Genetic identification of bat species for pathogen surveillance across France

With more than 1400 chiropteran species identified to date, bats comprise one-fifth of all mammalian species worldwide. Many studies have associated viral zoonoses with 45 different species of bats in the EU, which cluster within 5 families of bats. For example, the Serotine bats are infected by European Bat 1 Lyssavirus throughout Europe while Myotis bats are shown infected by coronavirus, herpesvirus and paramyxovirus. Correct host species identification is important to increase our knowledge of the ecology and evolutionary pattern of bat viruses in the EU. Bat species identification is commonly determined using morphological keys. Morphological determination of bat species from bat carcasses can be limited in some cases, due to the state of decomposition or nearly indistinguishable morphological features in juvenile bats and can lead to misidentifications. The overall objective of our study was to identify insectivorous bat species using molecular biology tools with the amplification of the partial cytochrome b gene of mitochondrial DNA. Two types of samples were tested in this study, bat wing punches and bat faeces. A total of 163 bat wing punches representing 22 species, and 31 faecal pellets representing 7 species were included in the study. From the 163 bat wing punches tested, a total of 159 were genetically identified from amplification of the partial cyt b gene. All 31 faecal pellets were genetically identified based on the cyt b gene. A comparison between morphological and genetic determination showed 21 misidentifications from the 163 wing punches, representing ~12.5% of misidentifications of morphological determination compared with the genetic method, across 11 species. In addition, genetic determination allowed the identification of 24 out of 25 morphologically non-determined bat samples. Our findings demonstrate the importance of a genetic approach as an efficient and reliable method to identify bat species precisely.

Dissecting the Genetics of Early Vigour to Design Drought-Adapted Wheat

Due to the climate change and an increased frequency of drought, it is of enormous importance to identify and to develop traits that result in adaptation and in improvement of crop yield stability in drought-prone regions with low rainfall. Early vigour, defined as the rapid development of leaf area in early developmental stages, is reported to contribute to stronger plant vitality, which, in turn, can enhance resilience to erratic drought periods. Furthermore, early vigour improves weed competitiveness and nutrient uptake. Here, two sets of a multi-reference nested association mapping (MR-NAM) population of bread wheat (Triticum aestivum ssp. aestivum L.) were used to investigate early vigour in a rain-fed field environment for 3 years, and additionally assessed under controlled conditions in a greenhouse experiment. The normalised difference vegetation index (NDVI) calculated from red/infrared light reflectance was used to quantify early vigour in the field, revealing a correlation (p < 0.05; r = 0.39) between the spectral measurement and the length of the second leaf. Under controlled environmental conditions, the measured projected leaf area, using a green-pixel counter, was also correlated to the leaf area of the second leaf (p < 0.05; r = 0.38), as well as to the recorded biomass (p < 0.01; r = 0.71). Subsequently, genetic determination of early vigour was tested by conducting a genome-wide association study (GWAS) for the proxy traits, revealing 42 markers associated with vegetation index and two markers associated with projected leaf area. There are several quantitative trait loci that are collocated with loci for plant developmental traits including plant height on chromosome 2D (log10 (P) = 3.19; PVE = 0.035), coleoptile length on chromosome 1B (–log10 (P) = 3.24; PVE = 0.112), as well as stay-green and vernalisation on chromosome 5A (–log10 (P) = 3.14; PVE = 0.115).

Gene-Cultura: E o Problema da Influência do Ambiente na Evolução dos Seres Vivos

O objetivo do presente artigo é expor e discutir a problemática relação da influência da cultura e da determinação genética no processo de evolução dos seres vivos, em especial dos seres humanos. Para tanto, dentre os procedimentos metodológicos foi realizada pesquisa bibliográfica e descritiva, analisando aspectos de natureza biológica, social e antropológica. O artigo buscou fazer conexões com a natureza genética dos seres humanos e sua evolução e coevolução relativa a aspectos socioambientais e culturais. É possível depreender pela análise dos resultados que as sociedades humanas modernas apresentam um processo de construção que tem influências mais significativas da natureza sociocultural que genética, apesar de que esses fatores sempre serão indissociáveis.Palavras-chave: Cultura, gene-cultura, coevolução, sociobiodiversidade, sustentabilidade Gene-Culture: And the Problem of the Influence of the Environment on the Evolution of Living BeingsABSTRACTThe aim of this article is to discuss the relationship between the influence of culture and genetic determination on the evolution process of living beings, especially human beings. Therefore, among the methodological procedures, bibliographical and descriptive research was carried out, analyzing aspects of the biological, social and anthropological nature. The article sought to search with the genetic nature of human beings and their evolution and co-evolution related to socio-environmental and cultural aspects. It is possible to infer from the analysis of the results that modern human societies present a construction process that has more important influences of sociocultural nature than genetics, although these factors will always be inseparable.Keywords: Culture, gene-culture, co-evolution, sociobiodiversity, sustainability

