) with 29 MF which was expanded to 148 MF by a covariance function (Γ148). The quality of the extrapolation of the Γpre matrix was studied by comparing average off-diagonal elements between breed groups. On average relationships among MF in Γ148 were 1.8% higher than in Γpre. The use of Γ148 increased the correlation between the G and A matrices by 0.13 and 0.11 for the diagonal and off-diagonal elements, respectively. [G]EBV were predicted using the ssGTBLUP and Pedigree-BLUP models with the MF and UPG. The prediction reliabilities were slightly higher for the ssGTBLUP model using MF than UPG. The ssGBLUP MF model showed less overprediction compared to other models.

Genetic groups have been widely adopted in tree breeding to account for provenance effects within pedigree-derived relationship matrices. However, provenances or genetic groups have not yet been incorporated into single-step genomic BLUP (“HBLUP”) analyses of tree populations. To quantify the impact of accounting for population structure in Eucalyptus globulus, we used HBLUP to compare breeding value predictions from models excluding base population effects and models including either fixed genetic groups or the marker-derived proxies, also known as metafounders. Full-sib families from 2 separate breeding populations were evaluated across 13 sites in the “Green Triangle” region of Australia. Gamma matrices (C) describing similarities among metafounders reflected the geographic distribution of populations and the origins of 2 land races were identified. Diagonal elements of C provided population diversity or allelic covariation estimates between 0.24 and 0.56. Genetic group solutions were strongly correlated with metafounder solutions across models and metafounder effects influenced the genetic solutions of base population parents. The accuracy, stability, dispersion, and bias of model solutions were compared using the linear regression method. Addition of genomic information increased accuracy from 0.41 to 0.47 and stability from 0.68 to 0.71, while increasing bias slightly. Dispersion was within 0.10 of the ideal value (1.0) for all models. Although inclusion of metafounders did not strongly affect accuracy or stability and had mixed effects on bias, we nevertheless recommend the incorporation of metafounders in prediction models to represent the hierarchical genetic population structure of recently domesticated populations. [ABSTRACT FROM AUTHOR]

Abstract Ongoing adaptive evolution, and resulting “evolutionary rescue” of declining populations, requires additive genetic variation in fitness. Such variation can be increased by gene flow resulting from immigration, potentially facilitating evolution. But, gene flow could in fact constrain rather than facilitate local adaptive evolution if immigrants have low additive genetic values for local fitness. Local migration‐selection balance and micro‐evolutionary stasis could then result. However, key quantitative genetic effects of natural immigration, comprising the degrees to which gene flow increases the total local additive genetic variance yet counteracts local adaptive evolutionary change, have not been explicitly quantified in wild populations. Key implications of gene flow for population and evolutionary dynamics consequently remain unclear. Our quantitative genetic analyses of long‐term data from free‐living song sparrows (Melospiza melodia) show that mean breeding value for local juvenile survival to adulthood, a major component of fitness, increased across cohorts more than expected solely due to drift. Such micro‐evolutionary change should be expected given nonzero additive genetic variance and consistent directional selection. However, this evolutionary increase was counteracted by negative additive genetic effects of recent immigrants, which increased total additive genetic variance but prevented a net directional evolutionary increase in total additive genetic value. These analyses imply an approximate quantitative genetic migration‐selection balance in a major fitness component, and hence demonstrate a key mechanism by which substantial additive genetic variation can be maintained yet decoupled from local adaptive evolutionary change.

Heritable genetic variation among free-living animals or plants is essential for populations to respond to selection and adapt. It is therefore important to be able to estimate additive genetic variance VA, which can be obtained using a GLMM known as the animal model. An underlying assumption of the standard animal model is that the study population is genetically unstructured, which is often unrealistic. In fact, admixture might be the norm rather than the exception in the wild, like in geographically structured populations, in the presence of (im)migration or in reintroduction and conservation contexts. Unfortunately, animal model estimators may be biased in such cases. The so-called genetic group animal models that account for genetically differentiated subpopulations have recently become popular, but methodology is currently only available for cases where relatedness among individuals can be estimated from pedigrees. 2. To ensure that genetic group animal models with heterogeneous VA remain applicable to populations with genomic data but no pedigrees, there is a clear need to generalize these models to the case when exclusively genomic data are available. We therefore introduce such methodology for wild admixed systems by extending methods that were recently suggested in the context of plant breeding. Our extension relaxes the limiting assumptions that currently restrict their use to artificial breeding set-ups. 3. We illustrate the usefulness of the extended genomic genetic group animal model on a wild admixed population of house sparrows resident in an island system in Northern Norway, where genome-wide data on more than 180,000 single nucleotide polymorphisms (SNPs) are available to derive genomic relatedness. We compare our estimates of quantitative genetic parameters to those derived from a corresponding pedigree-based genetic group animal model. The satisfactory agreement indicates that the new method works as expected. 4. Our extension of the very popular animal model ensures that the upcoming challenges with increasing availability of genomic data for quantitative genetic studies of wild admixed populations can be handled. To make the method widely available to the scientific community, we offer guidance in the form of a tutorial including step-by- step instructions to facilitate implementation. [ABSTRACT FROM AUTHOR]

