Geno‐Diver: A combined coalescence and forward‐in‐time simulator for populations undergoing selection for complex traits

Geno‐Diver is a combined coalescence and forward‐in‐time simulator designed to simulate complex traits with a quantitative and/or fitness component and implement multiple selection and mating strategies utilizing pedigree or genomic information. The simulation is carried out in two steps. The first step generates whole‐genome sequence data for founder individuals. A variety of trait architectures can be generated for quantitative and fitness traits along with their covariance. The second step generates new individuals forward‐in‐time based on a variety of selection and mating scenarios. Genetic values are predicted for individuals utilizing pedigree or genomic information. Relationship matrices and their associated inverses are generated using computationally efficient routines. We benchmarked Geno‐Diver with a previous simulation program and described how to simulate a traditional quantitative trait along with a quantitative and fitness trait. A user manual with examples, source code in C++11 and executable versions of Geno‐Diver for Linux are freely available at https://github.com/jeremyhoward/Geno-Diver .     

Genetic relationships of fertility traits with test‐day milk yield and fat‐to‐protein ratio in tropical smallholder dairy farms

The test‐day milk fat‐to‐protein ratio (TD‐FPR) could serve as a measure of energy balance status and might be used as a criterion to improve metabolic stability and fertility through genetic selection. Therefore, genetic parameters for fertility traits, test‐day milk yield (TD‐MY) and TD‐FPR, as well as, their relationships during different stages of lactation, were estimated on data collected from 25 968 primiparous Thai dairy crossbred cows. Gibbs sampling algorithms were implemented to obtain (co)variance components using both univariate linear and threshold animal models and bivariate linear‐linear and linear‐threshold animal models with random regression. Average TD‐MY and TD‐FPR were 12.60 and 1.15. Heritability estimates for TD‐MY, TD‐FPR and selected fertility traits ranged from 0.31 to 0.58, 0.17 to 0.19 and 0.02 to 0.05, respectively. Genetic correlations among TD‐FPR and TD‐MY, TD‐FPR and fertility traits, and TD‐MY and fertility traits ranged from 0.05 to ‐0.44, from ‐0.98 to 0.98 and ‐0.22 to 0.79, respectively. Selection for lower TD‐FPR would decrease numbers of inseminations per conception and increase conception at first service and pregnancy within 90 days. In addition, cow selection based only on high milk production has strong effects to prolong days to first service, days open and calving interval.     

Effects of a DHA‐rich unextracted microalgae as a dietary supplement on performance,carcass traits and meat fatty acid profile in growing‐finishing pigs

Two 125‐day experiments of the same design were conducted to evaluate the effects of a heterotrophically grown microalgae (AURA) containing docosahexaenoic acid (DHA) on pig performance, carcass traits and the fatty acid composition of lean and adipose tissue. In each experiment, 144 Hypor pigs were blocked by sex, allocated to three treatment groups, and fed 0, 0.25% or 0.50% AURA in isonutritive, isocaloric diets. Pigs were weighed on days 0, 28, 56, 84 and 112. Feed and water intakes were measured every 28 days. Pigs were slaughtered on day 125. Data from the two studies were analysed as a single data set. Performance and carcass traits did not differ between treatments. Both microalgae treatment levels enriched (p < .05) Longissimus lumborum (LL) and backfat in DHA and improved (p < .05) their ratios of n‐6 to n‐3 fatty acids.     

Importance of bird traits for seed dispersal patterns of co‐fruiting trees in a patchy forest

Habitat fragmentation is globally one of the most important drivers of change in biodiversity. Seed dispersal by birds is crucial for tree regeneration in remnant patchy forests, yet how bird traits affect seed dispersal pattern is still poorly understood. We studied the extent to which bird traits affect seed‐removal networks and whether these traits affect seed deposition and seedling recruitment for 3 co‐fruiting tree species (Taxus chinensis, Cinnamomum bodinieri and Machilus thunbergii) in a patchy forest. A total of 17, 18 and 10 bird species were recorded foraging for seeds of T. chinensis, M. thunbergii and C. bodinieri, respectively. Frequency of bird visitation increased with tail length, wing length and body length. Furthermore, bird body length, bill length, body weight and wing length were important in the strength of the seed removal network. During foraging, 6 bird species exhibited different patterns of microhabitat utilization and their perching frequency increased with bird weight and tarsus length. As a consequence, frequency of habitat use, bird length and tarsus length were important in determining the number of deposited seeds. For seedling recruitment, seedling number increased with bird tarsus length and weight, but decreased with wing length. Overall, our results showed that various bird traits not only affected seed removal, but also influenced the subsequent processes of seed deposition and seedling distribution in a patchy forest. These results thus highlight the importance of large‐bodied birds for plant recruitment and point out the need to prioritize the protection and conservation of these birds in remnant patchy forests.     

