Prediction of haplotypes for ungenotyped animals and its effect on marker-assisted breeding value estimation

Background

In livestock populations, missing genotypes on a large proportion of animals are a major problem to implement the estimation of marker-assisted breeding values using haplotypes. The objective of this article is to develop a method to predict haplotypes of animals that are not genotyped using mixed model equations and to investigate the effect of using these predicted haplotypes on the accuracy of marker-assisted breeding value estimation.

Methods

For genotyped animals, haplotypes were determined and for each animal the number of haplotype copies (nhc) was counted, i.e. 0, 1 or 2 copies. In a mixed model framework, nhc for each haplotype were predicted for ungenotyped animals as well as for genotyped animals using the additive genetic relationship matrix. The heritability of nhc was assumed to be 0.99, allowing for minor genotyping and haplotyping errors. The predicted nhc were subsequently used in marker-assisted breeding value estimation by applying random regression on these covariables. To evaluate the method, a population was simulated with one additive QTL and an additive polygenic genetic effect. The QTL was located in the middle of a haplotype based on SNP-markers.

Results

The accuracy of predicted haplotype copies for ungenotyped animals ranged between 0.59 and 0.64 depending on haplotype length. Because powerful BLUP-software was used, the method was computationally very efficient. The accuracy of total EBV increased for genotyped animals when marker-assisted breeding value estimation was compared with conventional breeding value estimation, but for ungenotyped animals the increase was marginal unless the heritability was smaller than 0.1. Haplotypes based on four markers yielded the highest accuracies and when only the nearest left marker was used, it yielded the lowest accuracy. The accuracy increased with increasing marker density. Accuracy of the total EBV approached that of gene-assisted BLUP when 4-marker haplotypes were used with a distance of 0.1 cM between the markers.

Conclusions

The proposed method is computationally very efficient and suitable for marker-assisted breeding value estimation in large livestock populations including effects of a number of known QTL. Marker-assisted breeding value estimation using predicted haplotypes increases accuracy especially for traits with low heritability.     

Hospital admissions for skin and soft tissue infections in a population with endemic scabies: A prospective study in Fiji, 2018–2019

Scabies is an important predisposing factor for impetigo but its role in more serious skin and soft tissue infections (SSTIs) is not well understood. Information is limited on incidence of SSTIs in the presence of endemic scabies. We conducted a prospective study of hospital admissions for SSTIs in the Northern Division of Fiji (population: 131,914). Prospective surveillance for admissions with impetigo, abscess, cellulitis, wound infection, pyomyositis, necrotizing fasciitis, infected scabies, and crusted scabies was conducted at the Division’s referral hospital between 2018 to 2019. Information was collected on demographic characteristics, clinical features, microbiology, treatment and outcomes. Over the study period, 788 SSTI admissions were recorded corresponding to a population incidence 647 per 100,000 person-years (95%CI 571–660). Incidence was highest at the extremes of age with peak incidence in children aged <5 years (908 per 100,000) and those aged ≥65 years (1127 per 100,000). Incidence was 1.7 times higher among the Indigenous Fijian population (753 per 100,000) compared to other ethnicities (442 per 100,000). Overall case fatality rate was 3.3%, and 10.8% for those aged ≥65 years. Scabies was diagnosed concurrently in 7.6% of all patients and in 24.6% of admitted children <5 years. There is a very high burden of hospital admissions for SSTIs in Fiji compared to high-income settings especially among the youngest, oldest and indigenous population which is concordant with scabies and impetigo distribution in this population. Our findings highlight the need for strategies to reduce the burden of SSTIs in Fiji and similar settings.     

