Construction of a strawberry breeding core collection to capture and exploit genetic variation.

BACKGROUND: Genetic diversity is crucial for the success of plant breeding programs and core collections are important resources to capture this diversity. Many core collections have already been constructed by gene banks, whose main goal is to obtain a panel of a limited number of genotypes to simplify management practices and to improve shareability while retaining as much diversity as possible. However, as gene banks have a different composition and goal than plant breeding programs, constructing a core collection for a plant breeding program should consider different aspects. RESULTS: In this study, we present a novel approach for constructing a core collection by integrating both genomic and pedigree information to maximize the representation of the breeding germplasm in a minimum subset of genotypes while accounting for future genetic variation within a strawberry breeding program. Our stepwise approach starts with selecting the most important crossing parents of advanced selections and genotypes included for specific traits, to represent also future genetic variation. We then use pedigree-genomic-based relationship coefficients combined with the 'accession to nearest entry' criterion to complement the core collection and maximize its representativeness of the current breeding program. Combined pedigree-genomic-based relationship coefficients allow for accurate relationship estimation without the need to genotype every individual in the breeding program. CONCLUSIONS: This stepwise construction of a core collection in a strawberry breeding program can be applied in other plant breeding programs to construct core collections for various purposes.

[IgG4-Related Orbitopathy as an Important Differential Diagnosis of Advanced Silent Sinus Syndrome. German version]. / IgG4-assoziierte Orbitopathie als wichtige Differenzialdiagnose eines fortgeschrittenen Silent-Sinus-Syndroms.

BACKGROUND: Immunoglobulin (Ig)G4-related disease is classified as an immune-mediated disease. The etiology of this condition has not been explained to date. Manifestations of the disease are diverse, and simultaneous involvement of multiple organs is not unusual. CASE REPORT: We report the case of a patient referred to us after multiple unsuccessful paranasal sinus operations who presented with enophthalmos and a resultant migratory keratitis with a suspected diagnosis of silent sinus syndrome. Preservation of the orbit was no longer feasible. After five years without a definitive diagnosis, we ascertained that this was a case of IgG4-related disease. DISCUSSION: IgG4-related disease represents an important element in the differential diagnosis of chronic advanced diseases of the orbit and paranasal sinuses. The diagnosis should be considered in the case of unclear disease presentations. Typical histological findings include a storiform pattern of fibrosis, vasculopathy, and tissue infiltration by IgG4 plasma cells.

IgG4-related orbitopathy as an important differential diagnosis of advanced silent sinus syndrome.

BACKGROUND: Immunoglobulin (Ig)G4-related disease is classified as an immune-mediated disease. The etiology of this condition has not been explained to date. Manifestations of the disease are diverse, and simultaneous involvement of multiple organs is not unusual. CASE REPORT: We report the case of a patient referred to us after multiple unsuccessful paranasal sinus operations who presented with enophthalmos and a resultant migratory keratitis with a suspected diagnosis of silent sinus syndrome. Preservation of the orbit was no longer feasible. After five years without a definitive diagnosis, we ascertained that this was a case of IgG4-related disease. DISCUSSION: IgG4-related disease represents an important element in the differential diagnosis of chronic advanced diseases of the orbit and paranasal sinuses. The diagnosis should be considered in the case of unclear disease presentations. Typical histological findings include a storiform pattern of fibrosis, vasculopathy, and tissue infiltration by IgG4 plasma cells.

A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits.

Rose is the world's most important ornamental plant, with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Roses are outbred and can have various ploidy levels. Our objectives were to develop a high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short reads, and anchoring to a high-density genetic map, and to study the genome structure and genetic basis of major ornamental traits. We produced a doubled haploid rose line ('HapOB') from Rosa chinensis 'Old Blush' and generated a rose genome assembly anchored to seven pseudo-chromosomes (512 Mb with N50 of 3.4 Mb and 564 contigs). The length of 512 Mb represents 90.1-96.1% of the estimated haploid genome size of rose. Of the assembly, 95% is contained in only 196 contigs. The anchoring was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features, including the pericentromeric regions, through annotation of transposable element families and positioned centromeric repeats using fluorescent in situ hybridization. The rose genome displays extensive synteny with the Fragaria vesca genome, and we delineated only two major rearrangements. Genetic diversity was analysed using resequencing data of seven diploid and one tetraploid Rosa species selected from various sections of the genus. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and the number of flower petals. A rose APETALA2/TOE homologue is proposed to be the major regulator of petal number in rose. This reference sequence is an important resource for studying polyploidization, meiosis and developmental processes, as we demonstrated for flower and prickle development. It will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae.