Calculating economic values for growth and functional traits in non‐dairy sheep

A bio‐economic model including a computer program was developed where a large number of parameters can be modified to describe a great variety of production systems. Economic values for up to 27 traits can be calculated. Seasonal feeding is considered and protein requirement in addition to net energy may be taken into account when calculating feed requirement. Furthermore, the model allows for the evaluation of individual parts of the growth curve. The model was applied to the Czech Suffolk breed used in pure‐breeding. An extensive pasture system with spring lambing and sale of surplus progeny for slaughter after weaning or after a finishing period was assumed. The economic values (in Euro cent per ewe, per year and per genetic standard deviation of the trait) were as follows: 9.9 for birth weight, ?72.6 for mature weight, 142, 32.1 and 16.9 for growth rates till weaning, in rearing of breeding animals and in fattening, respectively, 19.9 and 101 for conception rate of female lambs and ewes, respectively, 690 for litter size per ewe lambing, 172 for productive lifetime of ewes, 402 and 503 for survival rate of lambs at lambing and till weaning, respectively, and 16.5 for fleece weight.     

Wild‐Caught and Farm‐Reared Amphibians are Important Reservoirs of Salmonella,A Study in North‐East Thailand

The role of amphibians as Salmonella reservoirs has not been as well studied as in reptiles, where the literature is abundant. Recent outbreaks of salmonellosis associated with exotic pet frogs have occurred in United States. Frog farming and wild frog harvesting have increased the international trade in these species. This necessitates a better understanding of the risk of salmonellosis transmission from amphibians to humans. We explored the presence of Salmonella in amphibians (frogs and toads) in Thailand, where farmed and wild frogs as well as toads are present. These live animals are easily found in the local markets and are used as food. Exportation of frog meat from Thailand is common. During March–June 2014, ninety‐seven frogs were collected from several habitats, including frog farms, urban areas and protected natural areas. The collected amphibians were tested for the presence of Salmonella. The overall prevalence of Salmonella was 69.07% (90.00% in farm animals, 0% in urban area animals and 44.83% in protected area animals). Eight serovars of Salmonella were isolated: subsp. diarizonae ser. 50:k:z, Hvittingfoss, Muenchen, Newport, Stanley, Thompson, Panama and Wandsworth. Six of the identified serovars, Hvittingfoss, Newport, Panama, Stanley, Thompson and Wandsworth, have been detected in humans in Thailand. According to our results, amphibians are reservoirs of Salmonella and can be a public health concern when used as a source of protein for humans.     

Genetic association between GHSR1a 5′UTR‐microsatellite and nt‐7(C>A) loci and growth and carcass traits in Japanese Black cattle

We carried out a genetic association study between five nucleotide polymorphisms (5′UTR microsatellite ((TG)_n), nt‐7(C>A), L24V, DelR242 and Intron 1 microsatellite) of the GHSR1a gene and growth and carcass traits in 1285 steers sired by 117 Japanese Black bulls in a progeny testing program. We report herein, a significant association between the 5′UTR microsatellite and nt‐7(C>A) loci and growth and carcass traits. We also propose a translational hypothesis that the association is due to differences in the secondary structure of GHSR1b mRNA (the non‐spliced type with the 5′UTR microsatellite) among the GHSR1a gene haplotypes. Furthermore, we predicted the potential increase in profitability due to increased carcass weight in cow‐calf fattening enterprises through planned matings based on DNA testing of the 5′UTR microsatellite. Statistical analysis revealed that the 5′UTR microsatellite locus had a significant additive effect on carcass weight (CW) and average daily gain (ADG), but not on beef marbling score (BMS). One of the four major microsatellite alleles (19‐TG allele) with an allele frequency of 0.145, had a significantly (P < 0.0007) desirable effect on CW and ADG. We concluded that the 19‐TG allele could potentially be economically useful nucleotide markers for growth and carcass traits in Japanese Black cattle.     