COMPARATIVE CHARACTERISTICS OF COW AND GOAT MILK COMPONENT BY MIR-SPECTROSCOPY

На основе анализа компонентного состава молока проведено изучение белковой и жировой фракций, метаболитов веществ и соматических клеток для голштинизированных черно-пестрых коров и карачаевских коз в сравнительном аспекте. Молоко коров предназначалось для переработки, а молоко коз использовалось для выкармливания козлят. В этой связи представляет интерес использование экспресс-метода инфракрасной (ИК) спектроскопии для исследования точности прогностической модели анализа молока от разных видов животных, в частности, для определения в образцах содержания жирных кислот (ЖК). Скрининг молока по 25 показателям выполняли с помощью анализатора CombiFOSS 7 DSCC. Установлено, что в молоке коз было достоверно больше жира и белка, насыщенных ЖК (69,59% против 65,67% в коровьем) и более значимых для питания человека полиненасыщенных ЖК (4,05% против 3,66% у коров). Коэффициент детерминации показал высокую значимость совокупных факторов, включенных в GLM-уравнение, для массовой доли лактозы (23,9%), короткоцепочечных ЖК (28,1%), ацетона (24,3%), бетагидроксибутирата (37,9%), точки замерзания молока (46,0%) и мочевины (85,1%). Корреляции между компонентами имели биологическую направленность, характерную для процессов синтеза молока в организме жвачных животных. Проведенный комплексный анализ показал перспективность ИК-спектров для использования как в менеджменте стада коров и коз, так и в накоплении информации для изучения генетической детерминации процессов образования молока у сельскохозяйственных животных. The protein and fat fractions, metabolites and somatic cells count for Holsteinized Black-and-White cows and Karachai goats were studied by in a comparative aspect. The cows’ milk was intended for processing, and milk of goats was used to feed the goatlet. In this regard, to use the express method of infrared (MIR) spectroscopy to study the accuracy of the predictive model for analyzing milk from different animal species, in particular, to determine the content of fatty acids (FA) was interesting. Milk screening for 25 parameters was performed using a CombiFOSS 7 DSCC analyzer. It was found that under the same paratypical conditions, there was significantly more fat and protein in goat milk, however, in terms of lactose content, milk pH values were higher in cows’ milk. Goat milk has a higher content of saturated FAs (69.59% opp. 65.67% in cow milk) and polyunsaturated FAs that are more significant for human nutrition (4.05% opp. 3.66% in cows). The determination coefficient showed the high significance of the aggregate factors included in the GLM equation for the lactose percentage (23.9%), short-chain FA (28.1%), acetone (24.3%), betahydroxybutyrate (37.9%), milk freezing point (46.0%) and urea (85.1%). The correlations between components had a biological orientation that characterized for the milk synthesis processes into the body of ruminants. The analysis showed that MIR spectra are promising for use in the management of a herd of cows and goats, and in the information accumulation for studying the genetic determination of milk processes synthesis in animals.

Comprehensive functional core microbiome comparison in genetically obese and lean hosts under the same environment

Our study provides an exhaustive comparison of the microbiome core functionalities (captured by 3,936 microbial gene abundances) between hosts with divergent genotypes for intramuscular lipid deposition. After 10 generations of divergent selection for intramuscular fat in rabbits and 4.14 phenotypic standard deviations (SD) of selection response, we applied a combination of compositional and multivariate statistical techniques to identify 122 cecum microbial genes with differential abundances between the lines (ranging from −0.75 to +0.73 SD). This work elucidates that microbial biosynthesis lipopolysaccharides, peptidoglycans, lipoproteins, mucin components, and NADH reductases, amongst others, are influenced by the host genetic determination for lipid accretion in muscle. We also differentiated between host-genetically influenced microbial mechanisms regulating lipid deposition in body or intramuscular reservoirs, with only 28 out of 122 MGs commonly contributing to both. Importantly, the results of this study are of relevant interest for the efficient development of strategies fighting obesity.

Genotypic Variation and Talent Identification in Sports

Top performance of athletes is not limited to the demand of fame, public recognition, sponsorship, and prize money but genetic inheritance contributes a prime role to hold such traits. Recent years, we have witnessed the rise of sports specific tests that identify person’s athletic talents, but human vary on genetic factors which silently work to achieve success in sports. Recent progress on the genetic determination in the sports sciences offer great perspective to analyze the genotype profile associated with the athletes. One of the most used advances in this field is the identification of variations in the DNA sequence, known as Single Nucleotide Polymorphisms (SNPs). Genetic evaluations should be combined with other tools to get an accurate identification of athletes and their respective fields to achieve optimum success.