Abstract Background R is a multi-platform statistical software and an object oriented programming language. The package archive network for R provides CRAN repository that features over 15,000 free open source packages, at the time of writing this article ( https://cran.r-project.org/web/packages , accessed in October 2019). The package ggroups is introduced in this article. The purpose of this package is providing functions for checking and processing the pedigree, calculation of the additive genetic relationship matrix and its inverse, which are used to study the population structure and predicting the genetic merit of animals. Calculation of the dominance relationship matrix and its inverse are also covered. A concept in animal breeding is genetic groups, which is about the inequality of the average genetic merits for groups of unknown parents. The package provides functions for the calculation of the matrix of genetic group contributions (Q). Calculating Q is computationally demanding, and depending on the size of the pedigree and the number of genetic groups, it might not be feasible using personal computers. Therefore, a computationally optimised function and its parallel processing alternative are provided in the package. Results Using sample data, outputs from different functions of the package were presented to illustrate a real experience of working with the package. Conclusions The presented R package is a free and open source tool mainly for quantitative geneticists and ecologists, who deal with pedigree data. It provides numerous functions for handling pedigree data, and calculating various pedigree-based matrices. Some of the functions are computationally optimised for large-scale data.

Abstract Quantifying additive genetic variances and cross‐sex covariances in reproductive traits, and identifying processes that shape and maintain such (co)variances, is central to understanding the evolutionary dynamics of reproductive systems. Gene flow resulting from among‐population dispersal could substantially alter additive genetic variances and covariances in key traits in recipient populations, thereby altering forms of sexual conflict, indirect selection, and evolutionary responses. However, the degree to which genes imported by immigrants do in fact affect quantitative genetic architectures of key reproductive traits and outcomes is rarely explicitly quantified. We applied structured quantitative genetic analyses to multiyear pedigree, pairing, and paternity data from free‐living song sparrows (Melospiza melodia) to quantify the differences in mean breeding values for major sex‐specific reproductive traits, specifically female extra‐pair reproduction and male paternity loss, between recent immigrants and the previously existing population. We thereby quantify effects of natural immigration on the means, variances, and cross‐sex covariance in total additive genetic values for extra‐pair paternity arising within the complex socially monogamous but genetically polygynandrous reproductive system. Recent immigrants had lower mean breeding values for male paternity loss, and somewhat lower values for female extra‐pair reproduction, than the local recipient population, and would therefore increase the emerging degree of reproductive fidelity of social pairings. Furthermore, immigration increased the variances in total additive genetic values for these traits, but decreased the magnitudes of the negative cross‐sex genetic covariation and correlation below those evident in the existing population. Immigration thereby increased the total additive genetic variance but could decrease the magnitude of indirect selection acting on sex‐specific contributions to paternity outcomes. These results demonstrate that dispersal and resulting immigration and gene flow can substantially affect quantitative genetic architectures of complex local reproductive systems, implying that comprehensive theoretical and empirical efforts to understand mating system dynamics will need to incorporate spatial population processes.

INFINITy includes two classification models: one for complete HA sequences (FULL HA, for whole gene sequence length of 1700 bp) and other for the HA1 subunit coding sequence (HA1, for the initial 1030 bp of the HA gene). Influenza clade classification is usually performed by phylogenetic analysis of HA gene sequences from circulating strains along with reference sequences, which is a time-consuming process and requires specific training and equipment. Keywords: clades; genetic groups; hemagglutinin; influenza; machine learning; sequence; subclades; subtyping EN clades genetic groups hemagglutinin influenza machine learning sequence subclades subtyping 1 3 3 01/31/23 20230101 NES 230101 Influenza viruses are one of the main agents causing acute respiratory infections (ARI) in humans resulting in a large amount of illness and death globally.[[1]] The influenza viruses classification is based on the nomenclature proposed by the World Health Organization (WHO)[3] that is widely accepted and used by the medical and scientific communities throughout the world. [Extracted from the article]

Mammillaria hernandezii, M. dixanthocentron and M. lanata are endemic and threatened cactus species that inhabit the Tehuacán Valley, an arid zone in southern México that has an important richness of cacti. Their populations have been exposed to habitat alteration and poaching. Available information regarding genetic diversity is limited, but necessary for their conservation, and collection and use of germplasm. We used microsatellite markers to determine genetic diversity and population genetic structure of six populations of M. hernandezii, four of M. dixanthocentron and a single recorded population for M. lanata. The levels of heterozygosity were moderate in the three species (M. hernandezii Ho = 0.46, M. dixanthocentron Ho = 0.45 and M. lanata Ho = 0.52), with significant differences in their allelic richness. The genetic differentiation between populations was significant in M. hernandezii (RST 0.22) and M. dixanthocentron (RST 0.17), with evidence of isolation by distance in M. dixanthocentron. Geographic isolation and inbreeding are the processes that seem to shape the genetic variability of populations and differentiation in these species. We identified three genetic groups for M. hernandezii, and five groups for M. dixanthocentron. Conservation and protection must be guaranteed in all three species, with special emphasis on populations with high genetic diversity and private alleles. Finally, we recommended establishing a program for the development of germplasm banks, to promote Mammillaria ssp. propagation as an emerging measure of ex situ conservation. [ABSTRACT FROM AUTHOR]