Economic weights of production and functional traits for Holstein‐Friesian cattle in Hungary

A bio‐economic model was used to estimate economic values of 15 milk production, functional, growth and carcass traits for Hungarian Holstein‐Friesian cattle. The calculations were carried out for the situation in Hungary from 2000 to 2007, assuming no production quotas. The marginal economic values were defined as partial derivatives of the profit function with respect to each trait in a production system with dairy cow herds and with sales of surplus male calves. The economic weights for maternal and direct components of traits were calculated multiplying the marginal economic values by the number of discounted expression summed over a 25‐year investment period for 2‐year‐old bulls (candidates for selection). The standardized economic weight (economic weight × genetic standard deviation) of the trait or trait component expressed as percentage of the sum of the standardized economic weights for all traits and trait components represented the relative economic importance of this trait or trait component. The highest relative economic importance was obtained for milk yield (25%), followed by productive lifetime of cows (23%), protein yield and the direct component of a cow’s total conception rate (9% each), the maternal effect of the total conception rate of cows and the somatic cell score (approximately 7% each), fat yield (5%) and mature weight of cows and daily gain in rearing of calves (approximately 4% each). Other functional traits (clinical mastitis incidence, calving difficulty score, total conception rate of heifers and calf mortality) reached a relative economic importance between 0.5% and 2%. Birth weight and dressing percentage were least important (<0.5%). Based on these results, the inclusion of productive lifetime and cow fertility in the breeding programme for Holstein‐Friesian cattle in Hungary is advisable.     

An imputation‐based genome‐wide association study on traits related to male reproduction in a White Duroc × Erhualian F2 population

Boar reproductive traits are economically important for the pig industry. Here we conducted a genome‐wide association study (GWAS) for 13 reproductive traits measured on 205 F₂ boars at day 300 using 60 K single nucleotide polymorphism (SNP) data imputed from a reference panel of 1200 pigs in a White Duroc × Erhualian F₂ intercross population. We identified 10 significant loci for seven traits on eight pig chromosomes (SSC). Two loci surpassed the genome‐wide significance level, including one for epididymal weight around 60.25 Mb on SSC7 and one for semen temperature around 43.69 Mb on SSC4. Four of the 10 significant loci that we identified were consistent with previously reported quantitative trait loci for boar reproduction traits. We highlighted several interesting candidate genes at these loci, including APN, TEP1, PARP2, SPINK1 and PDE1C. To evaluate the imputation accuracy, we further genotyped nine GWAS top SNPs using PCR restriction fragment length polymorphism or Sanger sequencing. We found an average of 91.44% of genotype concordance, 95.36% of allelic concordance and 0.85 of r² correlation between imputed and real genotype data. This indicates that our GWAS mapping results based on imputed SNP data are reliable, providing insights into the genetic basis of boar reproductive traits.     

Effects of sinomenine in LPS‐associated diseases are related to inhibition of LBP,Mac‐1, and L‐selectin levels

The aim of the research was to investigate the anti‐endotoxin and anti‐inflammatory effects of Sinomenine, an agent commonly found in Chinese herbal medicines. Endotoxin (i.e., 1 mg lipopolysaccharide (LPS)/kg)) was administered via intraperitoneal (IP) injection to piglets in high‐, middle‐, and low‐dose sinomenine groups. Piglets were then treated with 1, 5 or 10 mg/kg sinomenine, intramuscularly (i.m.), 3 hr after LPS. Vehicle was administered, as above, to drug control group piglets followed 3 hr later by 10 mg/kg sinomenine i.m.. LPS control group piglets were challenged with 1 mg/kg LPS IP, followed by vehicle i.m., and naïve control piglets were treated with normal saline IP, followed by normal saline i.m., as above. Temperatures were measured, and blood samples were collected from the precaval veins of piglets at 12, 24, and 48 hr post‐LPS or vehicle injection. Clinical signs were recorded, and index levels were analyzed via ELISA. Sinomenine was found to reduce the incidence and severity of LPS‐induced toxicities, including body temperature elevation, cell adhesion, and systemic inflammation. These data suggest that sinomenine may be effective for regulating inflammatory responses and has the potential for use as an anti‐endotoxin therapy.     

