Microsatellite genotyping of post-PCR fluorescently labeled markers

We show that a post-PCR multicolor fluorescence-labeling technique is applicable to multiplex microsatellite genotyping. Forty-three dinucleotide microsatellite markers, which are located on 11q13-23, a candidate region for dominant familial exudative vitreoretinopathy (FEVR), were used to evaluate the quality of the marker profile produced by this technique. Thirty-eight people from six families with this disease were subjects for genotyping. The samples revealed clearly separated fragment peaks with signal intensities sufficient for analysis. All genotypes were consistent with Mendelian inheritance within each family. This method is cost effective because it does not use expensive fluorescently labeled primers. It also has the advantage of avoiding ambiguity in the analysis, which may arise from the addition of non-template nucleotides by Taq DNA polymerase.     

Microsatellite markers and genotyping procedures for Anopheles gambiae

The procedures outlined in this article by Rui Wang, Fotis Kafatos and Liangbiao Zheng are well suited to studies of field mosquito populations, and also to the genetic mapping of qualitative and quantitative traits of Anopheles gambiae, a major malaria vector in Africa. An accurate, reproducible and high-throughput microsatellite genotyping procedure has been established.     

Microsatellite genotyping by primer extension and MALDI-ToF mass spectrometry

A novel method for genotyping microsatellite alleles using primer extensions and mass spectrometry analysis has been developed. Following PCR amplification of the target region, a genotyping primer, with its 3′ end directly flanking the microsatellite repeats, was extended by a mixture of dNTPs complementary to the nucleotides composing the microsatellite. The length and molecular weight of extended primers vary with the number of repeats present in the allele(s) under examination. The weights of extension products were determined using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-ToF MS) and used to identify genotypes on the basis of differential primer extension. This is a platform that is not gel based and is amenable to multiplexing and automation. The technique enables identification of heterozygous progeny in which alleles differ by a single trinucleotide repeat. The method is illustrated by genotyping a polymorphic microsatellite identified in an intron of the barleyMlo gene.     

Microsatellite genotyping reveals end-Pleistocene decline in mammoth autosomal genetic variation

The last glaciation was a dynamic period with strong impact on the demography of many species and populations. In recent years, mitochondrial DNA sequences retrieved from radiocarbon-dated remains have provided novel insights into the history of Late Pleistocene populations. However, genotyping of loci from the nuclear genome may provide enhanced resolution of population-level changes. Here, we use four autosomal microsatellite DNA markers to investigate the demographic history of woolly mammoths (Mammuthus primigenius) in north-eastern Siberia from before 60 000 years ago up until the species' final disappearance c.4000 years ago. We identified two genetic groups, implying a marked temporal genetic differentiation between samples with radiocarbon ages older than 12 thousand radiocarbon years before present (ka) and those younger than 9ka. Simulation-based analysis indicates that this dramatic change in genetic composition, which included a decrease in individual heterozygosity of approximately 30%, was due to a multifold reduction in effective population size. A corresponding reduction in genetic variation was also detected in the mitochondrial DNA, where about 65% of the diversity was lost. We observed no further loss in genetic variation during the Holocene, which suggests a rapid final extinction event.     

Microsatellite genotyping of cryopreserved spermatozoa for the improvement of whitefish semen cryobanking

The cryobanking of semen is recognized as an emerging tool for the conservation of fish biodiversity. Microsatellite analysis of the DNA of cryopreserved sperm would facilitate the assessment of genetic variability of cryobanked semen specimens. The aim of this study was to compare microsatellite profiles of DNA extracted from adipose fins and cryopreserved semen collected from eleven male whitefish (Coregonus lavaretus L.). The following microsatellite loci were employed: Cocl–Lav-8, Cocl–Lav-18, Cocl–Lav-28, Cocl–Lav-80, Str-73 and Sfo-292. The chelex 100 method was used for the successful isolation of DNA from somatic tissue, and the DNeasy method with additional modifications was used for the successful isolation of DNA from sperm. Genotyping was possible with the use of a very low number of spermatozoa (5 × 10⁶ which is less than 0.1% of spermatozoa in standard 250 μL straw). The results of the DNA analysis from both the adipose tissue and spermatozoa were identical. Therefore, microsatellite analysis of cryopreserved spermatozoa can be recommended for future whitefish sperm banking.     

