scholarly journals qPCR assays with dual-labeled probes for genotyping honey bee variants associated with varroa resistance

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
David Claeys Boúúaert ◽  
Mario Van Poucke ◽  
Lina De Smet ◽  
Wim Verbeke ◽  
Dirk C. de Graaf ◽  
...  
Keyword(s):  
Honey Bee ◽  
Honey Bees ◽  
Binding Sites ◽  
Varroa Mite ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Mite Reproduction ◽  
Varroa Resistance ◽  
Development And Validation

Abstract Background The varroa mite is one of the main causes of honey bee mortality. An important mechanism by which honey bees increase their resistance against this mite is the expression of suppressed mite reproduction. This trait describes the physiological inability of mites to produce viable offspring and was found associated with eight genomic variants in previous research. Results This paper presents the development and validation of high-throughput qPCR assays with dual-labeled probes for discriminating these eight single-nucleotide variants. Amplicon sequences used for assay validation revealed additional variants in the primer/probe binding sites in four out of the eight assays. As for two of these the additional variants interfered with the genotyping outcome supplementary primers and/or probes were developed. Inclusion of these primers and probes in the assay mixes allowed for the correct genotyping of all eight variants of interest within our bee population. Conclusion These outcomes underline the importance of checking for interfering variants in designing qPCR assays. Ultimately, the availability of this assay allows genotyping for the suppressed mite reproduction trait and paves the way for marker assisted selection in breeding programs.

scholarly journals qPCR Assays with Dual-Labeled Probes for Genotyping Honey bee Variants Associated with Varroa Resistance

2021 ◽  
Author(s):  
David Claeys Bouuaert ◽  
Mario Van Poucke ◽  
Lina De Smet ◽  
Wim Verbeke ◽  
Dirk C. de Graaf ◽  
...  
Keyword(s):  
Honey Bee ◽  
Honey Bees ◽  
Binding Sites ◽  
Varroa Mite ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Mite Reproduction ◽  
Varroa Resistance ◽  
Development And Validation

Abstract Background: The varroa mite is one of the main causes of honey bee mortality. An important mechanism by which honey bees increase their resistance against this mite is the expression of suppressed mite reproduction. This trait describes the physiological inability of mites to produce viable offspring and was found associated with eight genomic variants in previous research. Results: This paper presents the development and validation of high-throughput qPCR assays with dual-labeled probes for discriminating these eight single-nucleotide variants. Within the sequenced samples, additional variants were detected in the primer/probe binding sites in four out of the eight variants of interest. As for two of these the additional variants interfered with the genotyping outcome supplementary primers and/or probes were developed. Inclusion of these primers and probes in the assay mixes allowed for the correct genotyping of all eight variants of interest.Conclusion: These outcomes underline the importance of checking for interfering variants in designing qPCR assays. Ultimately, the availability of this assay allows genotyping for the suppressed mite reproduction trait and paves the way for marker assisted selection in breeding programs.

scholarly journals Prediction of genome-wide effects of single nucleotide variants on transcription factor binding

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Sebastian Carrasco Pro ◽  
Katia Bulekova ◽  
Brian Gregor ◽  
Adam Labadorf ◽  
Juan Ignacio Fuxman Bass
Keyword(s):  
Binding Sites ◽  
Cancer Type ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Regulatory Regions ◽  
Genome Wide ◽  
Transcriptional Regulatory ◽  
Gene Regulatory ◽  
The Impact ◽  
The Relationship

Abstract Single nucleotide variants (SNVs) located in transcriptional regulatory regions can result in gene expression changes that lead to adaptive or detrimental phenotypic outcomes. Here, we predict gain or loss of binding sites for 741 transcription factors (TFs) across the human genome. We calculated ‘gainability’ and ‘disruptability’ scores for each TF that represent the likelihood of binding sites being created or disrupted, respectively. We found that functional cis-eQTL SNVs are more likely to alter TF binding sites than rare SNVs in the human population. In addition, we show that cancer somatic mutations have different effects on TF binding sites from different TF families on a cancer-type basis. Finally, we discuss the relationship between these results and cancer mutational signatures. Altogether, we provide a blueprint to study the impact of SNVs derived from genetic variation or disease association on TF binding to gene regulatory regions.

scholarly journals Neonicotinoid Clothianidin reduces honey bee immune response and contributes to Varroa mite proliferation

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Desiderato Annoscia ◽  
Gennaro Di Prisco ◽  
Andrea Becchimanzi ◽  
Emilio Caprio ◽  
Davide Frizzera ◽  
...  
Keyword(s):  
Immune Responses ◽  
Honey Bee ◽  
Honey Bees ◽  
Varroa Destructor ◽  
Negative Impact ◽  
Asymptomatic Infection ◽  
Varroa Mite ◽  
Deformed Wing Virus ◽  
Synergistic Interactions ◽  
Parasitic Mite