Abstract Background Forest trees can occupy extensive geography and environmentally highly variable areas which result in high genetic variability in the direction of pressure from natural selection. At the same time, the majority of conifer species are wind-pollinated from both short and long distances, resulting in wide-spread gene flow, which can lead to maladaptation to local conditions. Quantitative analyses of provenance/progeny tests correct for genetic differences between populations to ensure unbiased genetic parameters are obtained. Commonly, the provenance effect is fitted as a fixed term or can be implemented as a contemporary group in the pedigree. Results The use of a provenance effect, either as a fixed term or as the same contemporary groups in both maternal and paternal sides of the pedigree, resulted in fairly similar precision of genetic parameters in our case. However, when we developed a phantom contemporary group for the paternal side of the pedigree that considered a different genetic quality of pollen compared with the maternal contribution from trees in the local environment, the model fit and accuracy of breeding values increased. Conclusion Consideration of the mating dynamics and the vector of gene flow are important factors in modelling contemporary genetic groups, particularly when implementing pedigrees within a mixed model framework to obtain unbiased estimates of genetic parameters. This approach is especially important in traits involved in local adaptation.

The growing amount of genomic information in dairy cattle has increased computational and modeling challenges in the single-step evaluations. The computational challenges are due to the dense inverses of genomic (G) and pedigree (A 22) relationship matrices of genotyped animals in the single-step mixed model equations. An equivalent mixed model equation is given by single-step genomic BLUP that are based on the T matrix (ssGTBLUP), where these inverses are avoided by expressing G −1 through a product of 2 rectangular matrices, and (A 22)−1 through sparse matrix blocks of the inverse of full relationship matrix A −1. A proper way to account genetic groups through unknown parent groups (UPG) after the Quaas-Pollak transformation (QP) is one key factor in a single-step model. When the UPG effects are incompletely accounted, the iterative solving method may have convergence problems. In this study, we investigated computational and predictive performance of ssGTBLUP with residual polygenic (RPG) effect and UPG. The QP transformation used A −1 and, in the complete form, T and (A 22)−1 matrices as well. The models were tested with official Nordic Holstein milk production test-day data and model. The results show that UPG can be easily implemented in ssGTBLUP having RPG. The complete QP transformation was computationally feasible when preconditioned conjugate gradient iteration and iteration on data without explicitly setting up G or A 22 matrices were used. Furthermore, for good convergence of the preconditioned conjugate gradient method, a complete QP transformation was necessary. [ABSTRACT FROM AUTHOR]

The whitefly, Bemisia tabaci (Gennadius), is responsible for significant yield losses in many crops, including potato, by sucking the phloem sap and transmitting a number of plant viruses. B. tabaci is a complex of cryptic species which is commonly designated as genetic groups. The B. tabaci genetic groups differ biologically with respect to host plant preference, insecticidal resistance, reproduction capacity, and ability to transmit begomoviruses. Therefore, understanding genetic variation among populations is important for establishing crop-specific distribution profile and management. We sequenced the mitochondrial cytochrome oxidase I (mtCOI) gene of B. tabaci collected from major potato growing areas of India. BLAST analysis of the 24 mtCOI sequences with reference Gene Bank sequences revealed four B. tabaci genetic groups prevailing in this region. mtCOI analysis exhibited the presence of Asia II 1, Asia II 5, Asia 1, and MEAM1 B. tabaci genetic groups. Our study highlighted that a new genetic group Asia II 5 has been detected in Indo-Gangetic Plains. Further virus–vector relationship study of ToLCNDV with Asia II 5 B. tabaci revealed that females are efficient vector of this virus as compared to males. This behavior of females might be due to their ability to acquire more virus titer than males. This study will help in better understanding of whitefly genetic group mediated virus diseases. [ABSTRACT FROM AUTHOR]

Brettanomyces bruxellensis is described as a wine spoilage yeast with many mainly straindependent genetic characteristics, bestowing tolerance against environmental stresses and persistence during the winemaking process. Thus, it is essential to discriminate B. bruxellensis isolates at the strain level in order to predict their stress resistance capacities. Few predictive tools are available to reveal intraspecific diversity within B. bruxellensis species; also, they require expertise and can be expensive. In this study, a Random Amplified Polymorphic DNA (RAPD) adapted PCR method was used with three different primers to discriminate 74 different B. bruxellensis isolates. High correlation between the results of this method using the primer OPA-09 and those of a previous microsatellite analysis was obtained, allowing us to cluster the isolates among four genetic groups more quickly and cheaply than microsatellite analysis. To make analysis even faster, we further investigated the correlation suggested in a previous study between genetic groups and cell polymorphism using the analysis of optical microscopy images via deep learning. A Convolutional Neural Network (CNN) was trained to predict the genetic group of B. bruxellensis isolates with 96.6% accuracy. These methods make intraspecific discrimination among B. bruxellensis species faster, simpler and less costly. These results open up very promising new perspectives in oenology for the study of microbial ecosystems. [ABSTRACT FROM AUTHOR]

