scholarly journals Runs of homozygosity derived from pool-seq data reveal fine-scale population structures in Western honey bees (Apis mellifera)

2021 ◽  
Author(s):  
Annik Gmel ◽  
Matthieu Guichard ◽  
Benjamin Dainat ◽  
Geoffrey Williams ◽  
Sonia Eynard ◽  
...  
Keyword(s):  
Apis Mellifera ◽  
Honey Bee ◽  
Honey Bees ◽  
Uv Light ◽  
Whole Genome Sequencing Data ◽  
Runs Of Homozygosity ◽  
Sequencing Data ◽  
Stripe Pattern ◽  
Protein Coding ◽  
Fundamental Information

Runs of homozygosity (ROH) are continuous homozygous segments that arise through the transmission of haplotypes that are identical by descent (IBD). The length and distribution of ROH segments provide insight into the genetic diversity of populations and are useful to detect selection signatures. Here, we analysed pooled whole-genome sequencing data from 265 Western honey bee colonies from the two subspecies Apis mellifera mellifera and Apis mellifera carnica. Integrating individual ROH patterns and admixture levels in a high-resolution population network visualization allowed us to ascertain major differences between the two subspecies. Within A. m. mellifera, we identified well-defined substructures according to the genetic origin of the colonies and a fair amount of admixed colonies, despite the current applied conservation efforts. In contrast, A. m. carnica colonies were more inbred and could not be differentiated according to the geographical origin. We identified 29 coding genes in overlapping ROH segments within the two subspecies. Genes embedded in A. m. carnica specific homozygosity islands suggested a strong selection for production and behavioural traits, whilst the identified cuticula protein-coding genes (CPR3 and CPR4) were associated with their breed-specific stripe pattern. Local adaption of the two subspecies could be confirmed by the identification of two genes involved in the response to ultraviolet (UV) light. We demonstrated that colony genotypes derived from pooled honey bee workers are reliable to unravel the population dynamics in A. mellifera and provide fundamental information to conserve native honey bees.

Survey of feral honey bee (Apis mellifera) colonies for Nosema apis in Western Australia

2007 ◽  
Vol 47 (7) ◽  
pp. 883 ◽  
Author(s):  
Rob Manning ◽  
Kate Lancaster ◽  
April Rutkay ◽  
Linda Eaton
Keyword(s):  
Apis Mellifera ◽  
Honey Bee ◽  
Western Australia ◽  
Honey Bees ◽  
Nosema Apis ◽  
The South ◽  
South West ◽  
Feral Populations ◽  
Significant Difference

The parasite, Nosema apis, was found to be widespread among feral populations of honey bees (Apis mellifera) in the south-west of Western Australia. The location, month of collection and whether the feral colony was enclosed in an object or exposed to the environment, all affected the presence and severity of infection. There was no significant difference in the probability of infection between managed and feral bees. However, when infected by N. apis, managed bees appeared to have a greater severity of the infection.

scholarly journals Human-lineage-specific genomic elements are associated with neurodegenerative disease and APOE transcript usage

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Zhongbo Chen ◽  
◽  
David Zhang ◽  
Regina H. Reynolds ◽  
Emil K. Gustavsson ◽  
...  
Keyword(s):  
Neurological Diseases ◽  
Purifying Selection ◽  
Whole Genome Sequencing Data ◽  
Human Lineage ◽  
Sequencing Data ◽  
Protein Coding ◽  
Potential Association ◽  
High Depth ◽  
Specific Sequences ◽  
Human Specific

AbstractKnowledge of genomic features specific to the human lineage may provide insights into brain-related diseases. We leverage high-depth whole genome sequencing data to generate a combined annotation identifying regions simultaneously depleted for genetic variation (constrained regions) and poorly conserved across primates. We propose that these constrained, non-conserved regions (CNCRs) have been subject to human-specific purifying selection and are enriched for brain-specific elements. We find that CNCRs are depleted from protein-coding genes but enriched within lncRNAs. We demonstrate that per-SNP heritability of a range of brain-relevant phenotypes are enriched within CNCRs. We find that genes implicated in neurological diseases have high CNCR density, including APOE, highlighting an unannotated intron-3 retention event. Using human brain RNA-sequencing data, we show the intron-3-retaining transcript to be more abundant in Alzheimer’s disease with more severe tau and amyloid pathological burden. Thus, we demonstrate potential association of human-lineage-specific sequences in brain development and neurological disease.

scholarly journals Whole genome sequencing reveals high differentiation, low levels of genetic diversity and short runs of homozygosity among Swedish wels catfish