The Role of Intra-Clutch Variation of Magpie Clutches in Foreign Egg Rejection Depends on the Egg Trait Considered

The existence of a coevolutionary process between avian brood parasites and their hosts predicts a lower intra-clutch variation in egg appearance of host eggs among rejecters as this would favor egg discrimination of parasite eggs by hosts once parasitic egg mimicry had evolved. So far empirical tests of this prediction have ignored the fact that different aspects of host egg phenotypes may differ in the relative role of environmental vs. genetic determination, and hence that the role of intra-clutch variation in egg rejection within a population cannot be invariant. Here, we estimated whether the intra-clutch variation in several aspects of host eggshell features is consistently associated to rejection of parasitic foreign eggs across years in a magpie host population parasitized by great spotted cuckoos. We innovatively estimated spottiness by means of the fractal dimension of eggs, which considers the homogeneity of spot pattern complexity in eggshells. Our results show that low intra-clutch variation in the blue-green coloration at the middle area of the eggs associated with a high chance of rejection, but only in one of the 3 years we conducted the study. In addition, females that rejected foreign eggs presented more homogenous spot patterns in their clutches as estimated by their fractal dimension than females that accepted experimental eggs, independently of the year of study. Finally, intra-clutch variation in egg volume of host eggs was not associated to rejection. Analyses at the individual level revealed that the relative role of genetic vs. environmental factors that determine egg phenotype would be feature-specific in magpies, females having a characteristic spottiness, but not color or volume, pattern. Our work stresses the importance of considering a holistic approach including several aspects of variation in host egg phenotype (size, color, and homogeneity of spot pattern), as some aspects might be more susceptible to selection through egg rejection than others, presumably because they are less influenced by variation in the environmental conditions. Moreover, our study highlights the importance of replication in studies on the adaptive value of host traits in egg rejection.

Genome-Wide Association Studies Provide Insights into the Genetic Determination of Flower and Leaf Traits of Actinidia eriantha

Kiwifruit (Actinidia eriantha) is a dioecious vine, and the pollen of its male cultivars has a direct effect on the quality of its fruits. In this study, to facilitate molecular breeding and gene identification, we performed genome-wide association studies (GWAS) on 11 traits of flower and leaf. A total of 946,337 highly consistent SNP markers were obtained in the whole genome. Phylogenetic tree analysis and population structure analysis showed that the 143 germplasms can be divided into two groups. The linkage disequilibrium analysis showed that A. eriantha have a relatively fast attenuation rate, and that the average attenuation distance of LD was 0.1–0.3 Kb. The MLM (QK) model was determined as best for correlation analysis, and eight and three SNPs associated with flower- and leaf-related traits were identified, respectively, at 0.01 significance level. However, SNP markers associated with stamen number per flower, pollen viability, total chlorophyll content, and total flavonoid content were not identified at the 0.01 significant level, although it is worth noting that one, one, five, and two SNPs were identified to be associated with these traits at the 0.05 significant level. This study provides insights into the complex flower- and leaf-related biology, and identifies genes controlling important traits in A. eriantha through GWAS, which extends the genetic resources and basis for facilitating molecular breeding in kiwifruits.

Tools and applications for integrative analysis of DNA methylation in social insects

DNA methylation is a common epigenetic signaling tool and an important biological process which is widely studied in a large array of species. The presence, level, and function of DNA methylation varies greatly across species. In insects, DNA methylation systems are reduced, and methylation rates are often low. Low methylation levels probed by whole genome bisulfite sequencing require great care with respect to data quality control and intepretation. Here we introduce BWASP/R, a reproducible, scalable workflow, that allows efficient, scalable, and entirely reproducible analyses of raw DNA methylation sequencing data. Consistent application of quality control filters and analysis parameters provides fair comparisons among different studies and an integrated view of all experiments on one species. We describe the capabilities of the BWASP/R workflow by re-analyzing several publicly available social insect WGBS datasets, comprising 70 samples and cumulatively 147 replicates from four different species. We show that the CpG methylome comprises only about 1.5% of CpG sites in the honeybee genome and that the cumulative data are consistent with genetic signatures of site accessibility and physiological control of methylation levels.Significance StatementDNA methylation in the honeybee genome occurs almost entirely at CpG sites. Methylation rates are small compared to rates in mammalian or plant genomes. De novo analysis of all published honeybee methylation studies and statistical modeling suggests that the CpG methylome consists of about only 300,000 sites. The development of a fully reproducible, scalable, portable workflow allows for easy accessible updates of integrative views of all current experiments. The integrated results for the honeybee are consistent with genetic determination of methylation site accessibility by yet uncharacterized sequence features and physiological control of methylation levels at those sites.