Category Archives: ORIGINAL ARTICLE

Effects of reference population size and structure on genomic prediction of maternal traits in two pig lines using whole‐genome sequence‐, high‐density‐ and combined annotation‐dependent depletion genotypes

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Abstract

The aim of this study was to investigate the reference population size required to obtain substantial prediction accuracy within- and across-lines and the effect of using a multi-line reference population for genomic predictions of maternal traits in pigs. The data consisted of two nucleus pig populations, one pure-bred Landrace (L) and one Synthetic (S) Yorkshire/Large White line. All animals were genotyped with up to 30 K animals in each line, and all had records on maternal traits. Prediction accuracy was tested with three different marker data sets: High-density SNP (HD), whole genome sequence (WGS), and markers derived from WGS based on pig combined annotation dependent depletion-score (pCADD). Also, two different genomic prediction methods (GBLUP and Bayes GC) were compared for four maternal traits; total number piglets born (TNB), total number of stillborn piglets (STB), Shoulder Lesion Score and Body Condition Score. The main results from this study showed that a reference population of 3 K–6 K animals for within-line prediction generally was sufficient to achieve high prediction accuracy. However, when the number of animals in the reference population was increased to 30 K, the prediction accuracy significantly increased for the traits TNB and STB. For multi-line prediction accuracy, the accuracy was most dependent on the number of within-line animals in the reference data. The S-line provided a generally higher prediction accuracy compared to the L-line. Using pCADD scores to reduce the number of markers from WGS data in combination with the GBLUP method generally reduced prediction accuracies relative to GBLUP using HD genotypes. The BayesGC method benefited from a large reference population and was less dependent on the different genotype marker datasets to achieve a high prediction accuracy.

Mulch alleviates the continuous crop barriers of Codonopsis pilosula (Franch.) Nannf. by regulating the soil bacterial community

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Mulch alleviates the continuous crop barriers of Codonopsis pilosula (Franch.) Nannf. by regulating the soil bacterial community

This manuscript provides information using developed field experiments to systematically investigate the mechanisms of environment–microbe–plant occurrence of continuous cropping disorder of C. pilosula through 16S high-throughput sequencing in conjunction with actual production, and we explored the effect of the mulched film on the repair of C. pilosula continuous cropping obstacles and provided a theoretical basis for reducing C. pilosula continuous cropping obstacles. The findings of the study revealed a decline in organic matter and inorganic nitrogen content, as well as a decrease in soil microorganism abundance, following continuous cropping of C. pilosula. After mulching, the abundance of beneficial bacteria AKAU4049, Betaproteobacteriales and Gaiellales in the soil increased, and the content of organic matter and inorganic nitrogen was elevated, which improved the soil environment and promoted the growth of C. pilosula under continuous cropping conditions.


Abstract

Codonopsis pilosula (Franch.) Nannf. is an essential traditional medicinal herb in China. Soil sickness caused by continuous cropping is the main reason for the yield reduction of C. pilosula. However, because of the lack of systematic research on the mechanism of continuous cropping obstacles in C. pilosula, there is a lack of effective measures to reduce or even restrain the disorder of continuous cropping obstacles in C. pilosula. The root system, inter-root soil microorganisms and non-inter-root soil of C. pilosula under a continuous cropping system (e.g. crop rotation, two consecutive crops and three consecutive crops) as well as under different mulching methods (the mulched film and the uncovered) were used as experimental materials for the study. The plant growth of C. pilosula was significantly inhibited when continuous cropping reached 2 years. At the same time, the mulched film significantly (p < .05) promoted the development of C. pilosula under continuous cropping and considerably mitigated the plant death rate of C. pilosula in all fields. The content of soil nutrients, such as organic matter and inorganic nitrogen, decreased with increasing years of continuous cropping. In contrast, the mulched film improved this soil nutrient in continuous cropping. There was a tendency for the number of endemic operational taxonomic units (OTUs) to decrease in continuous cropping. Additionally, the mulched film altered the distribution of shared and endemic OTUs in the samples and had a recruiting effect on inter-root microorganisms in continuous cropping. Betaproteobacteriales flora abundance decreased with increasing years of continuous cropping, which showed a strong positive correlation with the immune system and environmental adaptation function. The mulched film increased the abundance of beneficial microorganisms, such as AKAU4049, Betaproteobacteriales and Gaiellales, to adapt and improve the continuous crop disorder of C. pilosula. In conclusion, mulching can enhance the soil environment and facilitate the growth and development of C. pilosula during continuous cultivation.