Efficient development of highly polymorphic microsatellite markers based on polymorphic repeats in transcriptome sequences of multiple individuals.

The first hurdle in developing microsatellite markers, cloning, has been overcome by next-generation sequencing. The second hurdle is testing to differentiate polymorphic from nonpolymorphic loci. The third hurdle, somewhat hidden, is that only polymorphic markers with a large effective number of alleles are sufficiently informative to be deployed in multiple studies. Both steps are laborious and still performed manually. We have developed a strategy in which we first screen reads from multiple genotypes for repeats that show the most length variants, and only these are subsequently developed into markers. We validated our strategy in tetraploid garden rose using Illumina paired-end transcriptome sequences of 11 roses. Of 48 tested two markers failed to amplify, but all others were polymorphic. Ten loci amplified more than one locus, indicating duplicated genes or gene families. Completely avoiding duplicated loci will be difficult because the range of numbers of predicted alleles of highly polymorphic single- and multilocus markers largely overlapped. Of the remainder, half were replicate markers (i.e. multiple primer pairs for one locus), indicating the difficulty of correctly filtering short reads containing repeat sequences. We subsequently refined the approach to eliminate multiple primer sets to the same loci. The remaining 18 markers were all highly polymorphic, amplifying on average 11.7 alleles per marker (range = 6-20) in 11 tetraploid roses, exceeding the 8.2 alleles per marker of the 24 most polymorphic markers genotyped previously. This strategy therefore represents a major step forward in the development of highly polymorphic microsatellite markers.

Cytogenetic studies on meiotic chromosome behaviors in sterile Oriental x Trumpet lily.

In order to determine the reasons for pollen sterility in lily hybrids, four diploid sterile Oriental x Trumpet (OT) lily cultivars ('Nymph', 'Gluhwein', 'Yelloween', and 'Shocking') were used to investigate the meiotic chromosome behaviors in pollen mother cells (PMCs), using genomic in situ hybridization and conventional cytological methods. At metaphase I, chromosome associations were quite variable, not only among different genotypes but also in different PMCs of the same genotype. In addition to bivalents, a certain amount of univalent, trivalents, and quadrivalents were observed in all of the investigated genotypes. In addition, ring octavalents and ring hexavalents were observed in 'Nymph'. Even dodecavalents were observed in 'Nymph'. These abnormal chromosome associations at metaphase I implied the occurrence of chromosome interchanges (translocation) in these intersectional hybrids. At anaphase-telophase, a large number of laggard chromosomes and different kinds of chromosome bridge configurations were observed. At the tetrad stage, micronuclei and polyads were also found in many PMCs. All of these abnormal chromosome behaviors in PMCs were responsible for the pollen sterility in lily hybrids.

Identification of low allergenic apple cultivars using skin prick tests and oral food challenges.

BACKGROUND: As oral allergy syndrome (OAS) symptoms to apple are frequent, we aimed to identify low allergenic apple cultivars and to validate the prick-to-prick skin prick test (SPT) as a suitable screening method. METHODS: Sixty-eight apple cultivars were tested by SPTs in 33 Dutch adults with OAS, before and during the birch pollen season in 2006 and 2007, respectively. Three cultivars yielding the largest number of negative SPTs (Elise, Santana and Pink Lady®) and one reference cultivar (Golden Delicious) were subsequently tested by single-blind oral food challenges (SBFC) just after picking in fall 2007 (fresh) and in spring 2008 (stored), outside the birch pollen season and preceded by SPTs. In spring, Santana was replaced by Modi®. RESULTS: In fresh apples, OAS symptoms of Elise, as measured by cumulative scores on a Visual Analogue Scale VASt, were significantly lower than those of Santana, Pink Lady and Golden Delicious (P = 0.021; 0.040 and 0.005, respectively). VASt scores of Santana were significantly lower than those of Golden Delicious (P = 0.049). In stored apples, VASt scores of Elise were significantly lower than that of Golden Delicious (P = 0.038). VASt scores of fresh apples did not differ significantly from stored apples, except in Golden Delicious (spring < fall: P = 0.021). The SPTs did not predict the severity of OAS. CONCLUSION: SPTs are not useful to assess the allergenicity of apple cultivars. By using SBFC, Elise and Santana were identified as low allergenic apple cultivars in patient with OAS. Our data on the effect of storage are inconclusive.