Heredity ◽  
2021 ◽  
Author(s):  
Axel Jensen ◽  
Mette Lillie ◽  
Kristofer Bergström ◽  
Per Larsson ◽  
Jacob Höglund
Keyword(s):  
Genetic Diversity ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome Sequencing Data ◽  
Peripheral Populations ◽  
Whole Genome ◽  
Runs Of Homozygosity ◽  
Sequencing Data ◽  
Isolated Populations ◽  
Native Populations

AbstractThe use of genetic markers in the context of conservation is largely being outcompeted by whole-genome data. Comparative studies between the two are sparse, and the knowledge about potential effects of this methodology shift is limited. Here, we used whole-genome sequencing data to assess the genetic status of peripheral populations of the wels catfish (Silurus glanis), and discuss the results in light of a recent microsatellite study of the same populations. The Swedish populations of the wels catfish have suffered from severe declines during the last centuries and persists in only a few isolated water systems. Fragmented populations generally are at greater risk of extinction, for example due to loss of genetic diversity, and may thus require conservation actions. We sequenced individuals from the three remaining native populations (Båven, Emån, and Möckeln) and one reintroduced population of admixed origin (Helge å), and found that genetic diversity was highest in Emån but low overall, with strong differentiation among the populations. No signature of recent inbreeding was found, but a considerable number of short runs of homozygosity were present in all populations, likely linked to historically small population sizes and bottleneck events. Genetic substructure within any of the native populations was at best weak. Individuals from the admixed population Helge å shared most genetic ancestry with the Båven population (72%). Our results are largely in agreement with the microsatellite study, and stresses the need to protect these isolated populations at the northern edge of the distribution of the species.

scholarly journals Exploring Two Honey Bee Traits for Improving Resistance Against Varroa destructor: Development and Genetic Evaluation

Insects ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 216
Author(s):  
Matthieu Guichard ◽  
Benoît Droz ◽  
Evert W. Brascamp ◽  
Adrien von Virag ◽  
Markus Neuditschko ◽  
...  
Keyword(s):  
Apis Mellifera ◽  
Honey Bee ◽  
Honey Bees ◽  
Varroa Destructor ◽  
Field Trial ◽  
Genetic Evaluation ◽  
Phenotypic Correlation ◽  
Apis Mellifera Mellifera ◽  
Novel Traits ◽  
Resistance Traits

For the development of novel selection traits in honey bees, applicability under field conditions is crucial. We thus evaluated two novel traits intended to provide resistance against the ectoparasitic mite Varroa destructor and to allow for their straightforward implementation in honey bee selection. These traits are new field estimates of already-described colony traits: brood recapping rate (‘Recapping’) and solidness (‘Solidness’). ‘Recapping’ refers to a specific worker characteristic wherein they reseal a capped and partly opened cell containing a pupa, whilst ‘Solidness’ assesses the percentage of capped brood in a predefined area. According to the literature and beekeepers’ experiences, a higher recapping rate and higher solidness could be related to resistance to V. destructor. During a four-year field trial in Switzerland, the two resistance traits were assessed in a total of 121 colonies of Apis mellifera mellifera. We estimated the repeatability and the heritability of the two traits and determined their phenotypic correlations with commonly applied selection traits, including other putative resistance traits. Both traits showed low repeatability between different measurements within each year. ‘Recapping’ had a low heritability (h2 = 0.04 to 0.05, depending on the selected model) and a negative phenotypic correlation to non-removal of pin-killed brood (r = −0.23). The heritability of ‘Solidness’ was moderate (h2 = 0.24 to 0.25) and did not significantly correlate with resistance traits. The two traits did not show an association with V. destructor infestation levels. Further research is needed to confirm the results, as only a small number of colonies was evaluated.

scholarly journals Varroa jacobsoni infestation of adult Africanized and Italian honey bees (Apis mellifera) in mixed colonies in Brazil

1999 ◽  
Vol 22 (3) ◽  
pp. 321-323 ◽  
Author(s):  
Geraldo Moretto ◽  
Leonidas João de Mello Jr.
Keyword(s):  
Apis Mellifera ◽  
Honey Bee ◽  
Honey Bees ◽  
Mite Infestation ◽  
Varroa Jacobsoni ◽  
Africanized Honey Bees ◽  
African Honey Bees ◽  
Africanized Bees ◽  
Bee Colonies ◽  
Different Levels

Different levels of infestation with the mite Varroa jacobsoni have been observed in the various Apis mellifera races. In general, bees of European races are more susceptible to the mite than African honey bees and their hybrids. In Brazil honey bee colonies are not treated against the mite, though apparently both climate and bee race influence the mite infestation. Six mixed colonies were made with Italian and Africanized honey bees. The percentage infestation by this parasite was found to be significantly lower in adult Africanized (1.69 ± 0.44) than Italian bees (2.79 ± 0.65). This ratio was similar to that found in Mexico, even though the Africanized bees tested there had not been in contact with varroa, compared to more than 20 years of the coexistence in Brazil. However, mean mite infestation in Brazil on both kinds of bees was only about a third of that found in Mexico.