Prevalence of sex‐chromosome aneuploidy estimated using SNP genotype intensity information in a large population of juvenile dairy and beef cattle

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Abstract

Aneuploidy is a genetic condition characterized by the loss or gain of one or more chromosomes. Aneuploidy affecting the sex chromosomes can lead to infertility in otherwise externally phenotypically normal cattle. Early identification of cattle with sex chromosomal aneuploidy is important to minimize the costs associated with rearing infertile cattle and futile breeding attempts. As most livestock breeding programs routinely genotype their breeding populations using single nucleotide polymorphism (SNP) arrays, this study aimed to assess the feasibility of integrating an aneuploidy screening tool into the existing pipelines that handle dense SNP genotype data. A further objective was to estimate the prevalence of sex chromosome aneuploidy in a population of 146,431 juvenile cattle using available genotype intensity data. Three genotype intensity statistics were used: the LogR Ratio (LRR), R-value (the sum of X and Y SNP probe intensities), and B-allele frequency (BAF) measurements. Within the female-verified population of 124,958 individuals, the estimated prevalence rate was 0.0048% for XO, 0.0350% for XXX, and 0.0004% for XXY. The prevalence of XXY in the male-verified population was 0.0870% (i.e., 18 out of 20,670 males). Cytogenetic testing was used to verify 2 of the XXX females who were still alive. The proposed approach can be readily integrated into existing genomic pipelines, serving as an efficient, large-scale screening tool for aneuploidy. Its implementation could enable the early identification of infertile animals with sex-chromosome aneuploidy.

Value of autotaxin for hepatocellular carcinoma risk assessment in chronic hepatitis B patients treated with nucleos(t)ide analogs

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Abstract

Aim

Autotaxin (ATX) is a newly identified liver fibrosis biomarker; however, its clinical usefulness remains unclear. Therefore, we analyzed the changes in patients with chronic hepatitis B virus infection treated with nucleos(t)ide analogs (NAs) to evaluate its usefulness. We also investigated the predictors of hepatocellular carcinoma development, including ATX, in patients with chronic hepatitis B based on their clinical characteristics.

Methods

This retrospective study included 179 patients with hepatitis B virus infection treated with NAs for >2 years. First, we measured the ATX levels before and up to 10 years after initiating entecavir (therapy for 88 patients whose serial ATX levels could be measured before and during entecavir therapy. Subsequently, for 179 patients whose ATX levels could be measured at the commencement of NAs, we examined the factors involved in developing hepatocellular carcinoma, including ATX.

Results

The ATX levels showed a gradual and significant decrease during the observation period of up to 10 years. Multivariable analysis showed that a baseline ATX/upper limits of normal ratio ≥1.214, age, and alkaline phosphatase levels were independent risk factors for hepatocellular carcinoma development. The combination of age and ATX/upper limits of normal ratio was used to stratify the high-risk groups for liver carcinogenesis.

Conclusions

A decrease in ATX levels up to 10 years after the commencement of therapy suggested that ATX is a helpful biomarker in evaluating fibrosis in patients undergoing long-term NA therapy. Furthermore, this study showed that combining age and the baseline ATX/upper limits of normal ratio may help identify high-risk carcinogenesis groups.

Sexual selection in Thaumatotibia leucotreta (Meyrick) is shaped by contrasting geographic adaptations, but does it matter for area‐wide sex pheromone control tools?

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Sexual selection in Thaumatotibia leucotreta (Meyrick) is shaped by contrasting geographic adaptations, but does it matter for area-wide sex pheromone control tools?

