In silico exploration of the effects of host genotype and nutrition on the genetic parameters of lambs challenged with gastrointestinal parasites

An in silico mathematical model was used to explore the effect of, and the interaction between, (i) nutrition, (ii) genotype for growth and (iii) genotype for resistance, on the estimates of genetic parameters for resistance and performance in a population of lambs trickle-challenged daily with 3,000 L3s of Teladorsagia circumcincta. A previously published model for nematode infections in sheep was developed to include heritable variation in sheep growth traits, as well as in immunologically controlled traits such as establishment of incoming larvae, mortality of the adult worms and fecundity of the adult female worms. The simulated population comprised 10,000 lambs, these being the offspring of 250 sires mated to 5,000 dams. The model assumed the lambs to be parasitologically naïve at weaning (2 months of age), at which point the trickle challenge commenced and the model was updated daily until slaughter (at 6 months of age). Dietary treatments included a good and a poor quality feed, offered ad libitum. Two genotypes for growth were assumed: (i) fast and (ii) slow growing. Three genotypes for resistance were used: (i) benchmark, (ii) susceptible and (iii) resistant, differing in their ability to cope with nematode infections. Genetic parameters for output traits, including growth rate, food intake, worm burden and faecal egg count were estimated using a linear mixed model, fitting sire as a random effect to capture genetic effects. Heritabilities and correlations were found to change over time. In general, the heritabilities of immunity traits increased over time, whereas genetic correlations between production and immunity traits became weaker. Diet had a significant effect on the means and the estimated correlations of output traits, while genotypes for growth and resistance had smaller effects. These results suggest that discrepancies between published genetic parameters for nematode resistance may be a function of environmental factors rather than differences in host genotype.     

Effect of Bt broccoli and resistant genotype of Plutella xylostella (Lepidoptera: Plutellidae) on life history and prey acceptance of the predator Coleomegilla maculata (Coleoptera: Coccinellidae)

The ecological implications on biological control of insecticidal transgenic plants, which produce crystal (Cry) proteins derived from the soil bacterium Bacillus thuringiensis (Bt), remains a contentious issue and affects risk assessment decisions. In this study, we used a unique system of resistant insects, Bt plants and a predator to critically evaluate this issue. The effects of broccoli type (normal or expressing Cry1Ac protein) and insect genotype (susceptible or Cry1Ac-resistant) of Plutella xylostella L. (Lepidoptera: Plutellidae) were examined for their effects on the life history of the predator, Coleomegilla maculata DeGeer (Coleoptera: Coccinellidae) over two generations. Additional behavioral studies were conducted on prey choice. C. maculata could not discriminate between Bt-resistant and susceptible genotypes of P. xylostella, nor between Bt and normal broccoli plants with resistant genotypes of P. xylostella feeding on them. The larval and pupal period, adult weight and fecundity of each female were not significantly different when C. maculata larvae fed on different genotypes (Bt-resistant or susceptible) of insect prey larvae reared on Bt or non-Bt broccoli plants. The life-history parameters of the subsequent generation of C. maculata fed on Bt broccoli-reared resistant P. xylostella were also not significantly different from those on non-Bt broccoli. These results indicated that Cry1Ac did not harm the life history or prey acceptance of an important predator after two generations of exposure. Plants expressing Cry1Ac are unlikely to affect this important predator in the field.     

Skipper genome sheds light on unique phenotypic traits and phylogeny

Background

Butterflies and moths are emerging as model organisms in genetics and evolutionary studies. The family Hesperiidae (skippers) was traditionally viewed as a sister to other butterflies based on its moth-like morphology and darting flight habits with fast wing beats. However, DNA studies suggest that the family Papilionidae (swallowtails) may be the sister to other butterflies including skippers. The moth-like features and the controversial position of skippers in Lepidoptera phylogeny make them valuable targets for comparative genomics.

Results

We obtained the 310 Mb draft genome of the Clouded Skipper (Lerema accius) from a wild-caught specimen using a cost-effective strategy that overcomes the high (1.6 %) heterozygosity problem. Comparative analysis of Lerema accius and the highly heterozygous genome of Papilio glaucus revealed differences in patterns of SNP distribution, but similarities in functions of genes that are enriched in non-synonymous SNPs. Comparison of Lepidoptera genomes revealed possible molecular bases for unique traits of skippers: a duplication of electron transport chain components could result in efficient energy supply for their rapid flight; a diversified family of predicted cellulases might allow them to feed on cellulose-enriched grasses; an expansion of pheromone-binding proteins and enzymes for pheromone synthesis implies a more efficient mate-recognition system, which compensates for the lack of clear visual cues due to the similarities in wing colors and patterns of many species of skippers. Phylogenetic analysis of several Lepidoptera genomes suggested that the position of Hesperiidae remains uncertain as the tree topology varied depending on the evolutionary model.