The study aimed to compare two grouping strategies for unknown parents or phantom parent groups (PPG) on the genetic evaluation of growth traits for Mexican Braunvieh cattle. Phenotypic data included birth (BW), weaning (WW) and yearling (YW) weights. Pedigree included 57,341 animals, fhe first strategy involved 12 PPG (G12) based on the birth year of the unknown parent's progeny and the sex of the unknown parent, while the second involved 24 PPG (G24) based on the birth year of the unknown parent's progeny and 4-selection pathways, fhe animal models included fixed effects and the random direct additive genetic effect; WW also included random maternal genetic and maternal permanent environmental effects. Product-moment correlations between EBV from GO (no PPG) and G12 were 0.96, 0.77 and 0.69 for BW, WW and YW, respectively, and between EBV from GO and G24 were 0.91, 0.54, and 0.53, respectively. Corresponding rank correlations between GO and G12 were 0.94, 0.77, and 0.72, and between GO and G24 were 0.89, 0.61, and 0.60. Genetic trends showed a base deviation from the genetic trend of GO, except for B W of G12. The results did not support the use of the two grouping strategies on the studied population and traits, and further research is required. Introducing PPG to the model, enough phenotype contribution from descendants to PPG, and avoiding collinearity between PPG and fixed effects are important. Genetic groups should reflect changes in the genetic structure of the population to the unknown parents, including different sources of genetic materials, and changes made by selection over time. [ABSTRACT FROM AUTHOR]

Common scab (CS) is a potato disease that significantly decreases the market value of potato tubers after the development of necrotic lesions on their surface. Streptomyces scabiei is the main causal agent of CS; however, other closely related species, including S. acidiscabies and S. turgidiscabies, have also been shown to cause the disease. In this study, we characterized the genetic and phenotypic diversity of Streptomyces spp. causing CS in Prince Edward Island, the main potato-producing province in Canada. Two hundred and ninety-six pathogenic Streptomyces spp. isolates were retrieved from diseased tubers harvested from six fields located across a longitudinal geographical gradient. Genome fingerprinting analyses using repetitive elements PCR (ERIC- and BOX-PCR) revealed 14 distinct genetic groups. Thirteen groups were taxonomically affiliated with S. scabiei, whereas the fourteenth group was affiliated with S. acidiscabies. Their geographical distribution was characterized and revealed that on average between six and eight different genetic groups were detected per field, with variable abundance. Virulence assays showed strong differences in virulence between the genetic groups, ranging from low to highly virulent. Interestingly, pathogenic Streptomyces spp. populations in each field seem to be dominated by the most virulent genetic groups. The results obtained will contribute to better understanding of the population dynamic of pathogenic Streptomyces spp. causing CS of potato and promoting the development of more efficient detection and intervention tools to manage this important potato disease. [ABSTRACT FROM AUTHOR]

The aim of this study was to evaluate the non-carcass components (NCC) of Berganês ecotype lambs of different sexual classes and genotypes using univariate and multivariate statistics, carrying out two experimental trials. In order to evaluate the effects of the sexual class, non-castrated males (BNC), castrated males (BC) and females (BF) of Berganês ecotype lambs were used, with mean initial body weight of 27 ± 3.1 kg. To evaluate crossbreeding, non-castrated male lambs of the genotypes Berganês (BG), Berganês × Santa Inês (BSI) and Berganês × Dorper (BD) were used, as well as the control Dorper × Santa Inês (DSI), all with mean initial body weight of 28 ± 3.8 kg. The weight and yield of the total by-products was higher for BNC. Regarding the genotype, BSI showed higher weight and yield of internal fat, but the weight and yield of the total by-products was higher for BG and BD. In factorial analysis (FA), the NCC, more correlated with empty body weight (EBW) and total weight gain (TWG), showed higher eigenvectors for factor 1. For factor 2, the weights and yields of internal fat and total viscera obtained higher eigenvectors. The discriminant analysis (DA) classified 100% of individuals in their respective sexes and genotypes. Therefore, the FA indicated that, among the NCC evaluated, the weights of liver, kidneys, GIT, skin and feets are determinant for obtaining EBW and TWG. The classification achieved by the DA indicates that the sexual classes and genotypes are heterogeneous. [ABSTRACT FROM AUTHOR]

