Automated 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).
We 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.
We 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.
The dissipation kinetics of glyphosate and its metabolite aminomethylphosphonic acid (AMPA) were studied in loess soil, under biotic and abiotic conditions, as affected by temperature, soil moisture ...(SM) and light/darkness. Nonsterile and sterile soil samples were spiked with 16mgkg−1 of glyphosate, subjected to three SM contents (20% WHC, 60% WHC, saturation), and incubated for 30days at 5°C and 30°C, under dark and light regimes. Glyphosate and AMPA dissipation kinetics were fit to single-first-order (SFO) or first-order-multicompartment (FOMC) models, per treatment combination. AMPA kinetic model included both the formation and decline phases. Glyphosate dissipation kinetics followed SFO at 5°C, but FOMC at 30°C. AMPA followed SFO dissipation kinetics for all treatments. Glyphosate and AMPA dissipation occurred mostly by microbial activity. Abiotic processes played a negligible role for both compounds. Under biotic conditions, glyphosate dissipation and AMPA formation/dissipation were primarily affected by temperature, but also by SM. Light regimes didn't play a significant role. Glyphosate DT50 varied between 1.5 and 53.5days, while its DT90 varied between 8.0 and 280days, depending on the treatment. AMPA persisted longer in soil than glyphosate, with its DT50 at 30°C ranging between 26.4 and 44.5days, and its DT90 between 87.8 and 148days. The shortest DT50/DT90 values for both compounds occurred at 30°C and under optimal/saturated moisture conditions, while the largest occurred at 5°C and reaching drought stress conditions. Based on these results, we conclude that glyphosate and AMPA dissipate rapidly under warm and rainy climate conditions. However, repeated glyphosate applications in fallows or winter crops in countries where cold and dry winters normally occur could lead to on-site soil pollution, with consequent potential risks to the environment and human health.
To our knowledge, this study is the first evaluating the combined effect of temperature, soil moisture and light/dark conditions on AMPA formation/dissipation kinetics and behaviour.
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•The combined effect of temp+SM+light on glyphosate & AMPA dissipation was studied in loess soil.•Glyphosate was 30 times more persistent under cold+dry than under warm+moist conditions.•AMPA persisted 21 (warm+moist) and 11 times (warm+dry) longer than glyphosate.•The use of SFO dissipation kinetics at high temperatures underestimates glyphosate DT90.•AMPA dissipation kinetics included the formation and decline phases, and followed SFO.
In nature, plants interact with multiple insect herbivores that may arrive simultaneously or sequentially. There is extensive knowledge on how plants defend themselves against single or dual attack. ...However, we lack information on how plants defend against the attack of multiple herbivores that arrive sequentially. In this study, we investigated whether
Brassica nigra
L. plants are able to defend themselves against caterpillars of the late-arriving herbivore
Plutella xylostella
L., when plants had been previously exposed to sequential attack by four other herbivores (
P. xylostella, Athalia rosae, Myzus persicae
and
Brevicoryne brassicae
). We manipulated the order of arrival and the history of attack by four herbivores to investigate which patterns in sequential herbivory determine resistance against the fifth attacker. We recorded that history of sequential herbivore attack differentially affected the capability of
B. nigra
plants to defend themselves against caterpillars of
P. xylostella.
Caterpillars gained less weight on plants attacked by a sequence of four episodes of attack by
P. xylostella
compared to performance on plants that were not previously damaged by herbivores. The number of times the plant was attacked by herbivores of the same feeding guild, the identity of the first attacker, the identity and the guild of the last attacker as well as the order of attackers within the sequence of multiple herbivores influenced the growth of the subsequent herbivory. In conclusion, this study shows that history of sequential attack is an important factor determining plant resistance to herbivores.
Genetic studies in tetraploids are lagging behind in comparison with studies of diploids as the complex genetics of tetraploids require much more elaborated computational methodologies. Recent ...advancements in development of molecular techniques and computational tools facilitate new methods for automated, high-throughput genotype calling in tetraploid species. We report on the upgrade of the widely-used fitTetra software aiming to improve its accuracy, which to date is hampered by technical artefacts in the data.
Our upgrade of the fitTetra package is designed for a more accurate modelling of complex collections of samples. The package fits a mixture model where some parameters of the model are estimated separately for each sub-collection. When a full-sib family is analyzed, we use parental genotypes to predict the expected segregation in terms of allele dosages in the offspring. More accurate modelling and use of parental data increases the accuracy of dosage calling. We tested the package on data obtained with an Affymetrix Axiom 60 k array and compared its performance with the original version and the recently published ClusterCall tool, showing that at least 20% more SNPs could be called with our updated.