Geographically isolated populations of Thaumatotibia leucotreta (Meyrick) (Lepidoptera: Tortricidae) occur in South Africa, causing speculations of loss of sexual communication between these isolated populations and compromise the efficiency of sex pheromone tools. Investigations into these speculations were conducted, and results indicate that local adaptation and other selection forces in contrasting environments are important in sexual communication and selection in T. leucotreta but do not necessarily prevent recognition of sexual signals and attraction between geographically isolated populations.


Abstract

Thaumatotibia leucotreta (Meyrick) (Lepidoptera: Tortricidae) is a quarantine pest for certain export markets due to its phytosanitary status in affected crops in sub-Saharan Africa, including citrus. Consequently, there is a zero-tolerance policy for T. leucotreta in export markets. In South Africa, an integrated pest management strategy, incorporating a systems approach is used to achieve complete control of T. leucotreta. Preharvest management is multi-faceted, including reliance on sex pheromone tools such as monitoring, attract-and-kill, mating disruptions, and sterile insect technique (SIT). Geographically isolated populations of T. leucotreta occur in South Africa, and there is speculation concerning the possible loss of sexual communication between these isolated populations, thereby compromising the efficiency of sex pheromone tools. To investigate this possibility, we collected samples from five geographically isolated populations of T. leucotreta and a population used for SIT in South Africa. These were subjected to sexual attraction trials under choice and no-choice scenarios in a semi-natural environment. Results of the choice tests revealed that males of each population preferred their corresponding population females, except irradiated males. However, when we deprived males of their preferred females, these preferences dissipated, and they were equally attracted to females from all populations. These results indicate that local adaptation and other selection forces in contrasting environments are important in sexual communication and selection in T. leucotreta but do not necessarily prevent recognition of sexual signals and attraction between geographically isolated populations. These findings are crucial for area-wide IPM and precision control of T. leucotreta.

Estimation of heritability with genomic information by method R

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Abstract

Estimating heritabilities with large genomic models by established methods such as restricted maximum likelihood (REML) or Bayesian via Gibbs sampling is computationally expensive. Alternatively, heritability can be estimated indirectly by method R and by maximum predictivity, referred to as MaxPred here, at a much lower computing cost. By method R, the heritability used for predictions with whole and partial data is considered the best estimate when the predictions based on partial data are unbiased relative to those with the complete data. By MaxPred, the heritability estimate is the one that maximizes predictivity. This study compared heritability estimation with genomic information using average information REML (AI–REML), method R and MaxPred. A simulated population was generated with ten generations of 5000 animals each and an effective population size of 80. Each animal had one record for a trait with a heritability of 0.3, a phenotypic variance of 10.0 and was genotyped at 50 k SNP. In method R, the heritability estimate is found when the expectation of a regression coefficient is equal to one. The regression is the EBV of selection candidates calculated with the whole dataset regressed on the EBV of candidates calculated from a partial dataset. In this study, we used the GBLUP framework and therefore, GEBV was calculated. The partial dataset was created by removing the last generation of phenotypes. Predictivity was defined as the correlation between the adjusted phenotypes of the selection candidates and their GEBV calculated from the partial data. We estimated the heritability for populations that included between three and 10 generations. In every scenario, predictivity increased as more data was used and was the highest at the simulated heritability. However, the predictivity for all data subsets and all heritabilities compared did not differ more than 0.01, suggesting MaxPred is not the best indication for heritability estimation. For the whole dataset, the heritability was estimated as 0.30 ± 0.01, 0.26 ± 0.01 and 0.30 ± 0.04 for AI–REML without genomics, AI–REML with genomics and method R with genomics, respectively. Heritability estimation with genomics by method R reduced timing by 83%, implying a reduction in computing time from 9.5 to 1.6 h, on average, compared to AI–REML with genomics. Method R has the potential to estimate heritabilities with large genomic information at a low cost when many generations of animals are present; however, the standard error can be high when only a few iterations are used.