Ongoing adaptive evolution, and resulting "evolutionary rescue" of declining populations, requires additive genetic variation in fitness. Such variation can be increased by gene flow resulting from immigration, potentially facilitating evolution. But, gene flow could in fact constrain rather than facilitate local adaptive evolution if immigrants have low additive genetic values for local fitness. Local migration‐selection balance and micro‐evolutionary stasis could then result. However, key quantitative genetic effects of natural immigration, comprising the degrees to which gene flow increases the total local additive genetic variance yet counteracts local adaptive evolutionary change, have not been explicitly quantified in wild populations. Key implications of gene flow for population and evolutionary dynamics consequently remain unclear. Our quantitative genetic analyses of long‐term data from free‐living song sparrows (Melospiza melodia) show that mean breeding value for local juvenile survival to adulthood, a major component of fitness, increased across cohorts more than expected solely due to drift. Such micro‐evolutionary change should be expected given nonzero additive genetic variance and consistent directional selection. However, this evolutionary increase was counteracted by negative additive genetic effects of recent immigrants, which increased total additive genetic variance but prevented a net directional evolutionary increase in total additive genetic value. These analyses imply an approximate quantitative genetic migration‐selection balance in a major fitness component, and hence demonstrate a key mechanism by which substantial additive genetic variation can be maintained yet decoupled from local adaptive evolutionary change. [ABSTRACT FROM AUTHOR]

Background: R is a multi-platform statistical software and an object oriented programming language. The package archive network for R provides CRAN repository that features over 15,000 free open source packages, at the time of writing this article (https://cran.r-project.org/web/packages, accessed in October 2019). The package ggroups is introduced in this article. The purpose of this package is providing functions for checking and processing the pedigree, calculation of the additive genetic relationship matrix and its inverse, which are used to study the population structure and predicting the genetic merit of animals. Calculation of the dominance relationship matrix and its inverse are also covered. A concept in animal breeding is genetic groups, which is about the inequality of the average genetic merits for groups of unknown parents. The package provides functions for the calculation of the matrix of genetic group contributions (Q). Calculating Q is computationally demanding, and depending on the size of the pedigree and the number of genetic groups, it might not be feasible using personal computers. Therefore, a computationally optimised function and its parallel processing alternative are provided in the package. Results: Using sample data, outputs from different functions of the package were presented to illustrate a real experience of working with the package. Conclusions: The presented R package is a free and open source tool mainly for quantitative geneticists and ecologists, who deal with pedigree data. It provides numerous functions for handling pedigree data, and calculating various pedigree-based matrices. Some of the functions are computationally optimised for large-scale data. [ABSTRACT FROM AUTHOR]

Quantifying additive genetic variances and cross‐sex covariances in reproductive traits, and identifying processes that shape and maintain such (co)variances, is central to understanding the evolutionary dynamics of reproductive systems. Gene flow resulting from among‐population dispersal could substantially alter additive genetic variances and covariances in key traits in recipient populations, thereby altering forms of sexual conflict, indirect selection, and evolutionary responses. However, the degree to which genes imported by immigrants do in fact affect quantitative genetic architectures of key reproductive traits and outcomes is rarely explicitly quantified. We applied structured quantitative genetic analyses to multiyear pedigree, pairing, and paternity data from free‐living song sparrows (Melospiza melodia) to quantify the differences in mean breeding values for major sex‐specific reproductive traits, specifically female extra‐pair reproduction and male paternity loss, between recent immigrants and the previously existing population. We thereby quantify effects of natural immigration on the means, variances, and cross‐sex covariance in total additive genetic values for extra‐pair paternity arising within the complex socially monogamous but genetically polygynandrous reproductive system. Recent immigrants had lower mean breeding values for male paternity loss, and somewhat lower values for female extra‐pair reproduction, than the local recipient population, and would therefore increase the emerging degree of reproductive fidelity of social pairings. Furthermore, immigration increased the variances in total additive genetic values for these traits, but decreased the magnitudes of the negative cross‐sex genetic covariation and correlation below those evident in the existing population. Immigration thereby increased the total additive genetic variance but could decrease the magnitude of indirect selection acting on sex‐specific contributions to paternity outcomes. These results demonstrate that dispersal and resulting immigration and gene flow can substantially affect quantitative genetic architectures of complex local reproductive systems, implying that comprehensive theoretical and empirical efforts to understand mating system dynamics will need to incorporate spatial population processes. [ABSTRACT FROM AUTHOR]

Genomic selection is widely used in dairy cattle breeding, but still, single-step models are rarely used in national dairy cattle evaluations. New computing methods have allowed the utilization of very large genomic data sets. However, an unsolved model problem is how to build genomic- (G) and pedigree- (A22) relationship matrices that satisfy the theoretical assumptions about the same scale and equal base populations. Incompatibility issues have also been observed in the manner in which the genetic groups are included in the model. In this study, we compared three approaches for accounting for missing pedigree information: (1) GT_H used the full Quaas and Pollak (QP) transformation for the genetic groups, including both the pedigree-based and the genomic-relationship matrices, (2) GT_A22 used the partial QP transformation that omitted QP transformation in G−1, and (3) GT_MF used the metafounder approach. In addition to the genomic models, (4) an official animal model with a unknown parent groups (UPG) from the QP transformation and (5) an animal model with the metafounder approach were used for comparison. These models were tested with Nordic Holstein test-day production data and models. The test-day data included 8.5 million cows with a total of 173.7 million records and 10.9 million animals in the pedigree, and there were 274,145 genotyped animals. All models used VanRaden method 1 in G and had a 30% residual polygenic proportion (RPG). The G matrices in GT_H and GT_A22 were scaled to have an average diagonal equal to that of A22. Comparisons between the models were based on Mendelian sampling terms and forward prediction validation using linear regression with solutions from the full- and reduced-data evaluations. Models GT_H and GT_A22 gave very similar results in terms of overprediction. The MF approach showed the lowest bias.