THE COMPETITIVE DEMANDS OF ELITE MALE RINK HOCKEY

The aim of this study was to simulate the activity pattern of rink hockey by designing a specific skate test (ST) to study the energy expenditure and metabolic responses to this intermittent high-intensity exercise and extrapolate the results from the test to competition. Six rink hockey players performed, in three phases, the 20-metre multi-stage shuttle roller skate test, a tournament match and the ST. Heart rate was monitored in all three phases. Blood lactate, oxygen consumption, ventilation and respiratory exchange ratio were also recorded during the ST. Peak HR was 190.7±7.2 beats · min⁻¹. There were no differences in peak HR between the three tests. Mean HR was similar between the ST and the match (86% and 87% of HR_max, respectively). Peak and mean ventilation averaged 111.0±8.8 L · min⁻¹ and 70.3±14.0 L ^· min⁻¹ (60% of V_Emax), respectively. VO_2max was 56.3±8.4 mL · kg⁻¹ · min⁻¹, and mean oxygen consumption was 40.9±7.9 mL · kg^{−1 ·} min⁻¹ (70% of VO_2max). Maximum blood lactate concentration was 7.2±1.3 mmol · L-1. ST yielded an energy expenditure of 899.1±232.9 kJ, and energy power was 59.9±15.5 kJ · min⁻¹. These findings suggest that the ST is suitable for estimating the physiological demands of competitive rink hockey, which places a heavy demand on the aerobic and anaerobic systems, and requires high energy consumption.     

Multimodal signals in male European treefrog (Hyla arborea) and the influence of population isolation on signal expression

In nocturnal treefrogs, mate choice implies the use of acoustic and visual signals. Multimodality is suspected to have evolved for either information redundancy or information complementariness. It is essential to explore multimodality in a natural context to understand the selection pressures operating on the signals. In the present study, we investigated calling and coloration in relation to male biometry and condition in four populations of European treefrog (Hyla arborea) varying in size and genetic isolation. We compared the signal intensity between core and satellite populations to estimate the impact of genetic diversity on male secondary sexual traits. The results obtained show important regional variations in both traits, likely as a result of local adaptations. Call and coloration are weakly correlated within an individual, implying that these traits likely convey different information about the signaller's identity or quality, thus supporting the hypothesis of complementariness of multiple messages. By contrast to the experimental evidence, we find that call and coloration are not related to male condition (as estimated by the residual of mass over size), suggesting that the condition‐dependence of these traits may be mediated by complex mechanisms not accurately reflected by the chosen estimator. Finally, male call and colour phenotypes present no robust pattern of variation with isolation status, probably because of variation in local selective pressures and in history of population dynamics. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 103 , 633–647.     

Identification of Mendelian inconsistencies between SNP and pedigree information of sibs

Background

Using SNP genotypes to apply genomic selection in breeding programs is becoming common practice. Tools to edit and check the quality of genotype data are required. Checking for Mendelian inconsistencies makes it possible to identify animals for which pedigree information and genotype information are not in agreement.

Methods

Straightforward tests to detect Mendelian inconsistencies exist that count the number of opposing homozygous marker (e.g. SNP) genotypes between parent and offspring (PAR-OFF). Here, we develop two tests to identify Mendelian inconsistencies between sibs. The first test counts SNP with opposing homozygous genotypes between sib pairs (SIBCOUNT). The second test compares pedigree and SNP-based relationships (SIBREL). All tests iteratively remove animals based on decreasing numbers of inconsistent parents and offspring or sibs. The PAR-OFF test, followed by either SIB test, was applied to a dataset comprising 2,078 genotyped cows and 211 genotyped sires. Theoretical expectations for distributions of test statistics of all three tests were calculated and compared to empirically derived values. Type I and II error rates were calculated after applying the tests to the edited data, while Mendelian inconsistencies were introduced by permuting pedigree against genotype data for various proportions of animals.

Results

Both SIB tests identified animal pairs for which pedigree and genomic relationships could be considered as inconsistent by visual inspection of a scatter plot of pairwise pedigree and SNP-based relationships. After removal of 235 animals with the PAR-OFF test, SIBCOUNT (SIBREL) identified 18 (22) additional inconsistent animals.Seventeen animals were identified by both methods. The numbers of incorrectly deleted animals (Type I error), were equally low for both methods, while the numbers of incorrectly non-deleted animals (Type II error), were considerably higher for SIBREL compared to SIBCOUNT.