Microsatellite genotyping of cryopreserved spermatozoa for the improvement of whitefish semen cryobanking

The cryobanking of semen is recognized as an emerging tool for the conservation of fish biodiversity. Microsatellite analysis of the DNA of cryopreserved sperm would facilitate the assessment of genetic variability of cryobanked semen specimens. The aim of this study was to compare microsatellite profiles of DNA extracted from adipose fins and cryopreserved semen collected from eleven male whitefish (Coregonus lavaretus L.). The following microsatellite loci were employed: Cocl–Lav-8, Cocl–Lav-18, Cocl–Lav-28, Cocl–Lav-80, Str-73 and Sfo-292. The chelex 100 method was used for the successful isolation of DNA from somatic tissue, and the DNeasy method with additional modifications was used for the successful isolation of DNA from sperm. Genotyping was possible with the use of a very low number of spermatozoa (5 × 10⁶ which is less than 0.1% of spermatozoa in standard 250 μL straw). The results of the DNA analysis from both the adipose tissue and spermatozoa were identical. Therefore, microsatellite analysis of cryopreserved spermatozoa can be recommended for future whitefish sperm banking.     

Development and application of SINE-based markers for genotyping of potato varieties

Potato variety discrimination based on morphological traits is laborious and influenced by the environment, while currently applied molecular markers are either expensive or time-consuming in development or application. SINEs, short interspersed nuclear elements, are retrotransposons with a high copy number in plant genomes representing a potential source for new markers. We developed a marker system for potato genotyping, designated inter-SINE amplified polymorphism (ISAP). Based on nine potato SINE families recently characterized (Wenke et al. in Plant Cell 23:3117-3128, 2011), we designed species-specific SINE primers. From the resulting 153 primer combinations, highly informative primer sets were selected for potato variety analysis regarding number of bands, quality of the banding pattern, and the degree of polymorphism. Fragments representing ISAPs can be separated by conventional agarose gel electrophoresis; however, automation with a capillary sequencer is feasible. Two selected SINE families, SolS-IIIa and SolS-IV, were shown to be highly but differently amplified in Solanaceae, Solaneae tribe, including wild and cultivated potatoes, tomato, and eggplant. Fluorescent in situ hybridization demonstrated the genome-wide distribution of SolS-IIIa and SolS-IV along potato chromosomes, which is the basis for genotype discrimination and differentiation of somaclonal variants by ISAP markers.     

Microsatellite genotyping for genetic quality testing using sperm cells in the mouse.

We attempted to determine the number of sperm cells required for genotyping of one microsatellite marker. The crude genomic DNA extracted from about 760 or more sperm cells gave sufficient quantity of PCR product using a 20 microl-scale PCR. We also studied the effects of non-ionic detergents on extraction of crude sperm genomic DNA. PCR products amplified with the crude sperm genomic DNA extracted using the lysis buffer supplemented with non-ionic detergents showed much clear bands. In conclusion, our results suggest that a small part of the frozen sperm, which is less than 1/10 of the original volume (10 microl), provides sufficient quantity of template DNA for genetic quality testing.     

Microsatellite genotyping errors: detection approaches, common sources and consequences for paternal exclusion