The aim of the present study was to evaluate the changes in physiological responses and serum biochemical panel in crossbred dairy cow populations kept in a hot climate environment. We used a population of 384 dairy cows of genetic groups ½Holstein × ½Guzerá (n = 105) and ¾Holstein × ¼Guzerá (n = 279) derived from the Brazilian semiarid region. The physiological responses analyzed were: respiratory rate (RR, movements/minute), rectal temperature (RT, °C), free thyroxine (T4, µg/mL) and thyroid-stimulating hormone (TSH, µUI/mL). The values of RR, RT, T4, TSH and serum levels of glucose, cholesterol, total protein, urea and creatinine were determined and correlated with milk production for 305 days, correlation lying only with TSH. Significant differences were observed just in milk production, RR and TSH comparing the genetic groups ½Holstein × ½Guzerá and ¾Holstein × ¼Guzerá. In conclusion, ¾Holstein × ¼Guzerá cows showed higher thyroid activity and milk production than ½Holstein × ½Guzerá cows, and may therefore be a better option for dairy production systems in semiarid regions.

The aim of this study was to evaluate thermoregulatory, behavioral, and production traits of Holstein/Gir dairy cows of different genetic compositions. The experiment was carried out in the municipality of Turvânia - GO, Brazil, from July to December 2017. Twenty lactating cows of two genetic groups (½ and ¾ Holstein/Gir [HG]) were used in a completely randomized design where they were subjected to a rotational-grazing system in 24 irrigated Mombasa grass pastures with one day of occupation and 24 days of rest, and fed a 22% CP supplemental concentrate diet. During the experimental period, thermoregulatory, behavioral, and production data were collected on 12 occasions, at 15-day intervals. Environmental data such as ambient temperature, air relative humidity, and temperature-humidity index were recorded. Number of hairs, hair length and thickness, body surface temperature, rectal temperature, and respiratory frequency were analyzed as thermoregulatory traits. The behavioral assessment was undertaken by observing the feeding behavior, rumination, rest, and other activities. To determine production traits, milk yield and composition were analyzed. A higher respiratory frequency was observed in ¾ HG cows compared with ½ HG cows (p0.05) between the two genetic groups, and the same was true for milk yield, fat and lactose contents, and somatic cell count.

Background: Forest trees can occupy extensive geography and environmentally highly variable areas which result in high genetic variability in the direction of pressure from natural selection. At the same time, the majority of conifer species are wind-pollinated from both short and long distances, resulting in wide-spread gene flow, which can lead to maladaptation to local conditions. Quantitative analyses of provenance/progeny tests correct for genetic differences between populations to ensure unbiased genetic parameters are obtained. Commonly, the provenance effect is fitted as a fixed term or can be implemented as a contemporary group in the pedigree. Results: The use of a provenance effect, either as a fixed term or as the same contemporary groups in both maternal and paternal sides of the pedigree, resulted in fairly similar precision of genetic parameters in our case. However, when we developed a phantom contemporary group for the paternal side of the pedigree that considered a different genetic quality of pollen compared with the maternal contribution from trees in the local environment, the model fit and accuracy of breeding values increased. Conclusion: Consideration of the mating dynamics and the vector of gene flow are important factors in modelling contemporary genetic groups, particularly when implementing pedigrees within a mixed model framework to obtain unbiased estimates of genetic parameters. This approach is especially important in traits involved in local adaptation. [ABSTRACT FROM AUTHOR]

An attack of a brown bear (Ursus arctos) on human was detected in November, 2014 in the Barabash village (Khasan region of the Primorski krai) located in close proximity to the national park Land of the Leopard. The bear was shot. The deviant behavior of the bear indicated the possibility of rabies. The diagnosis was confirmed by means of laboratory methods. The strain RABV/Ursus arctos/Russia/Primorye/PO 01/2014 (further PO 01) was isolated from the brain of the bear. PO 01 is the first completely sequenced Far Eastern strain of RABV. It can be considered as topotypic. PO 01 considerably differs from the vaccine strain RV 97 (GenBank EF542830) that is the basis of attenuated vaccine applied in the Land of the Leopard. At the same time, the immunodominant sites in PO 01 and RV 97 proteins differ slightly. It can be recommended to continue application of the vaccine. The analysis of the PO 01 genome (GenBank KP997032) revealed its belonging to the Eurasian genetic subgroup of the genotype 1 (street rage). Thus, this genetic subgroup stretches to the East. Expansion of the cross-border protected territories of Russia and China in the Far East demands the correct statistics of circulation of the lyssaviruses to be kept.