Epidemiology of Fontan‐associated liver disease in Japan: Results from a nationwide survey in 2021

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Epidemiology of Fontan-associated liver disease in Japan: Results from a nationwide survey in 2021

In Japan, the number of post-Fontan procedure patients was estimated to be 7810 in 2020, and 3120 (40%) of these patients were diagnosed with Fontan-associated liver disease (FALD) during the median follow-up of 13.8 years after the procedure. The most common sign leading to the diagnosis of FALD other than liver fibrosis was an elevated γ-glutamyl transpeptidase level. More than half of the patients without a diagnosis of FALD had increased liver enzymes, suggesting that the number of patients with FALD was underestimated.


Abstract

Aim

Although the Fontan procedure has improved the survival of patients with single-ventricle heart disease, the long-term consequences of the procedure have been a concern. This study aimed to explore the patients' postoperative clinical characteristics, including a diagnosis of Fontan-associated liver disease (FALD).

Methods

A nationwide Japanese epidemiological survey of post-Fontan patients was undertaken in 2021. The survey targets were selected from all departments of pediatrics, pediatric surgery, cardiology, cardiovascular surgery, and gastroenterology using stratified random sampling by the number of beds. Each department was asked to complete a mail-back questionnaire on the numbers of patients and their clinical characteristics. The diagnosis of FALD was made by each attending physician.

Results

The estimated number of post-Fontan patients was 7810 (95% confidence interval, 5430−10 200) in 2020, with a period prevalence of 61.9 per million. During the follow-up of 13.8 years after the Fontan procedure, 40% of patients were diagnosed with FALD. An elevated γ-glutamyl transpeptidase level was the most common finding leading to the FALD diagnosis (41%), and 45% of the patients also showed liver fibrosis. Compared with non-FALD patients, FALD patients were older, had longer duration since the Fontan procedure, and had more severe cardiac or liver conditions. However, more than half of the non-FALD patients had elevated liver enzyme levels, suggesting underestimation of the number of FALD patients.

Conclusions

In 2020, approximately 40% of post-Fontan patients underwent follow-up with a diagnosis of FALD, although the lack of established diagnostic criteria for FALD could affect the reported prevalence of FALD.

Changes in the prevalence of fungal species causing post‐harvest diseases of carrot in Finland

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Changes in the prevalence of fungal species causing post-harvest diseases of carrot in Finland

Carrot post-harvest diseases were analysed in samples from 52 different field plots in Finland, during 3 years. After 5 months at 0–1°C, the average loss due to diseases was 20%–21% every year. Decay of the root tip was the most common disease symptom, followed by pits on the side and black rot in the crown, detected in 69.2%, 15.0% and 9.0% of the symptomatic samples, respectively. The frequency of different fungal pathogens varied between the years and the time points during storage. At first Fusarium spp. were prevalent, whereas Mycocentrospora acerina and Botrytis cinerea peaked later.


Abstract

Post-harvest diseases cause significant economic losses in the carrot production chain. In this study, storage losses and fungal pathogens causing them were analysed in the carrot yield from 52 different field plots in four areas in Finland in 3 years (2016–2018). Over 30,000 carrots were sampled and analysed at three time points during cold storage at 0–1°C. In March, after 5–6 months' storage, the average loss due to diseases was 20%–21% every year. Decay of the root tip was the most common disease symptom, followed by pits on the side and black rot in the crown, detected in 69.2%, 15.0% and 9.0% of the symptomatic samples, respectively. Both intensive carrot cultivation practice and early timing of harvest increased storage losses. Pathogens in 3057 symptomatic carrot tissue samples were isolated by culturing, and fungal species were identified. The most common fungal species detected were Mycocentrospora acerina, Botrytis cinerea and Fusarium spp., especially F. avenaceum. However, the frequency of different pathogens varied between the different years and time points during storage. Species-specific PCR tests revealed that M. acerina and F. avenaceum were present in many early time-point samples where they could not yet be detected by the culturing method. In Finland, this study on carrot post-harvest diseases is the first large-scale survey in which the fungal pathogens were isolated and identified by laboratory tests. In comparison with the previous studies, Fusarium spp. were detected more frequently in this study, while grey mould and Sclerotinia rot were less frequent.

