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 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 Low genetic diversity among Francisella-like endosymbionts within different genotypes of Hyalomma dromedarii ticks infesting camels in Saudi Arabia

2020 ◽  
Vol 13 (7) ◽  
pp. 1462-1472
Author(s):  
Haitham Elbir ◽  
Faisal Almathen ◽  
Ayman Elnahas
Keyword(s):  
Genetic Diversity ◽  
Saudi Arabia ◽  
Population Structure ◽  
16S Rrna ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Hyalomma Dromedarii ◽  
Low Genetic Diversity

Background and Aim: Hyalomma dromedarii ticks are vectors of disease agents and hosts of Francisella-like endosymbionts (FLEs). Knowledge about intraspecific genetic variation among H. dromedarii and its Francisella species is limited. The aims of this study were to investigate whether certain H. dromedarii genotypes are specialized in carrying specific Francisella species genotypes and scrutinize the population structure of H. dromedarii ticks in Saudi Arabia. Materials and Methods: We collected 151 H. dromedarii ticks from 33 camels from 13 locations in Saudi Arabia. The second internal transcribed spacer (ITS2), cytochrome c oxidase subunit-1(COI), and 16S rRNA genes were used for single-and multi-locus sequence typing and phylogenetic analyses. H. dromedarii-borne Francisella was screened using the tul4 gene and 16S rRNA Francisella-specific primers followed by amplicon Sanger sequencing. Results: Single-locus typing of ticks using ITS2, 16S rRNA, and COI genes yielded 1, 10, and 31 sequence types (ST), respectively, with pairwise sequence similarity of 100% for ITS2, 99.18-99.86% for COI, and 99.50-99.75% for 16S rRNA. COI sequence analysis indicated a lack of strict geographical structuration, as ST15 was found in both Saudi Arabia and Kenya. In contrast, multilocus sequence typing resolved 148 H. dromedarii ticks into 39 genotypes of ticks and three genotypes of FLEs. The ST2-FLE genotype was carried by the tick genotype ST35, while the ST1-FLE genotype and 41.89% of the ST3-FLE genotype were carried by the tick genotype ST32. Accordingly, there appeared to be no specialization of certain tick genotypes to harbor-specific FLE genotypes. Conclusion: For the 1st time, we have provided an overview of the population structure of H. dromedarii ticks and FLE strains. We found a low level of genetic diversity among FLEs and non-specialized circulation of FLEs among H. dromedarii ticks.

scholarly journals Evaluation of genetic diversity of honey bee in Ukraine analyzed by the SSR-markers

2020 ◽  
Vol 26 ◽  
pp. 56-60
Author(s):  
D. I. Hryhorchuk ◽  
A. M. Rabokon ◽  
A. S. PostovoitovA ◽  
N. M. Pirko ◽  
Ya. V. Pirko ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Honey Bee ◽  
Ssr Markers ◽  
Honey Bees ◽  
Molecular Genetic ◽  
Molecular Genetic Analysis ◽  
Analysis Method ◽  
Ssr Analysis ◽  
Silver Nitrate Staining

Aim. The aim of the work was to analyze current genetic structure of honey bee populations in Ukraine that belong to different subspecies: A. meliffera meliffera, A. meliffera carnica, A. meliffera macedonica using microsatellite markers. Methods. SSR-analysis was used for evaluation of the honey bee polymorphism. Amplified fragments were fractionated by electrophoresis in non-denaturing polyacrylamide gel. DNA bands were detected using silver nitrate staining. Results. The analysis of the sample of honey bees (workers and male-bees) collected from different regions of Ukraine was performed by using two SSR-markers (Ac011 and A007). In this sample reasonably high polymorphism was observed, especially for the SSR-marker A007. Conclusions. It was estimated that SSR-analysis method can be applied in molecular-genetic analysis of honey bees for evaluation of genetic diversity and cross-subspecies hybridization. Keywords: microsatellite markers, Apis meliffera, PIC (Polymorphism Information Content).