Conclusion

Completion of the first genome from the family Hesperiidae allowed comparative analyses with other Lepidoptera that revealed potential genetic bases for the unique phenotypic traits of skippers. This work lays the foundation for future experimental studies of skippers and provides a rich dataset for comparative genomics and phylogenetic studies of Lepidoptera.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1846-0) contains supplementary material, which is available to authorized users.     

Prediction accuracies for growth and wood attributes of interior spruce in space using genotyping-by-sequencing

Background

Genomic selection (GS) in forestry can substantially reduce the length of breeding cycle and increase gain per unit time through early selection and greater selection intensity, particularly for traits of low heritability and late expression. Affordable next-generation sequencing technologies made it possible to genotype large numbers of trees at a reasonable cost.

Results

Genotyping-by-sequencing was used to genotype 1,126 Interior spruce trees representing 25 open-pollinated families planted over three sites in British Columbia, Canada. Four imputation algorithms were compared (mean value (MI), singular value decomposition (SVD), expectation maximization (EM), and a newly derived, family-based k-nearest neighbor (kNN-Fam)). Trees were phenotyped for several yield and wood attributes. Single- and multi-site GS prediction models were developed using the Ridge Regression Best Linear Unbiased Predictor (RR-BLUP) and the Generalized Ridge Regression (GRR) to test different assumption about trait architecture. Finally, using PCA, multi-trait GS prediction models were developed. The EM and kNN-Fam imputation methods were superior for 30 and 60% missing data, respectively. The RR-BLUP GS prediction model produced better accuracies than the GRR indicating that the genetic architecture for these traits is complex. GS prediction accuracies for multi-site were high and better than those of single-sites while multi-site predictability produced the lowest accuracies reflecting type-b genetic correlations and deemed unreliable. The incorporation of genomic information in quantitative genetics analyses produced more realistic heritability estimates as half-sib pedigree tended to inflate the additive genetic variance and subsequently both heritability and gain estimates. Principle component scores as representatives of multi-trait GS prediction models produced surprising results where negatively correlated traits could be concurrently selected for using PCA2 and PCA3.

Conclusions

The application of GS to open-pollinated family testing, the simplest form of tree improvement evaluation methods, was proven to be effective. Prediction accuracies obtained for all traits greatly support the integration of GS in tree breeding. While the within-site GS prediction accuracies were high, the results clearly indicate that single-site GS models ability to predict other sites are unreliable supporting the utilization of multi-site approach. Principle component scores provided an opportunity for the concurrent selection of traits with different phenotypic optima.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1597-y) contains supplementary material, which is available to authorized users.     

Induced resistance in the indeterminate growth of aspen (<Emphasis Type="Italic">Populus tremuloides</Emphasis>)

Studies of induction in trees have examined rapid induced resistance (RIR) or delayed induced resistance (DIR), but have not examined induction that occurs in leaves produced by indeterminately growing trees subsequent to, but in the same season as, damage. We refer to induction that occurs during this time period as intermediate-delayed induced resistance (IDIR). We assessed the influences of genetic and environmental factors, and their interactions, on temporal and spatial variation in induction and on tradeoffs between induced and constitutive levels of resistance in indeterminately growing saplings of aspen (Populus tremuloides). We utilized a common garden of 12 aspen genotypes experiencing two levels of defoliation and two levels of soil nutrients. We assessed concentrations of phenolic glycosides and condensed tannins in damaged leaf remnants collected 1 week after defoliation to examine rapid and local induction, and in undamaged leaves produced 8 weeks after defoliation to assess intermediate-delayed and systemic induction. In general, tannins showed RIR, while phenolic glycosides expressed IDIR. For both classes of allelochemicals, we found high estimates of broad-sense heritability and genetic variation in both induced and constitutive levels. Genetic variation may be maintained by both direct costs of allelochemicals and by costs of inducibility (phenotypic plasticity). Such costs may drive the tradeoff exhibited between induced and constitutive levels of phenolic glycosides. IDIR may be important in reducing total-season tissue loss by providing augmented resistance against late summer herbivores in trees that have experienced damage earlier in the season. Herbivore-resistant compensatory growth is especially beneficial to young trees growing in competitive environments.     

Genotypic and phenotypic diversity of a baculovirus population within an individual insect host

It is becoming increasingly apparent that many pathogen populations, including those of insects, show high levels of genotypic variation. Baculoviruses are known to be highly variable, with isolates collected from the same species in different geographical locations frequently showing genetic variation and differences in their biology. More recent studies at smaller scales have also shown that virus DNA profiles from individual larvae can show polymorphisms within and between populations of the same species. Here, we investigate the genotypic and phenotypic variation of an insect baculovirus infection within a single insect host. Twenty four genotypically distinct nucleopolyhedrovirus (NPV) variants were isolated from an individual pine beauty moth, Panolis flammea, caterpillar by in vivo cloning techniques. No variant appeared to be dominant in the population. The PaflNPV variants have been mapped using three restriction endonucleases and shown to contain three hypervariable regions containing insertions of 70-750 bp. Comparison of seven of these variants in an alternative host, Mamestra brassicae, demonstrated that the variants differed significantly in both pathogenicity and speed of kill. The generation and maintenance of pathogen heterogeneity are discussed.     