AbstractThe neonicotinoid Clothianidin has a negative impact on NF-κB signaling and on immune responses controlled by this transcription factor, which can boost the proliferation of honey bee parasites and pathogens. This effect has been well documented for the replication of deformed wing virus (DWV) induced by Clothianidin in honey bees bearing an asymptomatic infection. Here, we conduct infestation experiments of treated bees to show that the immune-suppression exerted by Clothianidin is associated with an enhanced fertility of the parasitic mite Varroa destructor, as a possible consequence of a higher feeding efficiency. A conceptual model is proposed to describe the synergistic interactions among different stress agents acting on honey bees.

scholarly journals Geographical Distribution and Selection of European Honey Bees Resistant to Varroa destructor

Insects ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 873
Author(s):  
Yves Le Conte ◽  
Marina D. Meixner ◽  
Annely Brandt ◽  
Norman L. Carreck ◽  
Cecilia Costa ◽  
...  
Keyword(s):  
Honey Bees ◽  
Mite Population ◽  
Varroa Mite ◽  
Local Conditions ◽  
Colony Management ◽  
Selection Strategies ◽  
Mite Reproduction ◽  
Natural Infestation ◽  
Practical Experiences ◽  
Colony Survival

Developing resistance to the varroa mite in honey bees is a major goal for apicultural science and practice, the development of selection strategies and the availability of resistant stock. Here we present an extended literature review and survey of resistant populations and selection programs in the EU and elsewhere, including expert interviews. We illustrate the practical experiences of scientists, beekeepers, and breeders in search of resistant bees. We describe numerous resistant populations surviving without acaricide treatments, most of which developed under natural infestation pressure. Their common characteristics: reduced brood development; limited mite population growth; and low mite reproduction, may cause conflict with the interests of commercial beekeeping. Since environmental factors affect varroa mite resistance, particular honey bee strains must be evaluated under different local conditions and colony management. The resistance traits of grooming, hygienic behavior and mite reproduction, together with simple testing of mite population development and colony survival, are significant in recent selection programs. Advanced breeding techniques and genetic and physiological selection tools will be essential in the future. Despite huge demand, there is no well-established market for resistant stock in Europe. Moreover, reliable experience or experimental evidence regarding the resistance of stocks under different environmental and management conditions is still lacking.

scholarly journals Initial Insights Into the Genetic Epidemiology of SARS-CoV-2 Isolates From Kerala Suggest Local Spread From Limited Introductions

2021 ◽  
Vol 12 ◽  
Author(s):  
Chandni Radhakrishnan ◽  
Mohit Kumar Divakar ◽  
Abhinav Jain ◽  
Prasanth Viswanathan ◽  
Rahul C. Bhoyar ◽  
...  
Keyword(s):  
Genetic Epidemiology ◽  
Binding Sites ◽  
Haplotype Analysis ◽  
Rt Pcr ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Functional Variants ◽  
Local Spread ◽  
Novel Variants ◽  
The World

Coronavirus disease 2019 (COVID-19) rapidly spread from a city in China to almost every country in the world, affecting millions of individuals. The rapid increase in the COVID-19 cases in the state of Kerala in India has necessitated the understanding of SARS-CoV-2 genetic epidemiology. We sequenced 200 samples from patients in Kerala using COVIDSeq protocol amplicon-based sequencing. The analysis identified 166 high-quality single-nucleotide variants encompassing four novel variants and 89 new variants in the Indian isolated SARS-CoV-2. Phylogenetic and haplotype analysis revealed that the virus was dominated by three distinct introductions followed by local spread suggesting recent outbreaks and that it belongs to the A2a clade. Further analysis of the functional variants revealed that two variants in the S gene associated with increased infectivity and five variants mapped in primer binding sites affect the efficacy of RT-PCR. To the best of our knowledge, this is the first and most comprehensive report of SARS-CoV-2 genetic epidemiology from Kerala.

scholarly journals Genetic diversity of the complementary sex-determiner (csd) gene in two closed breeding stocks of Varroa -resistant honey bees

Apidologie ◽  
2020 ◽  
Vol 51 (6) ◽  
pp. 1125-1132
Author(s):  
Lelania Bilodeau ◽  
Arian Avalos ◽  
Robert G. Danka
Keyword(s):  
Genetic Diversity ◽  
Honey Bee ◽  
Honey Bees ◽  
Sequence Similarity ◽  
Variable Region ◽  
Breeding Programs ◽  
Frequency Distributions ◽  
Low Genetic Diversity ◽  
Breeding Populations ◽  
Periodic Monitoring