Conclusions

Tests to remove Mendelian inconsistencies between sibs should be preceded by a test for parent-offspring inconsistencies. This parent-offspring test should not only consider parent-offspring pairs based on pedigree data, but also those based on SNP information. Both SIB tests could identify pairs of sibs with Mendelian inconsistencies. Based on type I and II error rates, counting opposing homozygotes between sibs (SIBCOUNT) appears slightly more precise than comparing genomic and pedigree relationships (SIBREL) to detect Mendelian inconsistencies between sibs.     

Expression of high-affinity human antibody fragments in bacteria

Here we describe protocols for the expression of human antibody fragments in Escherichia coli. Antigen-specific clones are identified by soluble fragment ELISA and concentrated by periplasmic preparation. They are then further purified by affinity chromatography. This article provides an overview of expression and purification strategies for human antibody fragments, as well as detailed protocols for the identification of high-affinity binders and for affinity maturation.     

Change in community phylogenetic structure during tropical forest succession: evidence from New Guinea

Ecologists have recently interpreted patterns of phylogenetic distance among coexisting species as indicative of processes affecting community assembly during forest succession. We investigated plant community phylogenetic structure along a successional gradient in New Guinean lowland rain forest. We surveyed all trees with diameter at breast height ≥ 5 cm in nineteen 0.25 ha plots representing younger secondary, older secondary, and primary forest. We estimated plant community phylogeny from rbcL gene sequences to quantify change in phylogenetic structure during succession. Mean phylogenetic distance among co‐occurring trees increased with total basal area per plot, a proxy for forest age. Significant phylogenetic clustering was detected in secondary forest whereas primary forest was significantly over‐dispersed relative to null expectations. We examined the sensitivity of these patterns to various methods of branch length estimation and phylogenetic uncertainty. Power to detect community phylogenetic patterns when equal branch lengths were assumed was weak in comparison to direct molecular and time‐calibrated measures of divergence. Inferred change during forest succession was also robust to phylogenetic uncertainty so long as temporal information was incorporated in estimates of divergence. The observed patterns are consistent with processes of environmental filtering during tropical forest succession giving way to other processes in primary forests including density‐dependence.     

Anatomy of flower and fruit of <i>Vassobia breviflora</i> (Solanaceae) in the south of the southern Yungas (Argentina)

Solanaceae is a family with nearly 2400 species of cosmopolitan distribution. Vassobia breviflora is the only species of the genus present in Argentina. The goal of this work was to review and characterize the anatomy of the flower and fruit of V. breviflora from samples collected in populations of Yungas in the argentine Northwest. Conventional anatomical techniques were applied. The results showed that most flower, fruit and seed structures did not differ from those previously reported regarding the structural organization described for other species of the Solanaceae family. However, for the first time, we described the androecium, fruit, seed, floral and fruit pedicels, five types of tricomes and five types of stomata in the perianth. We found some differences in the shape of the transmission tissue and in the type of ovule with respect to that previously reported. Also, we located the parenchyma and the epidermic secretory cells of the nectary. In the context of the family Solanaceae, we discussed the function and diagnostic value of the described structures.     

Costs of mass drug administration for scabies in Fiji

In 2019, the Murdoch Children’s Research Institute in partnership with the Fiji Ministry of Health and Medical Services carried out an integrated mass drug administration (MDA) for the treatment of scabies and lymphatic filariasis in the Northern Division of Fiji (population estimate 131,914). We conducted a retrospective micro-costing exercise focused on the cost of scabies control in order to inform budgeting and policy decision making in an endemic setting. We collected detailed information on financial and economic costs incurred by both parties during the course of the MDA campaign (April 2018 to July 2019). We also conducted interviews with personnel involved in the financial administration of the MDA campaign. The economic cost of delivering two doses of ivermectin was US$4.88 per person. The cost of donated drugs accounted for 36.3% of total MDA costs. In this first large-scale MDA for the public health control of scabies, the estimated cost of delivering MDA per person for scabies was considerably more expensive than the costs reported for other neglected tropical diseases. The important cost drivers included the remuneration of health care workers who were extensively involved in the campaign, coverage of hard-to-reach, mainly rural populations and the two-dose regimen of ivermectin. These results highlight the importance of these cost determinants and can be used to plan current and future MDA programs.