ABSTRACT We aimed to evaluate the impact of using embryo transfer (ET) information on weaning weight estimated breeding values (EBV) and its accuracy. Data from Hereford and Braford cattle, raised under extensive conditions in Southern Brazil, were used. A model that included ET information in addition to maternal (genetic and permanent environmental) effects as a function of foster dams was compared to a model without ET information. Accuracy of both bulls and calves increased due to inclusion of ET records in 0.04 and 0.12 points, respectively. In general, the inclusion of ET records provided a greater amount of phenotypic variance and most accurate EBV for sires and progeny. The results obtained in this study encourage the use of ET phenotypic records in large-scale genetic evaluation programs, especially for bulls that have most of their progeny coming from ET. Most of the Brazilian genetic evaluation programs do not use phenotypic records of ET animals. Therefore, breeding values are predicted based only on parentage average, which implies in underestimated accuracies. Considering that ET has been widely used in Brazil and that such information improves genetic predictions, we suggest modifying the traditional adopted models by considering ET information in the Brazilian genetic evaluations.

Abstract: Joint Nordic (Denmark, Finland, Sweden) genetic evaluation of female fertility is currently based on the multiple trait multilactation animal model (BLUP). Here, single step genomic model (ssGBLUP) was applied for the Nordic Red dairy cattle fertility evaluation. The 11 traits comprised of nonreturn rate and days from first to last insemination in heifers and first three parities, and days from calving to first insemination in the first three parities. Traits had low heritabilities (0.015–0.04), but moderately high genetic correlations between the parities (0.60–0.88). Phenotypic data included 4,226,715 animals with records and pedigree 5,445,392 animals. Unknown parents were assigned into 332 phantom parent groups (PPG). In mixed model equations animals were associated with PPG effects through the pedigree or both the pedigree and genomic information. Genotype information of 46,914 SNPs was available for 33,969 animals in the pedigree. When PPG used pedigree information only, BLUP converged after 2,420 iterations whereas the ssGBLUP evaluation needed over ten thousand iterations. When the PPG effects were solved accounting both the pedigree and the genomic information, the ssGBLUP model converged after 2,406 iterations. Also, with the latter model breeding values by ssGBLUP and BLUP became more consistent and genetic trends followed each other well. Models were validated using forward prediction of the young bulls. Reliabilities and variance inflation of predicted genomic breeding values (values for parent averages in brackets) for the 11 traits ranged 0.22–0.31 (0.10–0.27) and 0.81–0.95 (0.83–1.06), respectively. The ssGBLUP model gave always higher validation reliabilities than BLUP, but largest increases were for the cow fertility traits. [ABSTRACT FROM AUTHOR]

Quantifying sex‐specific additive genetic variance (VA) in fitness, and the cross‐sex genetic correlation (rA), is prerequisite to predicting evolutionary dynamics and the magnitude of sexual conflict. Further, quantifying VA and rA in underlying fitness components, and genetic consequences of immigration and resulting gene flow, is required to identify mechanisms that maintain VA in fitness. However, these key parameters have rarely been estimated in wild populations experiencing natural environmental variation and immigration. We used comprehensive pedigree and life‐history data from song sparrows (Melospiza melodia) to estimate VA and rA in sex‐specific fitness and underlying fitness components, and to estimate additive genetic effects of immigrants alongside inbreeding depression. We found evidence of substantial VA in female and male fitness, with a moderate positive cross‐sex rA. There was also substantial VA in male but not female adult reproductive success, and moderate VA in juvenile survival but not adult annual survival. Immigrants introduced alleles with negative additive genetic effects on local fitness, potentially reducing population mean fitness through migration load, but alleviating expression of inbreeding depression. Our results show that VA for fitness can be maintained in the wild, and be broadly concordant between the sexes despite marked sex‐specific VA in reproductive success. [ABSTRACT FROM AUTHOR]

The records of Mambí de Cuba dairy cows (3/4 Holstein 1/4 Cebu), Siboney de Cuba (5/8 Holstein 3/8 Cebu) and Holstein, from three herds were used to determine the effect of the genetic group (GG) and various non-genetic factors, for milk production traits (131 658 lactations of 63 066 cows), reproduction (117 794 reproductive events of 36 331 cows), longevity (18 741 cows) and milk production per life (56 536 cows). The traits of cumulative milk production up to 305 days (M305), duration of lactation (DL), age at first service (A first service), parturition-first service interval (PSI), parturition-gestation interval (PGI), parturition interval (PI),productive life (PL), number of parturition per life (PN) and milk production per life (MPLife) were studied. A mixed linear model was applied, with the use of the SAS MIXED procedure. This model included the fixed effects of the genetics, herd, lactation number, year, parturition time, genetic group interactions x lactation number, genetic group x parturition year and genetic group x parturition time. As random, the cow nested in the herd and the errors were included. For the A first S, PL, PN and MPLife traits, the model did not include the lactation number or its interaction. The fixed effects were significant, except for the parturition time and its interaction with the genetic group in the reproductive and longevity traits. It is concluded that the Mambí de Cuba showed better milk production accumulated during life and high longevity. [ABSTRACT FROM AUTHOR]