Our updated software package shows clearly improved performance in genotype calling accuracy. Estimation of mixing proportions of the underlying dosage distributions is separated for full-sib families (where mixture proportions can be estimated from the parental dosages and inheritance model) and unstructured populations (where they are based on the assumption of Hardy-Weinberg equilibrium). Additionally, as the distributions of signal ratios of the dosage classes can be assumed to be the same for all populations, including parental data for some subpopulations helps to improve fitting other populations as well. The R package fitTetra 2.0 is freely available under the GNU Public License as Additional file with this article.
Black soldier fly (BSF) larvae have gained significant attention as ingredients for poultry feed to improve value chain circularity and sustainability. Black soldier fly larvae contain bioactive ...compounds which can potentially improve broiler health and thereby performance. However, the functionality of bioactive compounds likely depends on how larvae are processed prior to feeding and to which extent larvae products are included in the diet. This may explain the variable results reported in literature on broiler performance and carcass characteristics when feeding them different types of BSF larvae products at different inclusion levels. Therefore, the present research aimed to investigate the effects of different BSF larvae products and inclusion levels in diets on performance and carcass characteristics of slow-growing broilers. The experiment started with 1,728 one-day-old slow-growing male broilers (Hubbard JA757). Nine dietary treatments were used, each replicated eight times. One group of broilers was given a control diet. The following BSF larvae products were investigated: live larvae, a combination of BSF larvae meal and oil mimicking the nutritional composition of the live larvae, and BSF larvae meal and oil separately. All insect products were tested at two inclusion levels. All diet programs were nutritionally comparable (isoenergetic and based on balanced levels of digestible essential amino acids). During the 7-wk trial, several performance parameters and carcass characteristics were measured. The results show that comparable or better broiler performance was achieved with the inclusion of BSF larvae products in the diets compared to the control. Based on the feed conversion ratio (FCR), the unprocessed larvae product and the highest inclusion level led to the most favorable results. Carcass characteristics remained unchanged when BSF larvae products were used in the diets compared to the control group, indicating favorable production output. The BSF larvae products investigated seem suitable feed ingredients for broilers at the current levels tested, generating performance benefits.
Intersexual dominance relations are important for female mammals, because of their consequences for accessing food and for the degree of sexual control females experience from males. Female mammals ...are usually considered to rank below males in the dominance hierarchy, because of their typical physical inferiority. Yet, in some groups or species, females are nonetheless dominant over some males (partial female dominance). Intersexual dominance, therefore, also depends on traits other than sexual dimorphism, such as social support, social exchange, group adult sex-ratio, and the widespread self-reinforcing effects of winning and losing fights, the "winner-loser effect." The importance of sex-ratio and the winner-loser effect remains poorly understood. A theoretical model, DomWorld, predicts that in groups with a higher proportion of males, females are dominant over more males when aggression is fierce (not mild). The model is based on a small number of general processes in mammals, such as grouping, aggression, the winner-loser effect, the initially greater fighting capacity of males than females, and sex ratio. We expect its predictions to be general and suggest they be examined in a great number of species and taxa. Here, we test these predictions in four groups of wild vervet monkeys (Chlorocebus pygerythrus) in Mawana game reserve in Africa, using 7 years of data. We confirm that a higher proportion of males in the group is associated with greater dominance of females over males; a result that remains when combining these data with those of two other sites (Amboseli and Samara). We additionally confirm that in groups with a higher fraction of males there is a relatively higher (a) proportion of fights of males with other males, and (b) proportion of fights won by females against males from the fights of females with any adults. We reject alternative hypotheses that more dominance of females over males could be attributed to females receiving more coalitions from males, or females receiving lowered male aggression in exchange for sexual access (the docile male hypothesis). We conclude that female dominance relative to males is dynamic and that future empirical studies of inter-sexual dominance will benefit by considering the adult sex-ratio of groups.
Abstract The spread of invasive species often follows a jump-dispersal pattern. While jumps are typically fostered by humans, local dispersal can occur due to the specific traits of a species, which ...are often poorly understood. This holds true for small hive beetles ( Aethina tumida ), which are parasites of social bee colonies native to sub-Saharan Africa. They have become a widespread invasive species. In 2017, a mark-release-recapture experiment was conducted in six replicates (A–F) using laboratory reared, dye-fed adults (N = 15,690). Honey bee colonies were used to attract flying small hive beetles at fixed spatial intervals from a central release point. Small hive beetles were recaptured (N = 770) at a maximum distance of 3.2 km after 24 h and 12 km after 1 week. Most small hive beetles were collected closest to the release point at 0 m (76%, replicate A) and 50 m (52%, replicates B to F). Temperature and wind deviation had significant effects on dispersal, with more small hive beetles being recaptured when temperatures were high (GLMM: slope = 0.99, SE = 0.17, Z = 5.72, P < 0.001) and confirming the role of wind for odour modulated dispersal of flying insects (GLMM: slope = − 0.39, SE = 0.14, Z = − 2.90, P = 0.004). Our findings show that the small hive beetles is capable of long-distance flights, and highlights the need to understand species specific traits to be considered for monitoring and mitigation efforts regarding invasive alien species.