The east-west-north colonization history of the Mediterranean and Europe by the coastal plant Carex extensa (Cyperaceae).

Coastal plants are ideal models for studying the colonization routes of species because of the simple linear distributions of these species. Carex extensa occurs mainly in salt marshes along the Mediterranean and European coasts. Variation in cpDNA sequences, amplified fragment length polymorphisms (AFLPs) and simple sequence repeats (SSRs) of 24 populations were analysed to reconstruct its colonization history. Phylogenetic relationships indicate that C. extensa together with the South American Carex vixdentata and the southern African Carex ecklonii form a monophyletic group of halophilic species. Analyses of divergence times suggest that early lineage diversification may have occurred between the late Miocene and the late Pliocene (Messinian crisis). Phylogenetic and network analyses of cpDNA variation revealed the monophyly of the species and an ancestral haplotype contained in populations of the eastern Mediterranean. The AFLP and SSR analyses support a pattern of variation compatible with these two lineages. These analyses also show higher levels of genetic diversity and differentiation in the eastern population group, which underwent an east-to-west Mediterranean colonization. Quaternary climatic oscillations appear to have been responsible for the split between these two lineages. Secondary contacts may have taken place in areas near the Ligurian Sea in agreement with the gene flow detected in Corsican populations. The AFLP and SSR data accord with the 'tabula rasa' hypothesis in which a recent and rapid colonization of northern Europe took place from the western Mediterranean after the Last Glacial Maximum. The unbalanced west-east vs. west-north colonization may be as a result of 'high density blocking' effect.

Autosomal and sex-linked microsatellite loci in the green oak leaf roller Tortrix viridana L. (Lepidoptera, Tortricidae).

Eight microsatellite markers were developed for the lepidopteran species Tortrix viridana using an enrichment protocol. The loci were highly variable with number of alleles ranging from four to 38. Six of the eight loci were in Hardy-Weinberg equilibrium. The other two were linked to the Z-chromosome. Values of observed heterozygosity ranged for the autosomal loci from 0.510 to 0.957. All loci will be useful to study dispersal and the autosomal loci, as well for phylogeographical studies.

Prediction uncertainty of environmental change effects on temperate European biodiversity.

Observed patterns of species richness at landscape scale (gamma diversity) cannot always be attributed to a specific set of explanatory variables, but rather different alternative explanatory statistical models of similar quality may exist. Therefore predictions of the effects of environmental change (such as in climate or land cover) on biodiversity may differ considerably, depending on the chosen set of explanatory variables. Here we use multimodel prediction to evaluate effects of climate, land-use intensity and landscape structure on species richness in each of seven groups of organisms (plants, birds, spiders, wild bees, ground beetles, true bugs and hoverflies) in temperate Europe. We contrast this approach with traditional best-model predictions, which we show, using cross-validation, to have inferior prediction accuracy. Multimodel inference changed the importance of some environmental variables in comparison with the best model, and accordingly gave deviating predictions for environmental change effects. Overall, prediction uncertainty for the multimodel approach was only slightly higher than that of the best model, and absolute changes in predicted species richness were also comparable. Richness predictions varied generally more for the impact of climate change than for land-use change at the coarse scale of our study. Overall, our study indicates that the uncertainty introduced to environmental change predictions through uncertainty in model selection both qualitatively and quantitatively affects species richness projections.

Regional gene flow and population structure of the wind-dispersed plant species Hypochaeris radicata (Asteraceae) in an agricultural landscape.