scholarly journals GENETIC DIVERSITY OF HONEY BEE POPULATIONS IN TURKEY BASED ON MICROSATELLITE MARKERS: A COMPARISON BETWEEN MIGRATORY VERSUS STATIONARY APIARIES AND ISOLATED REGIONS VERSUS REGIONS OPEN TO MIGRATORY BEEKEEPING

2019 ◽  
Author(s):  
Mert Kükrer
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
Honey Bee ◽  
Honey Bees ◽  
Phylogenetic Trees ◽  
The Status ◽  
Genetic Impact ◽  
Geographic Populations ◽  
Ecological Importance

The honey bee (Apis mellifera L.) is a globally significant species of apparent economic and ecological importance. Recent reports from Spain, Italy and Greece point to an intense admixture of honey bee populations signified by a loss of population structure. This is mostly attributed to migratory beekeeping practices and replacement of queens or colonies with commercial ones that are usually from non-native races or hybrids of different subspecies. These two practices are also heavily carried out in parts of Turkey where almost three-quarters of the 6 million colonies are transferred seasonally from one region to other.Past research using microsatellite and RAPD markers, mtDNA, allozymes and geometric morphometry revealed the presence of five different subspecies of honey bees (meda, syriaca,caucasica, anatoliaca and an ecotype from Carniolan subspecies group) inTurkey. Here, we carried out an analysis of population structure of Turkish honeybees sampled from six different regions (n = 250) during the period 2010-2012. A total of 29 microsatellite markers were used in four multiplex reactions. The results show that population structure is preserved in general although there are signs of gene flow between the clusters.Overall FST between stationary colonies was calculated as 0,067. For migratory colonies the value was 0,015 and for all the 250 samples the value was 0,047. Four different clusters corresponding to geographical distributions of four subspecies were revealed in structure analysis. The differentiation between the clusters was also apparent in PCA and FCA as well as phylogenetic trees constructed based on genetic distances.The genetic impact of migratory beekeeping was demonstrated for the first time based on a comparison of assignment probabilities of individuals from migratory and stationary colonies to their geographic populations. Another comparison between regions that are either open to migratory beekeeping or closed let us to evaluate the status of isolated regions and showed the importance of establishing such regions. The effects of queen and colony trade were revealed by the presence of introgression from the highly commercial Caucasian bees. Our findings confirm the previously observed high levels geographically structured genetic diversity in honey bees of Turkey and emphasize the need to develop policies to maintain this diversity.

scholarly journals Genetic diversity of tropical-adapted onion germplasm assessed by RAPD markers

2012 ◽  
Vol 30 (1) ◽  
pp. 112-118 ◽  
Author(s):  
Maria do Desterro M dos Santos ◽  
Carlos Francisco Ragassi ◽  
Maria Esther de N Fonseca ◽  
Anne Gizelle R Buzar ◽  
Valter R Oliveira ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Germplasm Collection ◽  
Rio Grande ◽  
Breeding Programs ◽  
Tropical Regions ◽  
Low Genetic Diversity ◽  
Tropical Conditions ◽  
Average Similarity ◽  
Onion Germplasm