Effect of dietary kapok oil supplementation on growth performance,carcass traits,meat quality and sensory traits of pork in finishing‐pigs

Kapok seed and oil from the tropical zone are widely used as pig feed to harden porcine fat in Japan. This study evaluated the effect of dietary kapok oil supplementation on pork quality and sensory traits. Five Duroc pigs each were assigned to an experimental group supplemented with kapok oil and a control group. Dietary kapok oil supplementation had no effect on growth performance and intramuscular fat content in the Longissimus dorsi muscle (LM). Supplemental kapok oil increased saturated fatty acid contents in subcutaneous and intramuscular fat and decreased monounsaturated fatty acid levels (P < 0.05). Off‐flavor detection by a trained panel was higher in the experimental than the control group (P < 0.05), but tenderness, juiciness, texture and flavor intensity of LM chops were similar in both groups. The overall palatability of pork as judged by a consumer panel decreased with kapok oil supplementation (P < 0.01). These results indicate that while growth performance, intramuscular fat contents and carcass characteristics were unchanged, while dietary kapok oil supplementation makes firm fat to prevent inferior soft fat in pork, it can lower the palatability of pork due to a decrease in monounsaturated fatty acids.     

Congenital malformations of the lumbosacral vertebral column are common in neurologically normal French Bulldogs,English Bulldogs,and Pugs,with breed‐specific differences

Congenital vertebral malformations are common findings on diagnostic imaging of the vertebral column in “screw‐tailed” brachycephalic dogs. The aims of this study were to evaluate the prevalence and anatomical characteristics of lumbosacral congenital vertebral malformations in French Bulldogs, English Bulldogs, and Pugs presenting for problems unrelated to spinal disease, as well as possible associations with the degree of tail malformation, lumbosacral intervertebral disc herniation, or spondylosis deformans. In this retrospective cross‐sectional study, CT scans of vertebrae L6 to S3 and of the coccygeal vertebrae were reviewed for type of congenital vertebral malformations (hemivertebrae, block vertebrae, lumbosacral transitional vertebrae, and spina bifida), lumbosacral intervertebral disc herniation, lumbosacral spondylosis deformans, and degree of tail malformation. In 76 (51.0%) of the 149 included dogs (53 French Bulldogs, 37 English Bulldogs, and 59 Pugs) at least one type of congenital vertebral malformations was found, with lumbosacral transitional vertebrae being the most common (34.2%). There was a significantly higher prevalence of lumbosacral transitional vertebrae (54.2%) and lower prevalence of hemivertebrae (1.7%) in Pugs compared to English (13.5% and 24.3%, respectively) and French Bulldogs (26.4% and 32.0%, respectively). Tail malformation was significantly more severe in dogs with evidence of hemivertebrae. Congenital vertebral malformations are a common finding in the lumbosacral vertebral column of French Bulldogs, English Bulldogs, and Pugs. These anatomical variances need to be considered when interpreting diagnostic studies and when planning for neurosurgical and neurodiagnostic procedures. Furthermore, this study suggests a possible association between the degree of tail malformation and lumbosacral hemivertebrae.     

Cluster and meta‐analyses of genetic parameters for feed intake traits in growing beef cattle

A data set based on 50 studies including feed intake and utilization traits was used to perform a meta‐analysis to obtain pooled estimates using the variance between studies of genetic parameters for average daily gain (ADG); residual feed intake (RFI); metabolic body weight (MBW); feed conversion ratio (FCR); and daily dry matter intake (DMI) in beef cattle. The total data set included 128 heritability and 122 genetic correlation estimates published in the literature from 1961 to 2012. The meta‐analysis was performed using a random effects model where the restricted maximum likelihood estimator was used to evaluate variances among clusters. Also, a meta‐analysis using the method of cluster analysis was used to group the heritability estimates. Two clusters were obtained for each trait by different variables. It was observed, for all traits, that the heterogeneity of variance was significant between clusters and studies for genetic correlation estimates. The pooled estimates, adding the variance between clusters, for direct heritability estimates for ADG, DMI, RFI, MBW and FCR were 0.32 ± 0.04, 0.39 ± 0.03, 0.31 ± 0.02, 0.31 ± 0.03 and 0.26 ± 0.03, respectively. Pooled genetic correlation estimates ranged from ?0.15 to 0.67 among ADG, DMI, RFI, MBW and FCR. These pooled estimates of genetic parameters could be used to solve genetic prediction equations in populations where data is insufficient for variance component estimation. Cluster analysis is recommended as a statistical procedure to combine results from different studies to account for heterogeneity.     