Infections by gastrointestinal nematodes cause large losses to sheep breeders. In the study reported here, the resistance to gastrointestinal nematodes was analyzed in sheep of adapted and non-adapted breeds, maintained in naturally infected pastures. A total of 134 females from seven genetic groups were monitored during 20 months: Santa Inês (OSI), Dorper (ODO), Texel (OTX), Ile de France (OIF), and animals from crosses of Santa Inês ewes with Dorper (ODS), Texel (OTS) and Ile de France (OIS) rams. Blood samples were collected monthly to determine the packed cell volume (PCV), and feces were collected at the same time to count the eggs per gram (fecal egg counts = FEC) and identify the genera of the prevalent parasites. The statistical analyses of the data showed significant differences ( p  < 0.05) regarding the genetic group, collection month and interaction of month with the genetic group on the FEC. The correlation estimates between FEC and PCV were negative and significant ( p  <  0.01).The OTS genetic group presented the lowest mean of FEC value. Concerning the nematode genera, the greatest prevalence was observed for Haemonchus spp. (85.6%), followed by Trichostrongylus spp. (10.8%), Oesophagostomum spp. (2.9%) and Cooperia spp. (0.7%). The results obtained in this study show that the crossing of the Texel and Santa Inês breeds can be considered an alternative for sheep production in the Southeast region of Brazil due to the lower egg output by gastrointestinal nematodes. [ABSTRACT FROM AUTHOR]

A cross-sectional comparative study was carried out to investigate the productive and reproductive performances of different genetic groups of crossbred cows at three different farming conditions in Bangladesh. Crossbred cows (n=90) those already completed third lactations, were selected randomly from three different dairy farms (e.g. Jarip, Mullah and Nahar) located in Chittagong, Bangladesh. The numbers of animals of each of the genetic groups were 30 for 50% Holstein Friesian (HF) × 50% Sahiwal (SL) cross, 30 for 62.5% HF × 37.5% SL cross and 30 for 75% HF × 25% SL cross. Different productive and reproductive traits of crossbred cows such as age at first heat, calving interval, gestation length, service per conception, days open, lactation length and milk yield, etc., were measured in this study. Results demonstrated that gestation length of 50% HF × 50% SL, lactation length of 62.5% HF × 37.5% SL, gestation and lactation length of 75% HF × 25% SL crossbred cows between the farms were significantly influenced (P<0.05). Other parameters of crossbred cows such as age at first heat, age at first calving, service per conception, average daily milk yield, days open and calving interval of different genotypes were not influenced (P>0.05) by different farms. The highest (282.00±0.00 days) and lowest (276.43±0.92 days) gestation length were found in crossbred cows of the Jarip and Nahar dairy farm, respectively. The highest (297.50±3.50 days) and lowest (282.00±0.00 days) gestation length were found in crossbred cows of Mullah and the Jarip dairy farm, respectively. The overall productive and reproductive performance of different crossbred cows of the Nahar and Mulla dairy farm were superior to that of the Jarip dairy farm. [ABSTRACT FROM AUTHOR]

This study aimed at evaluating the body weight (BW) and biometric traits [breast girth (BG), neck circumference (NC), Back length (BL), wing length (WL), thigh length (TL), thigh circumference (TC), shank length (SL) and shank circumference (SC)] of two newly introduced and one Nigerian indigenous chicken strains using multivariate principal components (PCs) and to classify the three genotypes using discriminant analysis. A total of one hundred and fifty chickens of both sexes comprising equal number of Sasso, Kuroiler and the local Fulani ecotype were utilized in the study. The six-week old birds were managed intensively in a private farm in Nasarawa State, north central Nigeria. The fixed genotype and sex effects including their interaction on the body parameters were tested using general linear model. With the exception of BG, the univariate analysis showed that Kuroiler birds had higher (P<0.05) BW and morphometric traits than Sasso, which in turn, were superior (P<0.05) to their Fulani counterparts. Male chickens also exhibited better performance (P<0.05) than their female counterparts. There was genotype * sex interaction effect on all the body traits, except TC. The phenotypic correlations among the traits were positive and significant (P<0.05; P<0.01) ranging from 0.41-0.97, 0.47-0.96 and 0.42-0.94 in Sasso, Kuroiler and Fulani chickens, respectively. Factor analysis with varimax rotation of interrelated traits revealed three PCs (Sasso and Kuroiler) and two PCs (Fulani) which accounted for 87.4, 93.9 and 78.9% of the total variance in the genetic groups. The PC-based regression models, which are preferable for selecting birds for optimal balance, accounted for 92, 95 and 88% of the total variation in the BW of Sasso, Kuroiler and Fulani chickens, respectively. The chicken genotypes were best separated using BG, SC, BW and TC. [ABSTRACT FROM AUTHOR]