Gerrit Gort

Genotype calling in tetraploid species from bi-allelic marker data using mixture models

BackgroundAutomated genotype calling in tetraploid species was until recently not possible, which hampered genetic analysis. Modern genotyping assays often produce two signals, one for each allele of a bi-allelic marker. While ample software is available to obtain genotypes (homozygous for either allele, or heterozygous) for diploid species from these signals, such software is not available for tetraploid species which may be scored as five alternative genotypes (aaaa, baaa, bbaa, bbba and bbbb; nulliplex to quadruplex).ResultsWe present a novel algorithm, implemented in the R package fitTetra, to assign genotypes for bi-allelic markers to tetraploid samples from genotyping assays that produce intensity signals for both alleles. The algorithm is based on the fitting of several mixture models with five components, one for each of the five possible genotypes. The models have different numbers of parameters specifying the relation between the five component means, and some of them impose a constraint on the mixing proportions to conform to Hardy-Weinberg equilibrium (HWE) ratios. The software rejects markers that do not allow a reliable genotyping for the majority of the samples, and it assigns a missing score to samples that cannot be scored into one of the five possible genotypes with sufficient confidence.ConclusionsWe have validated the software with data of a collection of 224 potato varieties assayed with an Illumina GoldenGate™ 384 SNP array and shown that all SNPs with informative ratio distributions are fitted. Almost all fitted models appear to be correct based on visual inspection and comparison with diploid samples. When the collection of potato varieties is analyzed as if it were a population, almost all markers seem to be in Hardy-Weinberg equilibrium. The R package fitTetra is freely available under the GNU Public License from http://www.plantbreeding.wur.nl/UK/software_fitTetra.html and as Additional files with this article.

Comparison of Cultivars of Ornamental Crop Gerbera jamesonii on Production of Spider Mite-Induced Volatiles, and Their Attractiveness to the Predator, Phytoseiulus persimilis

We investigated whether volatiles produced by spider mite-damaged plants of four gerbera cultivars differ in attractiveness to Phytoseiulus persimilis, a specialist predator of spider mites, and how the mite-induced odor blends differ in chemical composition. The gerbera cultivars differed in resistance, as expressed in terms of spider mite intrinsic rate of population increase (rm). In order of increasing resistance these were Sirtaki, Rondena, Fame, and Bianca. To correct for differences in damage inflicted on the cultivars, we developed a method to compare the attractiveness of the blends, based on the assumption that a larger amount of spider mite damage leads to higher attraction of P. persimilis. Spider mite-induced volatiles of cultivars Rondena and Bianca were preferred over those of cultivar Sirtaki. Spider mite-induced volatiles of cultivars Sirtaki and Fame did not differ in attractiveness to P. persimilis. Sirtaki plants had a lower relative production of terpenes than the other three cultivars. This was attributed to a low production of cis-α-bergamotene, trans-α-bergamotene, trans-β-bergamotene, and (E)-β-farnesene. The emission of (E)-β-ocimene and linalool was lower in Sirtaki and Fame leaves than in Bianca and Rondena. The importance of these chemical differences in the differential attraction of predatory mites is discussed.

Diversity and linkage disequilibrium analysis within a selected set of cultivated tomatoes

Within the Dutch genomics initiative the “Centre for Biosystems Genomics” (CBSG) a major research effort is directed at the identification and unraveling of processes and mechanisms affecting fruit quality in tomato. The basis of this fruit quality program was a diverse set of 94 cultivated tomato cultivars, representing a wide spectrum of phenotypes for quality related traits. This paper describes a diversity study performed on these cultivars, using information of 882 AFLP markers, of which 304 markers had a known map position. The AFLP markers were scored as much as possible in a co-dominant fashion. We investigated genome distribution and coverage for the mapped markers and conclude that it proved difficult to arrive at a dense and uniformly distributed coverage of the genome with markers. Mapped markers and unmapped markers were used to investigate population structure. A clear substructure was observed which seemed to coincide with a grouping based on fruit size. Finally, we studied amount and decay of linkage disequilibrium (LD) along the chromosomes. LD was observed over considerable (genetic) distances. We discuss the feasibility of marker-trait association studies and conclude that the amount of genetic variation in our set of cultivars is limited, but that there exists scope for association studies.