Using microsatellites, we investigated population structure and gene flow of the short-lived, wind-dispersed plant species Hypochaeris radicata in a fragmented agricultural landscape where more than 99% of the nutrient-poor grasslands have disappeared over the last century. We sampled populations in the few remaining high density populations in conservation areas, as well as individuals that occurred, with lower densities, in linear landscape elements, at two spatial scales. In a re-inventory of the landscape, after 3 years, both extinctions and colonizations of populations were observed. Contrary to expectations, no differences in genetic diversity between high and low density populations were observed. Both types of populations had relatively high levels of diversity. Overall genetic differentiation (theta) was 0.04 and significantly different from zero (P < 0.01). A significant isolation-by-distance pattern was found when all populations were simultaneously analysed (r = 0.24, P = 0.013). Isolation by distance was (marginally) significant at the small scale (r = 0.32, P = 0.06), whereas nonsignificant at the large spatial scale (r = -0.05, P = 0.66). A maximization-of-explained-variance procedure resulted in a threshold distance of 3.5 km above which populations were effectively genetically isolated. An additional partial exclusion Bayesian-based assignment test showed that overall 32.3% of the individuals were assigned to their population of origin, 48% were assigned to another population in the area and 19.7% were not assigned. Together, these results suggest high levels of gene flow. Seed dispersal contributes to the observed gene flow up to several hundred metres, which is higher than previously modelled using aerodynamic models on seed dispersal of H. radicata. We discuss the consequences of these results for an evaluation of the probability of persistence of this species in the fragmented landscape.

Genetic structure in populations of an ancient woodland sedge, Carex sylvatica Hudson, at a regional and local scale.

Wood sedge (Carex sylvatica) is a well-known ancient woodland species with a long-term persistent seed bank and a caespitose growth habit. All thirteen isolated Carex sylvatica populations in the Dutch Rhine floodplain (including the river branches Waal and IJssel) were mapped in detail and analysed for genetic variation at a large number of AFLP loci and one microsatellite locus. Across all populations, only 40 % of the sampled individuals (n=216) represented a unique genotype. A high number of the studied patches (spatial clusters of tussocks, 2-10 m in diameter) within populations contained only one or a few genotypes. Identical plants (tussocks) were also found 20-500 m apart and in one case even 1000 m apart. Observed heterozygosity levels (H(O)=0.029) were low, indicating low levels of gene flow, which is in agreement with the selfing nature of other caespitose sedges. Although the number of genotypes in populations is low, these genotypes are genetically very distinct and variation within populations accounted for 55% of the total variation. The absence of a correlation between genetic and geographic distances among populations, and the scattered distribution of genotypes among patches within woodlands, support our hypothesis of rare establishments and subsequent local dispersal within woodlands in this forest floor species, which may benefit from and partly depend on human land use and forest management activities.

Factors influencing bruises and mortality of broilers during catching, transport, and lairage.

A multilevel analysis was performed to identify and quantify risk factors associated with mortality and bruises occurring between catching and slaughter of broiler flocks. The effect of each factor in the final model was expressed as an odds ratio (OR). Data included 1,907 Dutch and German broiler flocks slaughtered in 2000 and 2001 at a Dutch processing plant. The mean dead on arrival (DOA) percentage was 0.46. Percentage of bruises was corrected for economic value. The mean corrected bruises percentage was 2.20. Factors associated with corrected bruises percentage were season, moment of transport, and ambient temperature. Unfortunately, these factors are quite difficult to manipulate. Factors associated with DOA percentage were ambient temperature, moment of transport, catching company, breed, flock size, mean BW, mean compartment stocking density, transport time, lairage time, and the interaction term transport time x ambient temperature. The most important factors that influence DOA percentage, and which can be reduced relatively easily, were compartment stocking density (OR = 1.09 for each additional bird in a compartment), transport time (OR = 1.06 for each additional 15 min), and lairage time (OR = 1.03 for each additional 15 min). In particular, reduction of transport and lairage times might have a major influence due to their large variations. Reducing or removing these factors will reduce DOA percentage. Consequently, profitability and animal welfare will increase.

Factors to be considered concerning the corrosion of copper tubes.

Various corrosion processes in copper tubes may lead to elevated copper concentrations in drinking water, if the water is stagnant. Incorrect application of copper tubes in households may lead to elevated copper concentrations in tap water. Owners of private wells should carefully check the properties of the water to be used for human consumption.

Microsatellite retrieval in lettuce (Lactuca sativa L.).