Onion is a crop of significant socioeconomic importance to Brazil. Onion germplasm with adaptation to tropical and sub-tropical conditions has played an important role in the development of this crop in the country. In this context, we studied the genetic diversity in a germplasm collection potentially useful for the development of cultivars for tropical and subtropical regions. The genetic variability of 21 accessions/cultivars that have been used as germplasm and/or were developed by onion breeding programs in Brazil was evaluated via RAPD markers. The following accessions were included in the study :'Red Creole', 'Roxa IPA-3', 'Valenciana 14', 'Beta Cristal', 'Diamante', 'Composto IPA-6', 'Aurora', 'Bojuda Rio Grande', 'Alfa Tropical', 'Pêra IPA-4', 'Primavera', 'Belém IPA-9', 'Crioula Alto Vale', 'Conquista', 'Pira-Ouro', 'Vale-Ouro IPA-11', 'Franciscana IPA-10', 'Serrana', 'CNPH 6400', 'Petroline', and 'Baia Periforme'. From the 520 primers used in the initial screening only 38 displayed stable polymorphisms. They produced 624 amplicons, of which 522 (83.7%) were monomorphic and 102 (16.3%) were polymorphic. An average similarity coefficient of 0.72 was calculated among accessions based upon this subgroup of polymorphic amplicons. This allowed the discrimination of this germplasm collection into six groups with only one of them comprising more than one accession. The main group was formed by 16 accessions ('Diamante', 'Composto IPA-6', 'Aurora', 'Bojuda Rio Grande', 'Conquista', 'Pira-Ouro', 'Serrana', 'Vale-Ouro IPA-11', 'Baia Periforme', 'Primavera', 'Franciscana IPA-10', 'Belém IPA-9', 'Crioula Alto Vale', 'Petroline', 'Pêra IPA-4' and 'Alfa Tropical'), for which the genetic origin (with few exceptions) can be traced back to the variety 'Baia Periforme'. The populations 'Red Creole', 'Roxa IPA-3', 'Beta Cristal', 'CNPH 6400', and 'Valenciana 14' comprised a set of five isolated groups, showing genetic divergence among them and in relation to main 'Baia Periforme' group. This germplasm displayed a relatively low genetic diversity, with the predominance of materials originated from the base population 'Baia Periforme'. There are, however, some accessions, which can add genetic diversity to this germplasm and they can be exploited by onion breeding programs aiming to develop cultivars for tropical regions of the world.

scholarly journals Genetic Diversity and Relationships of Phalaenopsis Based on the rbcL and trnL-F Markers: In Silico Approach

2021 ◽  
Vol 13 (2) ◽  
pp. 212-221
Author(s):  
Dindin Hidayatul Mursyidin ◽  
Gusti Muhammad Zainal Ahyar ◽  
Ahmad Winarto Saputra ◽  
Aminoor Hidayat
Keyword(s):  
Genetic Diversity ◽  
In Silico ◽  
Nucleotide Diversity ◽  
Diversity Index ◽  
Likelihood Method ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Breeding Programs ◽  
Multiple Sequence Alignments ◽  
Low Genetic Diversity

In silico is the more comprehensive and applicable approach in supporting, both conservation and breeding programs of germplasm. The study aimed to analyze and determine the genetic diversity and relationships of 24 species of Phalaenopsis using two DNA barcoding markers, namely the rbcL and trnL-F, by in silico approach. All sequences of these markers were collected randomly from the NCBI website and analyzed using several softwares and methods, such as ClustalW and MultAlin for multiple sequence alignments and MEGA-X to determine its genetic diversity and relationships. Specifically, the genetic diversity was determined using a nucleotide diversity index and their relationships by the Maximum Likelihood method. The results showed that Phalaenopsis has a low genetic diversity of 0.24, 0.32, and 0.19, respectively. The phylogenetic analysis revealed that this orchid separated into five (for the rbcL), six (trnL-F), and seven clades (a combined one), where the closest relationship is shown by P. amboinensis vs. P. venosa, whereas the farthest by P. gibbosa vs. P. doweryensis, P. stuartiana vs. P. micholitzii, and P. celebensis vs. P. pulchra. The results have novel information on the diversity and relationships of Phalaenopsis on the in silico approach. Thus, our findings might be used in supporting the conservation and breeding program of Phalaenopsis, both locally and globally.

scholarly journals Evaluation of Genetic Diversity of Iranian Pomegranate Cultivars Using Fruit Morphological Characteristics and AFLP Markers

2012 ◽  
Vol 40 (1) ◽  
pp. 261 ◽  
Author(s):  
Zahra NEMATI ◽  
Ali TEHRANIFAR ◽  
Mohammad FARSI ◽  
Amin MIRSHAMSI KAKHKI ◽  
Hossein NEMATI ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Morphological Characteristics ◽  
Principal Component ◽  
Aflp Markers ◽  
Fruit Characteristics ◽  
Aflp Data ◽  
Breeding Programs ◽  
Low Genetic Diversity ◽  
Geographic Origins ◽  
The Relationship

