Browsing by Author "Kryger, Per"
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- Authoritative subspecies diagnosis tool for European honey bees based on ancestry informative SNPsPublication . Momeni, Jamal; Parejo, Melanie; Nielsen, Rasmus O.; Langa, Jorge; Montes, Iratxe; Papoutsis, Laetitia; Farajzadeh, Leila; Bendixen, Christian; Căuia, Eliza; Charrière, Jean Daniel; Coffey, Mary F.; Costa, Cecilia; Dall'Olio, Raffaele; De la Rúa, Pilar; Dražić, Marica Maja; Filipi, Janja; Galea, Thomas; Golubovski, Miroljub; Gregorc, Aleš; Grigoryan, Karina; Hatjina, Fani; Ilyasov, Rustem; Ivanova, Evgeniya Neshova; Janashia, Irakli; Kandemir, Irfan; Karatasou, Aikaterini; Kekecoglu, Meral; Kezic, Nikola; Matray, Enikö Sz; Mifsud, David; Moosbeckhofer, Rudolf; Nikolenko, Alexei G.; Papachristoforou, Alexandros; Petrov, Plamen; Pinto, M. Alice; Poskryakov, Aleksandr V.; Sharipov, Aglyam Y.; Siceanu, Adrian; Soysal, M. Ihsan; Uzunov, Aleksandar; Zammit Mangion, Marion; Vingborg, Rikke; Bouga, Maria; Kryger, Per; Meixner, Marina D.; Estonba, AndoneWith numerous endemic subspecies representing four of its five evolutionary lineages, Europe holds a large fraction of Apis mellifera genetic diversity. This diversity and the natural distribution range have been altered by anthropogenic factors. The conservation of this natural heritage relies on the availability of accurate tools for subspecies diagnosis. Based on pool-sequence data from 2145 worker bees representing 22 populations sampled across Europe, we employed two highly discriminative approaches (PCA and FST) to select the most informative SNPs for ancestry inference. Results: Using a supervised machine learning (ML) approach and a set of 3896 genotyped individuals, we could show that the 4094 selected single nucleotide polymorphisms (SNPs) provide an accurate prediction of ancestry inference in European honey bees. The best ML model was Linear Support Vector Classifier (Linear SVC) which correctly assigned most individuals to one of the 14 subspecies or different genetic origins with a mean accuracy of 96.2% ± 0.8 SD. A total of 3.8% of test individuals were misclassified, most probably due to limited differentiation between the subspecies caused by close geographical proximity, or human interference of genetic integrity of reference subspecies, or a combination thereof. Conclusions: The diagnostic tool presented here will contribute to a sustainable conservation and support breeding activities in order to preserve the genetic heritage of European honey bees.
- Complex population structure and haplotype patterns in the Western European honey bee from sequencing a large panel of haploid dronesPublication . Wragg, David; Eynard, Sonia E.; Basso, Benjamin; Canale‐Tabet, Kamila; Labarthe, Emmanuelle; Bouchez, Olivier; Bienefeld, Kaspar; Bieńkowska, Małgorzata; Costa, Cecilia; Gregorc, Aleš; Kryger, Per; Parejo, Melanie; Pinto, M. Alice; Bidanel, Jean‐Pierre; Servin, Bertrand; Le Conte, Yves; Vignal, AlainHoney bee subspecies originate from specific geographical areas in Africa, Europe and the Middle East, and beekeepers interested in specific phenotypes have imported genetic material to regions outside of the bees' original range for use either in pure lines or controlled crosses. Moreover, imported drones are present in the environ-ment and mate naturally with queens from the local subspecies. The resulting ad-mixture complicates population genetics analyses, and population stratification can be a major problem for association studies. To better understand Western European honey bee populations, we produced a whole genome sequence and single nucleotide polymorphism (SNP) genotype data set from 870 haploid drones and demonstrate its utility for the identification of nine genetic backgrounds and various degrees of admixture in a subset of 629 samples. Five backgrounds identified correspond to sub-species, two to isolated populations on islands and two to managed populations. We also highlight several large haplotype blocks, some of which coincide with the position of centromeres. The largest is 3.6 Mb long and represents 21% of chromosome 11, with two major haplotypes corresponding to the two dominant genetic backgrounds identified. This large naturally phased data set is available as a single vcf file that can now serve as a reference for subsequent populations genomics studies in the honey bee, such as (i) selecting individuals of verified homogeneous genetic backgrounds as references, (ii) imputing genotypes from a lower-density data set generated by an SNP- chip or by low- pass sequencing, or (iii) selecting SNPs compatible with the re-quirements of genotyping chips.