By using enriched genomic libraries, microsatellite-containing sequences were isolated from lettuce (Lactuca sativa) with high efficiency. With this approach, a sizeable fraction (up to 55%) of the clones contained a microsatellite. In about half of these clones, primers could be designed for PCR amplification of the microsatellite. This yielded 28 primer sets amplifying unambiguously scorable products, of which 26 showed polymorphisms in a test set of six lettuce varieties. Practically all microsatellite-amplifying primer sets yielded products in lettuce's nearest relative, L. serriola, but only half of the primer sets yielded products in the more distant species L. saligna and L. virosa. An average polymorphism information content (PIC) value of 0.55 and an average number of 3.5 alleles per locus were in the normal range for a self-fertilizing species like lettuce. In addition, the incidental cloning of a microsatellite-containing repeat family, apparently specific for Lactuca, is reported and the implications for the efficient retrieval of single-locus microsatellite sequences are discussed. The microsatellite loci isolated will be useful for distinguishing lettuce cultivars and for screening diversity of genetic resources.

Microsatellite fingerprinting in lettuce (Lactuca sativa L.) and wild relatives.

Southern hybridisation with a single microsatellite probe, (TCT)10, sufficed to discriminate between a representative set of cultivars/accessions of lettuce, Lactuca sativa L., and its wild relatives L. serriola, L. saligna and L. virosa. Variability within cultivars was tested in a relatively modern cultivar (Hector), where no variation was found, and in an older and morphologically more variable cultivar (Madrilene), where heterogeneity was observed in the TCT fingerprint. (TCT)10 fingerprinting should be useful for variety identification and homogeneity testing in lettuce.

Molecular characterization of GATA/GACA microsatellite repeats in tomato.

Microsatellite repeats like GATA or GACA display a degree of variability that allows their use in cultivar identification. Southern hybridization with oligonucleotide probes complementary to these microsatellites were used for the detection of polymorphisms. To understand the molecular structure of the detected DNA, fragments hybridizing to GATA and GACA probes were cloned and sequenced. In the four clones analyzed, repeats of GATA and GACA were found intertwined. The GATA and GACA arrays were not perfect but were heavily degenerated, in that they contained many tetranucleotides that might have been derived by a single point mutation from GATA or GACA. Some of these derived sequences, like GGTA and GGAT, were present as relatively long stretches that also contained some point mutations. This supports the hypothesis that long stretches of repeats are stabilized by the accumulation of point mutations. Analysis of the flanking sequences of the fragments obtained with the GACA probe showed that one of them was homologous to a Lilium henryi retrotransposon and the other to a sequence upstream of a potato patatin gene. The two fragments obtained using the GATA probe were flanked by DNA that had no homology to any known sequence but they were highly homologous to each other. This DNA was frequently associated with GATA elements and was present in the tomato genome in approximately 4300 copies. The function of this new class of repetitive DNA, here termed U30, is presently unknown.

GATA- and GACA-repeats are not evenly distributed throughout the tomato genome.

This paper describes the distribution of highly polymorphic GATA- and GACA-containing DNA regions in tomato. To study the distribution of these polymorphic regions, a mapping experiment was done. The segregation of 32 GATA- and GACA-containing loci was analyzed in a F2 population from a cross between Lycopersicon esculentum and L. pennellii. From these loci, 28 could be mapped to 8 of the 12 tomato chromosomes. Both the GATA- and GACA-containing loci seem to cluster in the same chromosomal regions. To our knowledge, this is the first report on mapping of GATA- and GACA-containing loci in plants.

Indicators for microbiologically induced corrosion of copper pipes in a cold-water plumbing system.

Corrosion damage in the copper cold-water plumbing system of a large building was investigated. An unusual combination of corrosion patterns was found on the inner copper pipe surfaces that were in contact with water. Damage was in the form of shallow cavities, a surface cover or pinprick-like pits. The corrosion system was influenced by thermal treatment and also by cefoxitin dosing. The latter fact in particular is a clear indication of microbiological involvement in this corrosive action. Different parameters, to be measured in standing water (24-h stagnation), are considered typical for this type of corrosion: the detection of Sphingomonas spec. and other species in whose cell wall regions copper can accumulate, a copper content of more than 2 mg/l, oxygen consumption of more than 4 mg/l and an increase in pH. With the help of these indicators, it is possible to recognize microbiologically induced corrosion in copper plumbing systems before pipe perforation occur.