Plants are commonly exposed to abiotic and biotic stresses.
We used 350 Arabidopsis thaliana accessions grown under controlled conditions. We employed genome-wide association analysis to investigate ...the genetic architecture and underlying loci involved in genetic variation in resistance to: two specialist insect herbivores, Pieris rapae and Plutella xylostella; and combinations of stresses, i.e. drought followed by P. rapae and infection by the fungal pathogen Botrytis cinerea followed by infestation by P. rapae.
We found that genetic variation in resistance to combined stresses by drought plus P. rapae was limited compared with B. cinerea plus P. rapae or P. rapae alone. Resistance to the two caterpillars is controlled by different genetic components. There is limited overlap in the quantitative trait loci (QTLs) underlying resistance to combined stresses by drought plus P. rapae or B. cinerea plus P. rapae and P. rapae alone. Finally, several candidate genes involved in the biosynthesis of aliphatic glucosinolates and proteinase inhibitors were identified to be involved in resistance to P. rapae and P. xylostella, respectively.
This study underlines the importance of investigating plant responses to combinations of stresses. The value of this approach for breeding plants for resistance to combinatorial stresses is discussed.
In most group-living animals, a dominance hierarchy reduces the costs of competition for limited resources. Dominance ranks may reflect prior attributes, such as body size, related to fighting ...ability or reflect the history of self-reinforcing effects of winning and losing a conflict (the winner-loser effect), or both. As to prior attributes, in sexually dimorphic species, where males are larger than females, males are assumed to be dominant over females. As to the winner-loser effect, the computational model DomWorld has shown that despite the female's lower initial fighting ability, females achieve some degree of dominance of females over males. In the model, this degree of female dominance increases with the proportion of males in a group. This increase was supposed to emerge from the higher fraction of fights of males among themselves. These correlations were confirmed in despotic macaques, vervet monkeys, and in humans. Here, we first investigate this hypothesis in DomWorld and next in long-term data of 9,300 observation hours on six wild groups of robust capuchin monkeys (Sapajus libidinosus; S. nigritus, and S. xanthosternos) in three Brazilian sites. We test whether both the proportion of males and degree of female dominance over males are indeed associated with a higher relative frequency of aggression among males and a higher relative frequency of aggression of females to males. We confirm these correlations in DomWorld. Next, we confirm in empirical data of capuchin monkeys that with the proportion of males in the group there is indeed an increase in female dominance over males, and in the relative frequency of both male-male aggression and aggression of females to males and that the female dominance index is significantly positively associated with male male aggression. Our results reveal that adult sex ratio influences the power relation between the sexes beyond predictions from socioecological models.
Intensive and widespread use of pesticides raises serious environmental and human health concerns. The presence and levels of 209 pesticide residues (active substances and transformation products) in ...625 environmental samples (201 soil, 193 crop, 20 outdoor air, 115 indoor dust, 58 surface water, and 38 sediment samples) have been studied. The samples were collected during the 2021 growing season, across 10 study sites, covering the main European crops, and conventional and organic farming systems. We profiled the pesticide residues found in the different matrices using existing hazard classifications towards non-target organisms and humans. Combining monitoring data and hazard information, we developed an indicator for the prioritization of pesticides, which can support policy decisions and sustainable pesticide use transitions. Eighty-six percent of the samples had at least one residue above the respective limit of detection. One hundred residues were found in soil, 112 in water, 99 in sediments, 78 in crops, 76 in outdoor air, and 197 in indoor dust. The number, levels, and profile of residues varied between farming systems. Our results show that non-approved compounds still represent a significant part of environmental cocktails and should be accounted for in monitoring programs and risk assessments. The hazard profiles analysis confirms the dominance of compounds of low-moderate hazard and underscores the high hazard of some approved compounds and recurring "no data available" situations. Overall, our results support the idea that risk should be assessed in a mixture context, taking environmentally relevant mixtures into consideration. We have uncovered uncertainties and data gaps that should be addressed, as well as the policy implications at the EU approval status level. Our newly introduced indicator can help identify research priority areas, and act as a reference for targeted scenarios set forth in the Farm to Fork pesticide reduction goals.
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