- Effect of linkage disequilibrium on inferences of population structure and introgression of iberian and black honey beesPublication . Chávez-Galarza, Julio; Henriques, Dora; Kryger, Per; De la Rúa, Pilar; Johnston, J. Spencer; Rufino, José; Pinto, M. AliceIdentification of population structure, a primary goal in population genetics, is easily performed because there is a number of methods available, implemented by user-friendly software packages. However, the user must be cautious when inferring population structure because spurious results may be obtained when there is strong linkage disequilibrium. With recent development of high-density SNPs we have now more power to interrogate the honey bee genome. However, the greater the number of loci genotyped the greater the chance of scoring loci that are linked. In addition, events such as population bottleneck, small effective population size, genetic drift, and admixture may also generate strong linkage disequilibrium. According to Kaeuffer et al. (2007), correlation rLD is the best way to deal with linkage disequilibrium. These authors recommend removing loci with rLD higher than 0.5 when inferring structure. In this study we used the GoldenGate Assay of Illumina to genotype over 1221 loci in individuals sampled from populations of A.m. iberiensis and A.m. mellifera. In this dataset we used the genetic distance between SNPs and rLD to test the effect of linkage in the number of clusters and the introgression level inferred by the clustering method implemented in the software STRUCTURE.
- Effect of linkage disequilibrium on inferences of population structure and introgression of iberian and black honey beesPublication . Chávez-Galarza, Julio; Henriques, Dora; Kryger, Per; De la Rúa, Pilar; Johnston, J. Spencer; Rufino, José; Pinto, M. AliceIdentification of population structure, a primary goal in population genetics, is easily performed because there is a number of methods available, implemented by user-friendly software packages. However, the user must be cautious when inferring population structure because spurious results may be obtained when there is strong linkage disequilibrium. With recent development of high-density SNPs we have now more power to interrogate the honey bee genome. However, the greater the number of loci genotyped the greater the chance of scoring loci that are linked. In addition, events such as population bottleneck, small effective population size, genetic drift, and admixture may also generate strong linkage disequilibrium. According to Kaeuffer et al. (2007), correlation rLD is the best way to deal with linkage disequilibrium. These authors recommend removing loci with rLD higher than 0.5 when inferring structure. In this study we used the GoldenGate Assay of Illumina to genotype over 1221 loci in individuals sampled from populations of A.m. iberiensis and A.m. mellifera. In this dataset we used the genetic distance between SNPs and rLD to test the effect of linkage in the number of clusters and the introgression level inferred by the clustering method implemented in the software STRUCTURE.
- Evaluation of suppressed mite reproduction (Smr) reveals potential for varroa resistance in european honey bees (apis mellifera l.)Publication . Mondet, Fanny; Parejo, Melanie; Meixner, Marina D.; Costa, Cecilia; Kryger, Per; Andonov, Sreten; Servin, Bertrand; Basso, Benjamin; Bieńkowska, Małgorzata; Bigio, Gianluigi; Căuia, Eliza; Cebotari, Valentina; Dahle, Bjørn; Dražić, Marica Maja; Hatjina, Fani; Kovačić, Marin; Kretavicius, Justinas; Lima, Ana S.; Panasiuk, Beata; Pinto, M. Alice; Uzunov, Aleksandar; Wilde, Jerzy; Büchler, RalphIn 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.