AbstractHoney bee (Apis mellifera) breeding programs that use a closed mating system are particularly vulnerable to low genetic diversity. Inadequate diversity at the complementary sex-determiner (csd) locus is problematic and potentially catastrophic in honey bee populations because it causes low brood viability. In typical commercial populations, queens are open mated and csd diversity is fostered by high rates of introgression. In this study, we examine genetic diversity within the highly variable region (HVR) of csd in two stocks bred for resistance to Varroa destructor: Pol-line and Hilo, both of which use closed mating systems. We sampled 47 Pol-line colonies and 41 Hilo colonies and found 60 protein alleles that were condensed into 35 allele groupings by sequence similarity. We found that proportionately, HVR diversity levels were comparable with those in other closed breeding populations as well as open-mated populations of A. mellifera worldwide. Distinct patterns are observed among Pol-line and Hilo csd protein alleles in both the phylogeny and allele frequency distributions, suggesting early divergence of the two stocks. When compared with an African outgroup, both stocks shared alleles with the outgroup, suggesting ancestral lineages are present and not all diversity is due to new mutations. Periodic monitoring of csd diversity is recommended for closed breeding programs. The csd diversity data reported here are currently being used to make breeding decisions in these two mite-resistant populations of honey bees.

scholarly journals Molecular Assessment of Genes Linked to Immune Response Traits of Honey Bees in Conventional and Organically Managed Apiaries

Insects ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 637
Author(s):  
Shalom C. Siebert ◽  
Lambert H. B. Kanga ◽  
Sheikh M. Basha ◽  
Jesusa C. Legaspi
Keyword(s):  
Gene Expression ◽  
Immune Response ◽  
Superoxide Dismutase ◽  
Young Adult ◽  
Honey Bee ◽  
Honey Bees ◽  
Mite Infestation ◽  
Varroa Mite ◽  
Mite Infestations ◽  
Organically Managed

Honey bees are of great economic importance, not only for honey production but also for crop pollination. However, honey bee populations continue to decline mainly due to exposure to pesticides, pathogens and beekeeping practices. In this study, total soluble protein was measured, total RNA was extracted and first-strand cDNAs were generated. Quantitative PCR was used to assess the relative expression (transcript abundances) of immune function-related genes in honey bees collected from organically and conventionally managed hives. Honey bees collected from conventionally managed hives with 0% Varroa mite infestation levels displayed an upregulated expression of the prophenoloxidase gene (cellular defense). Similarly, honey bees collected from organically managed hives had increased levels of the vitellogenin gene (immune function and longevity). The gene expression for malvolio (sucrose responsiveness) was highest in organically managed hives with 0% Varroa mite infestations. Young adult bees collected from organically managed hives with 5% Varroa mite infestation levels had upregulated expressions of the gene spaetzle, whereas bees from similarly infested, conventionally managed hives did not, suggesting that honey bees from organically managed hives could mount an immune response. In young adult bees collected from organically managed hives only, the expression of the immune deficiency gene (antimicrobial defense) was upregulated. The relative gene expression for superoxide dismutase 1 increased in young adult bees collected from hives with 5% Varroa mite infestation levels as expected. However, for superoxide dismutase 2, there was a high level of gene expression in adult bees from both conventionally managed hives with 0% Varroa mite infestation levels and organically managed hives with 5% Varroa mite infestations. The gene CYP9Q3 (pesticide detoxification) that metabolizes coumaphos and fluvalinate was upregulated in adult bees collected from organically managed bees. Overall, these findings provide useful insights into the genetic response of honey bees to some environmental stressors and could be an important component of best beekeeping practices that intend to enhance honey bee health.

scholarly journals Esterase Activity is Affected by Genetics, Age, Insecticide Exposure, and Viral Infection in the Honey Bee, Apis mellifera

2018 ◽  
Author(s):  
Frank D. Rinkevich ◽  
Joseph W. Margotta ◽  
Michael Simone-Finstrom ◽  
Lilia I. de Guzman ◽  
Kristen B. Healy
Keyword(s):  
Viral Infection ◽  
Honey Bee ◽  
Honey Bees ◽  
Esterase Activity ◽  
Pesticide Exposure ◽  
Mite Infestation ◽  
Activity Levels ◽  
Varroa Mite ◽  
Genetic Stock ◽  
Insecticide Exposure