Sequential generations of honey bee (Apis mellifera) queens produced using cryopreserved semen

2012 ◽  
Vol 24 (8) ◽  
pp. 1079 ◽  
Author(s):  
Brandon K. Hopkins ◽  
Charles Herr ◽  
Walter S. Sheppard
Keyword(s):  
Apis Mellifera ◽  
Honey Bee ◽  
Honey Bees ◽  
Food Production ◽  
Effective Means ◽  
Eastern Asia ◽  
Pollination Services ◽  
Instrumental Insemination ◽  
Diploid Female ◽  
Frozen Semen

Much of the world’s food production is dependent on honey bees for pollination, and expanding food production will further increase the demand for managed pollination services. Apiculturists outside the native range of the honey bee, in the Americas, Australia and eastern Asia, have used only a few of the 27 described subspecies of honey bees (Apis mellifera) for beekeeping purposes. Within the endemic ranges of a particular subspecies, hybridisation can threaten native subspecies when local beekeepers import and propagate non-native honey bees. For many threatened species, cryopreserved germplasm can provide a resource for the preservation of diversity and recovery of endangered populations. However, although instrumental insemination of queen honey bees is well established, the absence of an effective means to cryopreserve honey bee semen has limited the success of efforts to preserve genetic diversity within the species or to develop repositories of honey bee germplasm for breeding purposes. Herein we report that some queens inseminated with cryopreserved semen were capable of producing a substantial number of fertilised offspring. These diploid female larvae were used to produce two additional sequential generations of new queens, which were then back-crossed to the same stock of frozen semen. Our results demonstrate the ability to produce queens using cryopreserved honey bee spermatozoa and the potential for the establishment of a honey bee genetic repository.

scholarly journals Ancestry-dependent Enrichment of Deleterious Homozygotes in Runs of Homozygosity

2018 ◽  
Author(s):  
Zachary A. Szpiech ◽  
Angel C.Y. Mak ◽  
Marquitta J. White ◽  
Donglei Hu ◽  
Celeste Eng ◽  
...  
Keyword(s):  
Native American ◽  
Mexican American ◽  
Complex Disease ◽  
Disease Risk ◽  
African Ancestry ◽  
Population History ◽  
Whole Genome Sequencing Data ◽  
Runs Of Homozygosity ◽  
Sequencing Data ◽  
Local Ancestry

AbstractRuns of homozygosity (ROH) are important genomic features that manifest when an individual inherits two haplotypes that are identical-by-descent. Their length distributions are informative about population history, and their genomic locations are useful for mapping recessive loci contributing to both Mendelian and complex disease risk. We have previously shown that ROH, and especially long ROH that are likely the result of recent parental relatedness, are enriched for homozygous deleterious coding variation in a worldwide sample of outbred individuals. However, the distribution of ROH in admixed populations and their relationship to deleterious homozygous genotypes is understudied. Here we analyze whole genome sequencing data from 1,441 individuals from self-identified African American, Puerto Rican, and Mexican American populations. These populations are three-way admixed between European, African, and Native American ancestries and provide an opportunity to study the distribution of deleterious alleles partitioned by local ancestry and ROH. We re-capitulate previous findings that long ROH are enriched for deleterious variation genome-wide. We then partition by local ancestry and show that deleterious homozygotes arise at a higher rate when ROH overlap African ancestry segments than when they overlap European or Native American ancestry segments of the genome. These results suggest that, while ROH on any haplotype background are associated with an inflation of deleterious homozygous variation, African haplotype backgrounds may play a particularly important role in the genetic architecture of complex diseases for admixed individuals, highlighting the need for further study of these populations.

scholarly journals Mitochondrial DNA Variation of Feral Honey Bees (Apis mellifera L.) from Utah (USA)

2018 ◽  
Vol 62 (2) ◽  
pp. 223-232
Author(s):  
Dylan Cleary ◽  
Allen L. Szalanski ◽  
Clinton Trammel ◽  
Mary-Kate Williams ◽  
Amber Tripodi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Apis Mellifera ◽  
Honey Bee ◽  
Honey Bees ◽  
Western Europe ◽  
Dna Variation ◽  
Bee Colony ◽  
The Us ◽  
Coii Gene