Reduced competitive ability due to Wolbachia infection in the parasitoid wasp Trichogramma kaykai

Several hymenopteran parasitoids are infected with parthenogenesis‐inducing (PI) Wolbachia. Infected wasps produce daughters instead of sons from unfertilized eggs. Thus far, little is known about the direct effects of PI Wolbachia on their hosts fitness. Here, we report reduced competitive ability due to Wolbachia infection in a minute parasitoid wasp, Trichogramma kaykai Pinto and Stouthamer (Hymenoptera: Trichogrammatidae). Immature survival of infected individuals in a host parasitized by a single infected female, laying a normal clutch of eggs, was lower than those parasitized by a single uninfected individual. When the offspring of infected and uninfected females shared the same host, the infected immatures had significantly lower survival rates than their uninfected counterparts. The survival rate of infected immatures was higher when they competed with other infected immatures from a different infected parent than in competition with uninfected immatures of conspecific wasps. Thus, the host Trichogramma can suffer a substantial reduction in fitness when it is infected with the PI Wolbachia. We discuss why such a reduction is to be expected when populations of infected and uninfected individuals co‐occur, and how the reduced competitive ability of PI Wolbachia influences the spread of the bacteria in the field.

Rapid divergence of genetic variance-covariance matrix within a natural population.

The matrix of genetic variances and covariances (G matrix) represents the genetic architecture of multiple traits sharing developmental and genetic processes and is central for predicting phenotypic evolution. These predictions require that the G matrix be stable. Yet the timescale and conditions promoting G matrix stability in natural populations remain unclear. We studied stability of the G matrix in a 20‐year evolution field experiment, where a population of the cosmopolitan parthenogenetic soil nematode Acrobeloides nanus was subjected to drift and divergent selection (benign and stress environments). Selection regime did not influence the level of absolute genetic constraints: under both regimes, two genetic dimensions for three life‐history traits were identified. A substantial response to selection in principal components structure and in general matrix pattern was indicated by three statistical methods. G structure was also influenced by drift, with higher divergence under benign conditions. These results show that the G matrix might evolve rapidly in natural populations. The observed high dynamics of G structure probably represents the general feature of asexual species and limits the predictive power of G in phenotypic evolution analyses.

Swim-training changes the spatio-temporal dynamics of skeletogenesis in zebrafish larvae (Danio rerio)

Fish larvae experience many environmental challenges during development such as variation in water velocity, food availability and predation. The rapid development of structures involved in feeding, respiration and swimming increases the chance of survival. It has been hypothesized that mechanical loading induced by muscle forces plays a role in prioritizing the development of these structures. Mechanical loading by muscle forces has been shown to affect larval and embryonic bone development in vertebrates, but these investigations were limited to the appendicular skeleton. To explore the role of mechanical load during chondrogenesis and osteogenesis of the cranial, axial and appendicular skeleton, we subjected zebrafish larvae to swim-training, which increases physical exercise levels and presumably also mechanical loads, from 5 until 14 days post fertilization. Here we show that an increased swimming activity accelerated growth, chondrogenesis and osteogenesis during larval development in zebrafish. Interestingly, swim-training accelerated both perichondral and intramembranous ossification. Furthermore, swim-training prioritized the formation of cartilage and bone structures in the head and tail region as well as the formation of elements in the anal and dorsal fins. This suggests that an increased swimming activity prioritized the development of structures which play an important role in swimming and thereby increasing the chance of survival in an environment where water velocity increases. Our study is the first to show that already during early zebrafish larval development, skeletal tissue in the cranial, axial and appendicular skeleton is competent to respond to swim-training due to increased water velocities. It demonstrates that changes in water flow conditions can result into significant spatio-temporal changes in skeletogenesis.

Food Preference of Wireworms Analyzed with Multinomial Logit Models

Many species of wireworms (larvae of click beetles, Elateridae) are poly- phagous root herbivores. In grasslands under restoration succession with various grass species, we aim to determine the role of wireworms in aboveground vegetation succession. Therefore, it is crucial to know whether wireworms prefer some food plants to others. We have investigated the root preference to different grass species for Agriotes obscurus and Athous haemorrhoidalis and whether these preferences can be explained by covariates. In Experiment 1, individual wireworms could choose between four different plants, one of each species (Anthoxanthum odoratum, Festuca rubra, Holcus lanatus, and Lolium perenne). In Experiment 2, groups of wireworms were released into the soil in the center of 16 plants (4 from each species). We used multinomial logit models (MLMs) to analze the data. In the appendix the use of multinomial response models is clarified with a fictitious example, using the SAS statistic software package. No preference was found in Experiment 1. In Experiment 2 we found differences in attractiveness of plant species depending on wireworm species: A. obscurus preferred grass species from nutrient-rich grasslands (L. perenne and H. lanatus). Both wireworm species disliked F. rubra. The distance from the release point influenced the probability of being found at a certain place at the end of the experiment: wireworms tended to stay in the proximity of the release point. A. haemorrhoidalis was more often found farther from the point of release than A. obscurus. Dispersal was farther from the release point in experiments with young plants (6 weeks) compared to older ones (9 weeks). Results are discussed in a broad ecological context.