Genetically altered mice: phenotypes,no phenotypes,and Faux phenotypes

Phenotype means different things, but whatever the measure, phenotype can be profoundly influenced by genetic, environmental and infectious variables. The laboratory mouse is a complex multisystemic organism which, despite its genetically inbred nature, as highly variable pathophysiologic characteristics. Mouse strains have background characteristics that can influence genomics research. In addition to the mouse itself, different approaches toward creating mutant mice each create variables that influence phenotype. Different background strains of mice are utilized for these different approaches, and various strains are preferred among different laboratories. Background genotype significantly influences phenotype of gene mutations, as can insufficient genetic stabilization of a mutation. Research programs engaged in functional mouse genomics not only must use genetically well-defined mice, but also must incorporate environmental and infectious disease quality assurance/prevention programs. Laboratory mice are subject to over 60 different infectious disease agents, including a wide variety of viruses, bacteria, protozoa, and metazoa. Although these agents can be readily diagnosed and prevented, a number of forces are resulting in their rise in prevalence in mouse colonies. Infectious disease, including clinically silent infections, can and do influence phenotype, and can jeopardize research considerably through lost time, wasted effort, cost, and even loss of valuable strains.     

烧伤病房MRSA医院感染暴发的PFGE分型研究

利用表型分型和基因分型的方法解析医院感染常见致病菌——耐甲氧西林金黄色葡萄球菌(MRSA)造成医院感染暴发的可能传播途径。本实验对某医院烧伤科、ICU、肿瘤科病房内从患者和环境分离的19株MRSA,进行了16种抗生素的耐药性实验和全基因组稀有位点限制性内切酶酶切脉冲凝胶电泳(PFGE)分析,并聚类分析归纳了菌株之间的相关性。结果发现在19株MRSA中有11株属于同一个菌种A型,在这些菌株中,有8株属于相同的克隆亚型A1型,分别来自烧伤科和ICU患者以及烧伤科医生、护士的手。4株属于B型,均分离自同一烧伤病房。这暗示该医院可能存在MRSA(A型)院内感染的暴发,并且存在B型流行的潜在危险。MRSA很有可能通过医护工作人员的手及鼻腔等媒介在患者间传播。因此,加强医护人员的感染控制观念,利用灵敏、可靠且分辨率强的分型技术加强MRSA感染监控至关重要。     

Detection of a serine proteinase gene in Acanthamoeba genotype T6 (Amoebozoa: Lobosea)

Cytopathic proteins are assumed to contribute to the pathogenicity of Acanthamoeba spp. due to their degrading capacity that is required for tissue invasion. In this study, a serine proteinase gene was demonstrated in a highly virulent Acanthamoeba keratitis causing strain with genotype T6. This gene was detected in both, the genomic DNA and the cDNA by PCR and subsequent sequencing. The gene fragment comprises about 500 bp and exhibits high sequence similarity to the serine proteinases of Acanthamoeba strains with genotype T4 and T12. The detection of a serine proteinase in this Acanthamoeba T6 strain is significant, because while T4 is the most common genotype among pathogenic Acanthamoeba strains and also T12 is known to be associated with disease, this is the only virulent Acanthamoeba T6 strain known to date. Obviously, this serine proteinase represents a common tool in pathogenic processes during Acanthamoeba infection.     

Variability in infection efficiency in vitro of different strains of the microsporidian Encephalitozoon hellem

The infection efficiency of different strains of Encephalitozoon hellem of human origin was tested in Vero E6 cell cultures, scoring the number of infection foci (NIF) after 9, 14, 20, and 24 days of inoculation. The results revealed a strong interaction of the strain type with time: different strains showed different proliferative dynamics. Number of infection foci was lower on the first sampling day for CDC: V257, EHVS-96, and PV6-96, with a subsequent increase at a higher rate for the first strain and lower for the latter. In contrast, PV7-96 showed the highest NIF at the first sampling, followed by a slight decrease. Since these strains were selected by their genotype for the polar tube protein (PTP)-1A, 1B, 1C, and 2C, respectively, it is tempting to suggest a major role of this protein in the differences detected, although the influence of other genes that hypothetically may also differ among the strains employed cannot be discarded. The different in vitro infection efficiencies raise the possibility that some strains of E. hellem will also produce more aggressive features in infected patients.