Microsatellite genotyping errors will be present in all but the smallest data sets and have the potential to undermine the conclusions of most downstream analyses. Despite this, little rigorous effort has been made to quantify the size of the problem and to identify the commonest sources of error. Here, we use a large data set comprising almost 2000 Antarctic fur seals Arctocephalus gazella genotyped at nine hypervariable microsatellite loci to explore error detection methods, common sources of error and the consequences of errors on paternal exclusion. We found good concordance among a range of contrasting approaches to error-rate estimation, our range being 0.0013 to 0.0074 per single locus PCR (polymerase chain reaction). The best approach probably involves blind repeat-genotyping, but this is also the most labour-intensive. We show that several other approaches are also effective at detecting errors, although the most convenient alternative, namely mother-offspring comparisons, yielded the lowest estimate of the error rate. In total, we found 75 errors, emphasizing their ubiquitous presence. The most common errors involved the misinterpretation of allele banding patterns (n = 60, 80%) and of these, over a third (n = 22, 36.7%) were due to confusion between homozygote and adjacent allele heterozygote genotypes. A specific test for whether a data set contains the expected number of adjacent allele heterozygotes could provide a useful tool with which workers can assess the likely size of the problem. Error rates are also positively correlated with both locus polymorphism and product size, again indicating aspects where extra effort at error reduction should be directed. Finally, we conducted simulations to explore the potential impact of genotyping errors on paternity exclusion. Error rates as low as 0.01 per allele resulted in a rate of false paternity exclusion exceeding 20%. Errors also led to reduced estimates of male reproductive skew and increases in the numbers of pups that matched more than one candidate male. Because even modest error rates can be strongly influential, we recommend that error rates should be routinely published and that researchers make an attempt to calculate how robust their analyses are to errors.     

SNP genotyping reveals genetic diversity between cultivated landraces and contemporary varieties of tomato

Background

The tomato (Solanum lycopersium L.) is the most widely grown vegetable in the world. It was domesticated in Latin America and Italy and Spain are considered secondary centers of diversification. This food crop has experienced severe genetic bottlenecks and modern breeding activities have been characterized by trait introgression from wild species and divergence in different market classes.

Results

With the aim to examine patterns of polymorphism, characterize population structure and identify putative loci under positive selection, we genotyped 214 tomato accessions (which include cultivated landraces, commercial varieties and wild relatives) using a custom-made Illumina SNP-panel. Most of the 175 successfully scored SNP loci were found to be polymorphic. Population structure analysis and estimates of genetic differentiation indicated that landraces constitute distinct sub-populations. Furthermore, contemporary varieties could be separated in groups (processing, fresh and cherry) that are consistent with the recent breeding aimed at market-class specialization. In addition, at the 95% confidence level, we identified 30, 34 and 37 loci under positive selection between landraces and each of the groups of commercial variety (cherry, processing and fresh market, respectively). Their number and genomic locations imply the presence of some extended regions with high genetic variation between landraces and contemporary varieties.

Conclusions

Our work provides knowledge concerning the level and distribution of genetic variation within cultivated tomato landraces and increases our understanding of the genetic subdivision of contemporary varieties. The data indicate that adaptation and selection have led to a genomic signature in cultivated landraces and that the subpopulation structure of contemporary varieties is shaped by directed breeding and largely of recent origin. The genomic characterization presented here is an essential step towards a future exploitation of the available tomato genetic resources in research and breeding programs.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-14-835) contains supplementary material, which is available to authorized users.     

Microsatellite scoring errors associated with noninvasive genotyping based on nuclear DNA amplified from shed hair

In the context of a study of wild chimpanzees, Pan troglodytes verus, we found that genotypes based on single PCR amplifications of microsatellite loci from single shed hair have a high error rate. We quantified error rates using the comparable results of 791 single shed hair PCR amplifications of 11 microsatellite loci of 18 known individuals. The most frequent error was the amplification of only one of the two alleles present at a heterozygous locus. This phenomenon, called allelic dropout, produced false homozygotes in 31% of single-hair amplifications. There was no difference in the probability of preferential amplification between longer and shorter alleles. The probability of scoring false homozygotes can be reduced to below 0.05 by three separate amplifications from single hairs of the same individual or by pooling hair samples from the same individual. In this study an additional 5.6% of the amplifications gave wrong genotypes because of contamination, labelling and loading errors, and possibly amplification artefacts. In contrast, amplifications from plucked hair taken from four dead individuals gave consistent results (error rate < 0.01%, n= 120). Allelic dropout becomes a problem when the DNA concentration falls below 0.05 ng/10 μL in the template as it can with shed hair, and extracts from faeces and masticated plant matter.     