- Genetic integrity of the Dark European honey bee (Apis mellifera mellifera) from protected populations: a genome-wide assessment using SNPs and mtDNA sequence dataPublication . Pinto, M. Alice; Henriques, Dora; Chávez-Galarza, Julio; Kryger, Per; Garnery, Lionel; Zee, Romée van der; Dahle, Bjørn; Soland-Reckeweg, Gabriele; De la Rúa, Pilar; Dall'Olio, Raffaele; Carreck, Norman L.; Johnston, J. SpencerThe recognition that the Dark European honey bee, Apis mellifera mellifera, is increasingly threatened in its native range has led to the establishment of conservation programmes and protected areas throughout western Europe. Previous molecular surveys showed that, despite management strategies to preserve the genetic integrity of A. m. mellifera, protected populations had a measurable component of their gene pool derived from commercial C-lineage honey bees. Here we used both sequence data from the tRNAleu-cox2 intergenic mtDNA region and a genome-wide scan, with over 1183 single nucleotide polymorphisms (SNPs), to assess genetic diversity and introgression levels in several protected populations of A. m. mellifera, which were then compared with samples collected from unprotected populations. MtDNA analysis of the protected populations revealed a single colony bearing a foreign haplotype, whereas SNPs showed varying levels of introgression ranging from virtually zero in Norway to about 14% in Denmark. Introgression overall was higher in unprotected (30%) than in protected populations (8%), and is reflected in larger SNP diversity levels of the former, although opposite diversity levels were observed for mtDNA. These results suggest that, despite controlled breeding, some protected populations still require adjustments to the management strategies to further purge foreign alleles, which can be identified by SNPs.
- High sample throughput genotyping for estimating C-lineage introgression in the dark honeybee: an accurate and cost-effective SNP-based toolPublication . Henriques, Dora; Browne, Keith A.; Barnett, Mark W.; Parejo, Melanie; Kryger, Per; Freeman, Tom C.; Muñoz, Irene; Garnery, Lionel; Highet, Fiona; Jonhston, J. Spencer; McCormack, Grace P.; Pinto, M. AliceThe natural distribution of the honeybee (Apis mellifera L.) has been changed by humans in recent decades to such an extent that the formerly widest-spread European subspecies, Apis mellifera mellifera, is threatened by extinction through introgression from highly divergent commercial strains in large tracts of its range. Conservation efforts for A. m. mellifera are underway in multiple European countries requiring reliable and cost-efficient molecular tools to identify purebred colonies. Here, we developed four ancestry-informative SNP assays for high sample throughput genotyping using the iPLEX Mass Array system. Our customized assays were tested on DNA from individual and pooled, haploid and diploid honeybee samples extracted from different tissues using a diverse range of protocols. The assays had a high genotyping success rate and yielded accurate genotypes. Performance assessed against whole-genome data showed that individual assays behaved well, although the most accurate introgression estimates were obtained for the four assays combined (117 SNPs). The best compromise between accuracy and genotyping costs was achieved when combining two assays (62 SNPs). We provide a ready-to-use cost-effective tool for accurate molecular identification and estimation of introgression levels to more effectively monitor and manage A. m. mellifera conservatories.