Abstract A study was conducted on the mitochondrial DNA genetic diversity of feral colonies and swarms of Apis mellifera from ten counties in Utah by sequencing the intergenic region of the cytochrome oxidase (COI-COII) gene region. A total of 20 haplotypes were found from 174 honey bee colony samples collected from 2008 to 2017. Samples belonged to the A (African) (48%); C (Eastern Europe) (43%); M (Western Europe) (4%); and O (Oriental) lineages (5%). Ten African A lineage haplotypes were observed with two unique to Utah among A lineage haplotypes recorded in the US. Haplotypes belonging to the A lineage were observed from six Utah counties located in the southern portion of the State, from elevations as high as 1357 m. All five C lineage haplotypes that were found have been observed from queen breeders in the US. Three haplotypes of the M lineage (n=7) and two of the O lineage (n=9) were also observed. This study provides evidence that honey bees of African descent are both common and diverse in wild populations of honey bees in southern Utah. The high levels of genetic diversity of A lineage honey bee colonies in Utah provide evidence that the lineage may have been established in Utah before the introduction of A lineage honey bees from Brazil to Texas in 1990.

scholarly journals Toxicity Evaluation of Selected Plant Water Extracts on a Honey Bee (Apis mellifera L.) Larvae Model

Animals ◽  
2022 ◽  
Vol 12 (2) ◽  
pp. 178
Author(s):  
Roksana Kruszakin ◽  
Paweł Migdal
Keyword(s):  
Apis Mellifera ◽  
Honey Bee ◽  
Honey Bees ◽  
Larval Rearing ◽  
Distilled Water ◽  
Chelidonium Majus ◽  
Freeze Dried ◽  
Study Laboratory ◽  
The Impact

So far, larval rearing in vitro has been an important method in the assessment of bee toxicology, particularly in pesticide risk assessment. However, natural products are increasingly used to control honey bee pathogens or to enhance bee immunity, but their effects on honey bee larvae are mostly unknown. In this study, laboratory studies were conducted to determine the effects of including selected aqueous plant infusions in the diet of honey bee (Apis mellifera L.) larvae in vitro. The toxicity of infusions from three different plant species considered to be medicinal plants was evaluated: tansy (Tanacetum vulgare L.), greater celandine (Chelidonium majus L.), and coriander (Coriandrum sativum L.). The impact of each on the survival of the larvae of honey bees was also evaluated. One-day-old larvae were fed a basal diet consisting of distilled water, sugars (glucose and fructose), yeast extract, and freeze-dried royal jelly or test diets in which distilled water was replaced by plant infusions. The proportion of the diet components was adjusted to the age of the larvae. The larvae were fed twice a day. The experiment lasted seven days. Significant statistical differences in survival rates were found between groups of larvae (exposed or not to the infusions of tansy, greater celandine, and coriander). A significant decrease (p < 0.05) in the survival rate was observed in the group with the addition of a coriander herb infusion compared to the control. These results indicate that plant extracts intended to be used in beekeeping should be tested on all development stages of honey bees.

scholarly journals Beeporter: a high-throughput tool for non-invasive analysis of honey bee virus infection

2021 ◽  
Author(s):  
Jay D. Evans ◽  
Olubukola Banmeke ◽  
Evan C. Palmer-Young ◽  
Yanping Chen ◽  
Eugene V. Ryabov
Keyword(s):  
Virus Infection ◽  
Honey Bee ◽  
High Throughput ◽  
Honey Bees ◽  
High Throughput Screening ◽  
Fluorescent Protein ◽  
Imaging System ◽  
Uv Light ◽  
Light Sources ◽  
Deformed Wing Virus

ABSTRACTHoney bees face numerous pests and pathogens but arguably none are as devastating as Deformed wing virus (DWV). Development of antiviral therapeutics and virus-resistant honey bee lines to control DWV in honey bees is slowed by the lack of a cost-effective high-throughput screening of DWV infection. Currently, analysis of virus infection and screening for antiviral treatments in bees and their colonies is tedious, requiring a well-equipped molecular biology laboratory and the use of hazardous chemicals. Here we utilize a cDNA clone of DWV tagged with green fluorescent protein (GFP) to develop the Beeporter assay, a method for detection and quantification of DWV infection in live honey bees. The assay involves infection of honey bee pupae by injecting a standardized DWV-GFP inoculum, followed by incubation for up to 44 hours. GFP fluorescence is recorded at intervals via commonly available long-wave UV light sources and a smartphone camera or a standard ultraviolet transilluminator gel imaging system. Nonlethal DWV monitoring allows high-throughput screening of antiviral candidates and a direct breeding tool for identifying honey bee parents with increased antivirus resistance. For even more rapid drug screening, we also describe a method for screening bees using 96-well trays and a spectrophotometer.

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