Investigations of carnation viruses

Carnation vein mottle virus (CarVMV) is rare in glasshouse carnations in Britain, although locally common in Dianthus barbatus in private gardens. In Sim carnations free from other viruses, CarVMV caused slight diffuse chlorotic mottling in the younger leaves, decreased flower yield by c. 22%, and caused flower breaking in cvs William Sim and Dusty. In non-Sim cultivars Pink Shibiuya, Orchid Beauty and Vesta, leaf symptoms and flower breaking were more pronounced. In mixed infections with carnation mottle virus, symptoms were much more severe. CarVMV was not eliminated from carnation or D. barbatus plants grown for 4 wk at 37^oC, and only rarely from cuttings then taken from them, but it was readily eliminated by meristem-tip culture. Myzus persicae adults or nymphs acquired and transmitted the virus within a total time of 4 min, and remained infective for 30–60 min if feeding, or for 75 min if starved. The carnation aphid, M. persicae f. dianthi, transmitted the virus much less efficiently. The virus was not transmitted by dodder (Cuscuta campestris), or through seed of D. barbatus or Chenopodium quinoa. The maximum infective dilution in sap of D. barbatus, carnation and C. quinoa ranged from 10^-2 to 10^-5. The virus withstood 10 min at 60 but not 65^oC, up to 9 days at c. 18^oC or 3–4 wk at c. 2^oC. CarVMV infected twenty-two of 107 plant species in six of thirty-seven families; suscepts were confined to the Chenopodiaceae, Caryophyllaceae and closely allied families. C. quinoa was the best local lesion assay host. Seedling clones of D. barbatus, selected as resistant to carnation mottle virus, proved the best indicator and propagation species. Up to 50 mg virus/kg tissue were obtained by butanol clarification followed by differential and density gradient centrifugation. The preparations contained a single sedimenting component, s_20w= 144S, and had flexuous filamentous particles, c. 790 times 12 run; the particles contained a single polypeptide, mol. wt 34800, and 5% of a single-stranded ribonucleic acid (RNA) with nucleotide base ratios of G21: A25: C25: U29. Serologically CarVMV was related distantly to turnip mosaic (cabbage black ring strain), pea mosaic, watermelon mosaic (Strain 2) and bean yellow mosaic viruses, more closely to pepper veinal mottle virus, but unrelated to twelve other potyviruses. CarVMV is not at present a danger to carnation crops in Britain, but the recent trend of sending carnation plants to overwinter outdoors in warmer countries involves potential risks of more rapid spread by effective vector races of M. persicae.     

Use of meristem tip culture to eliminate carnation latent virus from carnation plants

A successful protocol for meristem tip culture to eliminate carnation latent virus from carnation cv. scania has been described . The virus was found to be mechanically transmissible to Chenopodium quinoa, C. amaranticolor, Dianthus barbatus and Saponaria vaccaria. Murashige and Skoog'smedium (MS) supplemented with NAA (1.0 microM) and Kn (20.0 microM) proved best for meristem establishment and microshoots were rooted in MS medium supplemented with IBA (5.0 microM). Meristems measuring 0.1 and-0.2 mm yielded virus free plants and larger meristems were not effective.     

Microsatellite genotyping of cultivars of the Holy Land grapevine, Vitis vinifera ssp. sativa (Vitaceae)

Analysis of DNA microsatellites was used to assign genomic identity to the local grapevines ( Vitis vinifera ssp. sativa ) of the Holy Land. Most of the 24 analysed cultivars were sampled from the Indigenous Fruit Trees Rescue Gardens (Sataf collection) near Jerusalem. To determine the genotype identity of these cultivars, primers of the following microsatellites were used: VrZAG47, VrZAG62, VrZAG79, VVS2, VVMD5 and VVMD7. The amplicon sizes of the various microsatellites were measured by genotyping. The genetic similarity between cultivars within the local collection was computed and presented as a dendrogram. Three vines showed identical allele sizes for all six microsatellites. Two of these cultivars are likely to be genetically identical, whereas one, although potentially closely related, showed phenotypic difference at least in the colour of the berries. In comparing the allelic frequencies of the various microsatellite sizes with those of European cultivars (available in accessible web databases), it was found that the cultivar group most similar to the Holy Land grapevines is the Greek vine population. Historical and archaeological information indicates that the Sataf collection may represent only part of the expected diversity of local vines. It is thus possible that many of the missing vines still occur as unattended feral plants.  © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society , 2008, 156 , 513–521.     