The present research evaluated the diversity of a number of Iranian pomegranate cultivars using fruit morphological characteristics and AFLP markers. Thirty-one pomegranate cultivars were collected from Yazd Pomegranate Collection in Iran to study their diversity. Seven AFLP primer combinations were used to amplify a total of 112 polymorphic fragments (47.26%). By use of AFLPs, a low genetic diversity level was detected among cultivars. The relationship between fruit characteristics was analyzed using the principal component analysis (PCA). The cluster analysis based on both fruit characteristics and AFLP data indicated that cultivars were not grouped according to their geographic origins. Moreover, the correlation between the diversity matrix based on fruit characteristics and Dice’s genetic similarity coefficient was insignificant (r=0.06). The results obtained from this study can improve the conservation and management of pomegranate germplasm resources and could be helpful in optimizing breeding programs.

scholarly journals Genetic Composition of Korean Ginseng Germplasm by Collection Area and Resource Type

Agronomy ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 1643
Author(s):  
Kyung Jun Lee ◽  
Raveendar Sebastin ◽  
Seong-Hoon Kim ◽  
Eunae Yoo ◽  
Sookyeong Lee ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Source Material ◽  
Genetic Composition ◽  
Breeding Programs ◽  
Breeding Lines ◽  
Low Genetic Diversity ◽  
Resource Type ◽  
Genetic Source ◽  
Wild Ginseng ◽  
Korean Ginseng

To improve crops, it is important to secure plant genetic source material and evaluate the genetic diversity. Ginseng (Panax ginseng C.A. Meyer) has long been used as a medicinal herb in Korea and China. Since ginseng originated from wild ginseng with low genetic diversity, it is also expected to have low genetic diversity. In this study, the genetic diversity of 451 ginseng accessions conserved in the National Agrobiodiversity Center (NAC) at Korea was analyzed using 33 SSR markers. Another objective was to establish a strategy for NAC to manage ginseng germplasm based on these results. The 451 accessions were collected from 22 cities in six provinces in South Korea. Among the 451 ginseng accessions, 390 (86.5%) and 61 (13.5%) were landraces and breeding lines, respectively. In the STRUCTURE results for the accessions, there was no relationship between assigned genotypes and collection areas, but there was a population genetic structure. In addition, genetic differentiation within populations of each analysis was low, indicating that the ginseng accessions conserved at NAC are extensively dispersed throughout the collection areas. The results of this study suggest that NAC should increase the genetic diversity of ginseng accessions for breeding programs, and alternatives are needed for securing ginseng genetic resources.

scholarly journals In silico identification of off-target pesticidal dsRNA binding in honey bees (Apis mellifera)

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e4131 ◽  
Author(s):  
Christina L. Mogren ◽  
Jonathan Gary Lundgren
Keyword(s):  
Honey Bee ◽  
Honey Bees ◽  
In Silico ◽  
Target Genes ◽  
Sequence Similarity ◽  
Phenotypic Effect ◽  
High Sequence Similarity ◽  
Dsrna Molecule ◽  
Dsrna Binding ◽  
Genomic Regions

Background Pesticidal RNAs that silence critical gene function have great potential in pest management, but the benefits of this technology must be weighed against non-target organism risks. Methods Published studies that developed pesticidal double stranded RNAs (dsRNAs) were collated into a database. The target gene sequences for these pesticidal RNAs were determined, and the degree of similarity with sequences in the honey bee genome were evaluated statistically. Results We identified 101 insecticidal RNAs sharing high sequence similarity with genomic regions in honey bees. The likelihood that off-target sequences were similar increased with the number of nucleotides in the dsRNA molecule. The similarities of non-target genes to the pesticidal RNA was unaffected by taxonomic relatedness of the target insect to honey bees, contrary to previous assertions. Gene groups active during honey bee development had disproportionately high sequence similarity with pesticidal RNAs relative to other areas of the genome. Discussion Although sequence similarity does not itself guarantee a significant phenotypic effect in honey bees by the primary dsRNA, in silico screening may help to identify appropriate experimental endpoints within a risk assessment framework for pesticidal RNAi.

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.

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