Effects of a novel missense polymorphism within the SIGLEC5 gene on fertility traits in Holstein‐Friesian cattle

The aim of the study was to find functional polymorphism within two exons of the SIGLEC5 (sialic acid‐binding Ig‐like lectin‐5) gene and to examine its effects on the production and fertility traits of cows and bulls. Two hundred seventytwo Holstein‐Friesian cows and 574 bulls were included in the study. Novel missense polymorphism (A > G) within exon 3 causing substitution of amino acid arginine by glutamate in position 260 of SIGLEC5 protein (R260Q) was identified by sequencing and digestion by restriction enzyme Msp I. Basic production and fertility traits of cows and estimated breeding values (EBV) of bulls were analysed. The study demonstrated a significant association of SIGLEC5 R260Q polymorphism with days open and calving interval in cows as well as with breeding value for calving interval in bulls. An opposite effect of SIGLEC5 alleles for production and fertility traits was observed: the allele G increased the breeding value for the protein yield, while the allele A increased the breeding value for the calving interval. The current study suggests the involvement of SIGLEC5 R260Q polymorphism in biological processes related to fertility traits. This finding can be applied as a biomarker for a genetic improvement programme in Holstein‐Friesian cattle.     

Plant‐pollinator interactions in a biodiverse meadow are rather stable and tight for 3 consecutive years

Plant–pollinator interactions can be highly variable across years in natural communities. Although variation in the species composition and its basic structure has been investigated to understand the dynamic nature of pollination networks, little is known about the temporal dynamic of interaction strength between the same plant and pollinator species in any natural community. Pollinator‐mediated selection on the evolution of floral traits could be diminished if plant–pollinator interactions vary temporally. To quantify the temporal variation in plant–pollinator interactions and the interaction strength (observed visits), we compared weighted networks between plants and pollinators in a biodiverse alpine meadow in Shangri‐La, southwest China for 3 consecutive years. Although plant–pollinator interactions were highly dynamic such that identical interactions only accounted for 10.7% of the total between pair years, the diversity of interactions was stable. These identical interactions contributed 41.2% of total visits and were similar in strength and weighted nestedness. For plant species, 72.6% of species were visited by identical pollinator species between pair years, accounting for over half of the total visits and three‐quarters at the functional group level. More generalized pollinators contributed more connectiveness and were more central in networks across years. However, there was no similar or even opposite trend for plant species, which suggested that specialized plant species may also be central in pollinator networks. The variation in pollinator composition decreased as pollinator species numbers increased, suggesting that generalized plants experienced stable pollinator partition. The stable, tight interactions between generalized pollinators and specialized plants represent cornerstones of the studied community.     

Effects of fermented mushroom (Flammulina velutipes) by‐product diets on growth performance and carcass traits in growing‐fattening Berkshire pigs

This study was conducted to investigate effects of fermented mushroom (Flammulina velutipes) by‐product diets on the growth performance and carcass traits in growing‐fattening Berkshire pigs. The fermented diets mainly contained 40.0% mushroom by‐product, 20.0% formula feed, 26.0% rice bran and supplemental 0.1% probiotics. The mixed ingredients were fermented for 5 days at room temperature. Berkshire pigs (n = 225) were divided into five groups and three replications. The basal diets (C) were substituted by 10% (T1), 30% (T2), 50% (T3) and 70% (T4) fermented mushroom by‐product diets. Crude protein concentration and total calorie in fermented diets were significantly increased (P < 0.05) at the end of fermentation days compared with initial fermentation day. Body weight gain, feed efficiency and carcass weight were significantly lower (P < 0.05) in the T2, T3 and T4 groups than in the control group. Carcass grade was significantly better (P < 0.05) in the pigs fed fermented diets than in the pigs fed control diet and the ratio of high grade (1 plus 2 grades) was higher in the fermented diet groups compared with the control group. Therefore, although a diet of fermented mushroom by‐product decreased growth performance and feed efficiency, it improved the carcass grade in Berkshire pigs.     