Genomic analyses of nitrogen utilization efficiency, its indicator trait blood urea nitrogen and the relationship to classical growth performance and feed efficiency traits in a Landrace × Piétrain crossbred population

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Abstract

Improving the nutrient efficiency in pork production is required to reduce the resource competition between human food and animal feed regarding diet components edible for humans and to minimize emissions relevant to climate or the environment. Thereby, protein utilization efficiency and its equivalent nitrogen utilization efficiency (NUE) play a major role. Breeding for more nitrogen (N) efficient pigs bears a promising strategy to improve such traits, however, directly phenotyping NUE based on N balance data is neither cost-efficient nor straightforward and not applicable for routine evaluations. Blood urea nitrogen (BUN) levels in the pig are suitable to predict the NUE and, therefore, might be an indicator trait for NUE because BUN is a relatively easy-to-measure trait. This study investigated the suitability of NUE as a selection trait in future breeding programs. The relationships to classical growth performance and feed efficiency traits were analysed as well as the relationship to BUN to infer the role of BUN as an indicator trait to improve NUE via breeding. The analyzes were based on a Landrace F1 cross population consisting of 502 individuals who descended from 20 Piétrain sires. All animals were genotyped for 48,525 SNPs. They were phenotyped in two different fattening phases, i.e., FP1 and FP2, during the experiment. Uni- and bivariate analyses were run to estimate variance components and to determine the genetic correlation between different traits or between the same trait measured at different time points. Moderate heritabilities were estimated for all traits, whereby the heritability for NUE was h 2 = 0.293 in FP1 and h 2 = 0.163 in FP2 and BUN had the by far highest heritability (h 2 = 0.415 in FP1 and h 2 = 0.460 in FP2). The significant genetic correlation between NUE and BUN showed the potential of BUN to be considered an indicator trait for NUE. This was particularly pronounced when NUE was measured in FP1 (genetic correlations rg=−0.631$$ {r}_g=-0.631 $$ and rg=−0.688$$ {r}_g=-0.688 $$ between NUE and BUN measured in FP1 and FP2, respectively). The genetic correlations of NUE and BUN with important production traits suggest selecting pigs with high growth rates and low BUN levels to breed more efficient pigs in future breeding programs.

Effects of food resources on the longevity, survival, and fecundity of Paracentrobia subflava adults, an egg parasitoid of the corn leafhopper pest Dalbulus maidis

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Effects of food resources on the longevity, survival, and fecundity of Paracentrobia subflava adults, an egg parasitoid of the corn leafhopper pest Dalbulus maidis

Process of evaluating longevity and survival to different artificial diets and honeydew of the corn pest Dalbulus maidis in the egg parasitoid Paracentrobia subflava (A). In addition, assess P. subflava's fecundity with food (honey) and without food (B).


Abstract

The diet consumed by adult parasitoids can affect longevity, survival, and fecundity. Honeydew from sap-sucking insects is an abundant food resource in the field; however, artificial diets such as commercial bee honey are often used in lab rearing. The parasitoid Paracentrobia subflava (Girault) (Hymenoptera: Trichogrammatidae) is a natural enemy of Dalbulus maidis (DeLong) (Hemiptera: Cicadellidae). The longevity and survival of P. subflava when fed natural and artificial diets under controlled conditions have not been studied. Further, the fecundity of P. subflava when fed a diet of honey has not been investigated. Therefore, our first objective was to analyse the longevity and survival of P. subflava when fed (1) honeydew of the corn leafhopper D. maidis, (2) honey + water, (3) honey + water + pollen, (4) water, and (5) nothing (control). Our second objective was to evaluate P. subflava fecundity upon exposure to D. maidis eggs, comparing parasitoids fed with honey + water versus controls (no food or water). In the second objective, honey was chosen since it was determined during the first objective to be the optimal food. The longevity of adult parasitoids (laboratory-reared and field-collected) was high when fed on honey and low when fed other diets. The highest longevity was achieved with honey + water: 17 days, while the survival of adult parasitoids was only 3 days for honeydew. Interestingly, fecundity, in terms of the percentage of parasitism and the percentage of emergence, did not differ between parasitoid females that had access to honey + water as a food resource and those that had no food or water.