CRISPR-Cas systems preferentially target the leading regions of MOBF conjugative plasmids

Most prokaryotes contain CRISPR-Cas immune systems that provide protection against mobile genetic elements. We have focused on the ability of CRISPR-Cas to block plasmid conjugation, and analyzed the position of target sequences (protospacers) on conjugative plasmids. The analysis reveals that protospacers are non-uniformly distributed over plasmid regions in a pattern that is determined by the plasmid’s mobilization type (MOB). While MOBP plasmids are most frequently targeted in the region entering the recipient cell last (lagging region), MOBF plasmids are mostly targeted in the region entering the recipient cell first (leading region). To explain this protospacer distribution bias, we propose two mutually non-exclusive hypotheses: (1) spacers are acquired more frequently from either the leading or lagging region depending on the MOB type (2) CRISPR-interference is more efficient when spacers target these preferred regions. To test the latter hypothesis, we analyzed Type I-E CRISPR-interference against MOBF prototype plasmid F in Escherichia coli. Our results show that plasmid conjugation is effectively inhibited, but the level of immunity is not affected by targeting the plasmid in the leading or lagging region. Moreover, CRISPR-immunity levels do not depend on whether the incoming single-stranded plasmid DNA, or the DNA strand synthesized in the recipient is targeted. Our findings indicate that single-stranded DNA may not be a target for Type I-E CRISPR-Cas systems, and suggest that the protospacer distribution bias might be due to spacer acquisition preferences.

Aroma exposure time and aroma concentration in relation to satiation

The present study investigated the effect of aroma exposure time and aroma concentration on ad libitum intake and subjective satiation. In a within-subject study, thirty-eight unrestrained, healthy female participants (age: 18-39 years; BMI: 18·5-26·0 kg/m²) were asked to consume tomato soup during lunchtime, until they felt comfortably full. Every 30 s, the participants consumed 10 g of a bland soup base while tomato soup aroma was delivered separately through the nose via a retronasal tube that was attached to an olfactometer. This gave the impression of consuming real tomato soup. For each sip, the aroma varied in exposure time (3 and 18 s) and concentration (5 × ), resulting in four different test conditions. Ad libitum food intake and appetite profile parameters were measured. A 9% lower food intake was observed when the participants were exposed to the condition with 18 s exposure time and a high concentration than when exposed to the other three conditions. These results indicate that changing the retronasal aroma release by aroma concentration and aroma exposure time affects food intake.

Effects of blood-feeding on olfactory sensitivity of the malaria mosquito Anopheles gambiae: Application of mixed linear models to account for repeated measurements

Olfaction plays an important role in the host-seeking behavior of the malaria mosquito Anopheles gambiae. After a complete blood meal, female mosquitoes will not engage in host-seeking behavior until oviposition has occurred. We investigated if peripheral olfactory sensitivity changed after a blood meal by recording electroantennograms (EAGs) of female mosquitoes at three time points (2h, 48 h and 72 h) to 15 volatile kairomones of either human origin or documented to emanate from oviposition sites. The EAG-sensitivity was compared with that of females of similar age post eclosion. As is common practice in electrophysiological studies, the EAG recordings were obtained by repeated stimulation of the same antennal preparations. We introduce mixed linear modeling as an improved statistical analysis for electrophysiological data. Two hours after blood ingestion, olfactory sensitivity as quantified through EAG-recording increased significantly and selectively, i.e. for seven compounds, compared to unfed females of the same age. Such short-term electrophysiological sensitization in the olfactory system as a result of feeding has not been documented before for insects. Sensitization to six compounds persisted until 48 h or 72 h post-blood meal at one or more concentrations. Desensitization was observed at 48 and 72 h pbm in response to two and three kairomones, respectively. For several compounds, sensitization at the EAG-level corresponded with sensitization found previously in single sensillum studies on olfactory neurons in antennal sensilla trichodea of An. gambiae females. These effects are likely to reflect sensitization to oviposition cues, as eggs have matured 48-72 h pbm. Knowledge of changes in olfactory sensitivity to kairomones can be applied to increase trap catches of malaria mosquitoes that have taken a blood meal and need to locate oviposition sites.