Effects of parent‐of‐origin models with different pedigree information on beef carcass traits and fatty acid composition in Japanese Black cattle

Genomic imprinting should be considered in animal breeding systems to avoid lead in bias in genetic parameter estimation. The objective of this study was to clarify the effects of pedigree information on imprinting variances for carcass traits and fatty acid composition in Japanese Black cattle. Carcass records [carcass weight, rib eye area, rib thickness (RT), subcutaneous fat thickness and beef marbling score (BMS)] and fatty acid composition were obtained for 11,855 Japanese Black feedlot cattle. To estimate and compare the imprinting variances for the traits, two imprinting models with different pedigree information [the sire–dam gametic relationship matrix (Model 1) and the sire–maternal grandsire (MGS) numerator relationship matrix (Model 2)] were fitted. The ratio of the imprinting variance to the total additive genetic variance for RT (6.33%) and BMS (19.00%) was significant in Model 1, but only that for BMS (21.09%) was significant in Model 2. This study revealed that fitting the sire–MGS model could be useful in estimating imprinting variance under certain conditions, such as when restricted pedigree information is available. Furthermore, the present result suggested that the maternal gametic effects on BMS should be included in breeding programmes for Japanese Black cattle to avoid selection bias caused by imprinting effects.     

Genetic correlations between dressage,show jumping and studbook‐entry inspection traits in a process of specialization in Dutch Warmblood horses

Sport performance in dressage and show jumping are two important traits in the breeding goals of many studbooks. To determine the optimum selection scheme for jumping and dressage, knowledge is needed on the genetic correlation between both disciplines and between traits measured early in life and performance in competition in each discipline. This study aimed to estimate genetic parameters to support decision‐making on specialization of breeding horses for dressage and show jumping in Dutch warmblood horses. Genetic correlations between performance of horses in dressage and show jumping were estimated as well as the genetic correlation between traits recorded during studbook‐entry inspections and performance in dressage and show jumping competitions. The information on competition comprised the performance of 82 694 horses in dressage and 62 072 horses in show jumping, recorded in the period 1993–2012. For 26 056 horses, information was available for both disciplines. The information on traits recorded at studbook‐entry inspections comprised 62 628 horses, recorded in the period 1992–2013. Genetic parameters were estimated from the whole dataset and from a subset without horses recorded in both disciplines. Additionally, the genetic parameters were estimated in three different time periods defined by horses' birth year. The genetic correlation between dressage and show jumping in the whole dataset was ?0.23, and it was ?0.03 when it was estimated from horses recorded in only one discipline. The genetic correlation between dressage and show jumping was more negative in the most recent time period in all the cases. The more negative correlation between disciplines in more recent time periods was not reflected in changes in the correlations between competitions traits and the traits recorded in the studbook‐first inspection. These results suggest that a breeding programme under specialization might be most effective defining two separate aggregate breeding goals for each of the disciplines.     

Aggressive behaviour of sows at mixing and maternal behaviour are heritable and genetically correlated traits

This study was designed to estimate genetic variation in aggressive behaviour of sows at mixing, and in maternal ability for the same sows. The study included 835 sows observed for number of mild or severe aggressions performed (F_A1, F_A2), or received (F_R1, F_R2) during 30 min after grouping. Maternal ability was recorded as sows' response to vocalisation from their piglets when these were handled. Maternal behaviour was studied in 1076 sows as a body reaction (MBR) to their piglets being handled after farrowing. Genetic covariances were estimated using a multi-trait animal model, assuming traits to be normally distributed. The heritabilities of performed aggression traits were intermediate (h² F_A1=0.17, h² F_A2=0.24), but lower for received aggression (h² F_R1=0.06, h² F_R2=0.04), and heritability of maternal behaviour was also low (h²=0.08). Although estimates of genetic correlations had large standard errors, they indicate that less aggressive sows were stronger responding mothers (r_g=−0.3). We conclude that performed aggression in sows is a heritable trait, and selection against aggression is possible without offsetting maternal behaviour.