AbstractNon-target impacts of insecticide treatments are a major public and environmental concern, particularly in contemporary beekeeping. Therefore, it is important to understand the physiological mechanisms contributing to insecticide sensitivity in honey bees. In the present studies, we sought to evaluate the role of esterases as the source of variation in insecticide sensitivity. To address this question, the following objectives were completed: 1) Evaluated esterase activity among honey bee stocks, 2) Assessed the correlation of esterase activity with changes in insecticide sensitivity with honey bee age, 3) Established if esterases can be used as a biomarker of insecticide exposure, and 4) Examined the effects of Varroa mite infestation and viral infection on esterase activity.Results indicated that honey bees have a dynamic esterase capacity that is influenced by genetic stock and age. However, there was no consistent connection of esterase activity with insecticide sensitivity across genetic stocks or with age, suggests other factors are more critical for determining insecticide sensitivity. The trend of increased esterase activity with age in honey bees suggests this physiological transition is consistent with enhanced metabolic rate with age. The esterase inhibition with naled but not phenothrin or clothianidin indicates that reduced esterase activity levels may only be reliable for sublethal doses of organophosphate insecticides. The observation that viral infection, but not Varroa mite infestation, reduced esterase activity shows viruses have extensive physiological impacts. Taken together, these data suggest that honey bee esterase activity toward these model substrates may not correlate well with insecticide sensitivity. Future studies include identification of esterase substrates and inhibitors that are better surrogates of insecticide detoxification in honey bees as well as investigation on the usefulness of esterase activity as a biomarker of pesticide exposure, and viral infection.

scholarly journals Population genetics of ectoparasitic mites Varroa spp. in Eastern and Western honey bees

Parasitology ◽  
2019 ◽  
Vol 146 (11) ◽  
pp. 1429-1439 ◽  
Author(s):  
Vincent Dietemann ◽  
Alexis Beaurepaire ◽  
Paul Page ◽  
Orlando Yañez ◽  
Ninat Buawangpong ◽  
...  
Keyword(s):  
Host Specificity ◽  
Honey Bee ◽  
Honey Bees ◽  
Nuclear Dna ◽  
Apis Cerana ◽  
Mite Species ◽  
Host Shifts ◽  
Mite Reproduction ◽  
Single Host ◽  
New Hosts

AbstractHost shifts of parasites are often causing devastating effects in the new hosts. The Varroa genus is known for a lineage of Varroa destructor that shifted to the Western honey bee, Apis mellifera, with disastrous effects on wild populations and the beekeeping industry. Despite this, the biology of Varroa spp. remains poorly understood in its native distribution range, where it naturally parasitizes the Eastern honey bee, Apis cerana. Here, we combined mitochondrial and nuclear DNA analyses with the assessment of mite reproduction to determine the population structure and host specificity of V. destructor and Varroa jacobsonii in Thailand, where both hosts and several Varroa species and haplotypes are sympatric. Our data confirm previously described mite haplogroups, and show three novel haplotypes. Multiple infestations of single host colonies by both mite species and introgression of alleles between V. destructor and V. jacobsonii suggest that hybridization occurs between the two species. Our results indicate that host specificity and population genetic structure in the genus Varroa is more labile than previously thought. The ability of the host shifted V. destructor haplotype to spillback to A. cerana and to hybridize with V. jacobsonii could threaten honey bee populations of Asia and beyond.

scholarly journals Evaluation of Suppressed Mite Reproduction (SMR) Reveals Potential for Varroa Resistance in European Honey Bees (Apis mellifera L.)

Insects ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 595
Author(s):  
Fanny Mondet ◽  
Melanie Parejo ◽  
Marina D. Meixner ◽  
Cecilia Costa ◽  
Per Kryger ◽  
...  
Keyword(s):  
Apis Mellifera ◽  
Honey Bee ◽  
Honey Bees ◽  
Selective Breeding ◽  
Evaluation Method ◽  
Selection Criterion ◽  
Mite Reproduction ◽  
Solution Selection ◽  
Parasitic Mite ◽  
Different Populations

In the fight against the Varroa destructor mite, selective breeding of honey bee (Apis mellifera L.) populations that are resistant to the parasitic mite stands as a sustainable solution. Selection initiatives indicate that using the suppressed mite reproduction (SMR) trait as a selection criterion is a suitable tool to breed such resistant bee populations. We conducted a large European experiment to evaluate the SMR trait in different populations of honey bees spread over 13 different countries, and representing different honey bee genotypes with their local mite parasites. The first goal was to standardize and validate the SMR evaluation method, and then to compare the SMR trait between the different populations. Simulation results indicate that it is necessary to examine at least 35 single-infested cells to reliably estimate the SMR score of any given colony. Several colonies from our dataset display high SMR scores indicating that this trait is present within the European honey bee populations. The trait is highly variable between colonies and some countries, but no major differences could be identified between countries for a given genotype, or between genotypes in different countries. This study shows the potential to increase selective breeding efforts of V. destructor resistant populations.

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