A possible virus cryptic in carnation

Small isometric virus-like particles were found in low concentration in apparently healthy carnations of the Mediterranean, miniature and Chinese type but not in eleven Sim cultivars tested. Most carnations containing these particles were from Italy but some were from France and the USA. The particles were not transmitted by grafting or by mechanical inoculation but were seed-transmitted to a large proportion of seedlings. Antisera to partially purified particles were obtained. The particles did not react with antisera to twenty-eight isometric plant viruses or virus-like particles but were serologically related to similar particles found in carnations in England, Holland and Israel. When negatively stained, the particles were isometric with a diameter of about 29 nm and a rounded rather than angular profile, but without clear substructure; some particles were penetrated by the stain. The particles remained intact in neutral sodium phosphotungstate. After isopycnic centrifugation in CsCl solution, preparations of particles formed a main band of mean density 1.377 g/ml and other fainter bands that varied in intensity and position in different preparations. In thin sections of carnations, no virus-like particles or cytological abnormalities were observed.     

Microsatellite genotyping of red imported fire ant (Hymenoptera: Formicidae) colonies reveals that most colonies persist in plowed pastures

Our study focused on colony dynamics of the red imported fire ant, Solenopsis invicta Buren (Hymenoptera: Formicidae), in relation to the standard practice of planting rye grass (i.e., plowing) in the fall in Louisiana. Microsatellite molecular markers were used to determine genotypes of individuals from red imported fire ant colonies. These markers allowed us to monitor treatment effect by detecting changes in number and location of colonies in response to disking of pasture plots. Previous research on mound disturbance as a form of cultural control in pastures has produced mixed results. We found that the majority of colonies persisted on plots after plowing. Mound density and mound area, 5 mo after plowing, were not significantly different among treatments. In contrast, April measurements of mound volume were significantly smaller on plowed plots compared with control plots. A closer look at the rebuilding of mounds on plowed plots, during the 5 mo, showed that mound heights stayed below pretreatment measurements and they were significantly smaller than those of undisturbed mounds. Whether plowing has potential for use as a cultural control technique in reducing the impact of red imported fire ant mounds on agricultural practices in pastures remains to be seen. Conceivably, the best application of this technique will be in combination with other control measures in an integrated pest management approach to control red imported fire ants in pastures.     

Fragrance volatiles of developing and senescing carnation flowers

Thirteen major volatiles of the carnation flower fragrance signature have been identified by GC/MS. Of these, ten, hexanal, (2E)-hexenal, 1-hexanol, 2-hexanol, 3-hexen-1-ol, nonanal, benzaldehyde, benzyl alcohol, benzyl benzoate and caryophyllene, were quantified. The steady-state levels of these ten volatiles change independently as the flowers develop and senesce, suggesting that their synthesis is developmentally regulated. In addition, the chemical composition of the fragrance signature in naturally senesced flowers proved to be very different from that for flowers that had been induced to senesce prematurely by treatment with ethylene. Thus, senescence-related changes in carnation floral scent appear not to be directly regulated by ethylene. From cellular fractionation studies, it is evident that all of the volatiles, except 2-hexanol, are present in both membranous and cytosolic compartments, suggesting that their synthesis is membrane-associated and that they subsequently partition into the cytosol in accordance with partition coefficients.     

Role of cytokinins in carnation flower senescence

Stem and leaf tissues of carnation (Dianthus caryophyllus) plants appear to contain a natural antisenescence factor since removal of most of these tissues from cut carnation flowers hastened their senescence. However, kinetin (5-10 μg/ml) significantly delayed senescence of flowers with stem and leaf tissues removed. In addition, the life span of cut flowers with intact (30-cm) stems was increased with kinetin treatment. Peak ethylene production by presenescent flowers was reduced 55% or more with kinetin treatment and was delayed by 1 day. Kinetin-treated flowers were less responsive to applied ethylene (100 μl/l for 3 hours) than untreated flowers. Possible natural roles of cytokinins in carnation flower senescence are discussed.