- High sample throughput genotyping for estimating C-lineage introgression in the dark honeybee: An accurate and cost-effective SNP-based toolPublication . Henriques, Dora; Browne, Keith A.; Barnett, Mark W.; Parejo, Melanie; Kryger, Per; Freeman, Tom C.; Muñoz, Irene; Garnery, Lionel; Highet, Fiona; Johnston, J. Spencer; McCormack, Grace P.; Pinto, M. AliceThe natural distribution of the honeybee (Apis mellifera L.) has been changed by humans in recent decades to such an extent that the formerly widest-spread European subspecies, Apis mellifera mellifera, is threatened by extinction through introgression from highly divergent commercial strains in large tracts of its range. Conservation efforts for A. m. mellifera are underway in multiple European countries requiring reliable and cost-efficient molecular tools to identify purebred colonies. Here, we developed four ancestry-informative SNP assays for high sample throughput genotyping using the iPLEX Mass Array system. Our customized assays were tested on DNA from individual and pooled, haploid and diploid honeybee samples extracted from different tissues using a diverse range of protocols. The assays had a high genotyping success rate and yielded accurate genotypes. Performance assessed against whole-genome data showed that individual assays behaved well, although the most accurate introgression estimates were obtained for the four assays combined (117 SNPs). The best compromise between accuracy and genotyping costs was achieved when combining two assays (62 SNPs). We provide a ready-to-use cost-effective tool for accurate molecular identification and estimation o
- Introgression of lineage c honey bees into black honey bee populations: a genome-wide estimation using single nucleotide polymorphisms (SNPS)Publication . Henriques, Dora; Chávez-Galarza, Julio; Kryger, Per; Johnston, J. Spencer; De la Rúa, Pilar; Rufino, José; Dall'Olio, Raffaele; Garnery, Lionel; Pinto, M. AliceThe black honey bee, Apis mellifera mellifera L., is probably the honey bee subspecies more threatened by introgression from foreign subspecies, specially lineage C A. m. carnica and A. m. ligustica. In fact, in some areas of its distributional range, intensive beekeeping with foreign subspecies has driven A. m. mellifera populations to nearly replacement. While massive and repeated introductions may lead to loss of native genetic patrimony, a low level of gene flow can also be detrimental because it may compromise honey bee survival and local adaptation by disrupting co-evolved gene complexes. Assessing levels of introgression is an important activity in breeding programs, especially when conservation of native races is a major concern. Previous surveys of A. m. mellifera populations estimated the introgression of lineage C honey bees by using mtDNA and microsatellites markers. In this presentation we used both mtDNA (sequence data of the tRNAleu-cox2 intergenic region) and over 1245 SNPs to ascertain introgression levels of A. m. carnica and A. m. ligustica in A. m. mellifera populations (some included in conservation programs) sampled in France, Switzerland, Denmark, Holland, Norway, England, and Scotland. We used different model-based approaches, implemented by different software applications (Structure, Admixture, NewHybrids). We found varying levels of introgression ranging from less than 3% (in Norway) to over 65% (in France).
- Introgression of lineage c honey bees into black honey bee populations: a genome-wide estimation using single nucleotide polymorphisms (SNPS)Publication . Henriques, Dora; Chávez-Galarza, Julio; Kryger, Per; Johnston, J. Spencer; De la Rúa, Pilar; Rufino, José; Dall'Olio, Raffaele; Garnery, Lionel; Pinto, M. AliceThe black honey bee, Apis mellifera mellifera L., is probably the honey bee subspecies more threatened by introgression from foreign subspecies, specially lineage C A. m. carnica and A. m. ligustica. In fact, in some areas of its distributional range, intensive beekeeping with foreign subspecies has driven A. m. mellifera populations to nearly replacement. While massive and repeated introductions may lead to loss of native genetic patrimony, a low level of gene flow can also be detrimental because it may compromise honey bee survival and local adaptation by disrupting co-evolved gene complexes. Assessing levels of introgression is an important activity in breeding programs, especially when conservation of native races is a major concern. Previous surveys of A. m. mellifera populations estimated the introgression of lineage C honey bees by using mtDNA and microsatellites markers. In this presentation we used both mtDNA (sequence data of the tRNAleu-cox2 intergenic region) and over 1245 SNPs to ascertain introgression levels of A. m. carnica and A. m. ligustica in A. m. mellifera populations (some included in conservation programs) sampled in France, Switzerland, Denmark, Holland, Norway, England, and Scotland. We used different model-based approaches, implemented by different software applications (Structure, Admixture, NewHybrids). We found varying levels of introgression ranging from less than 3% (in Norway) to over 65% (in France).