Genetic parameters for semen production traits in Swiss dairy bulls

Variance components (VC) were estimated for the semen production trait ejaculate volume, sperm concentration and sperm motility in the Swiss cattle breeds Brown Swiss (BS), Original Braunvieh (OB), Holstein (HO), Red‐Factor‐Carrier (RF), Red Holstein (RH), Swiss Fleckvieh (SF) and Simmental (SI). For this purpose, semen production traits from 2,617 bulls with 124,492 records were used. The data were collected in the years 2000–2012. The model for genetic parameter estimation across all breeds included the fixed effects age of bull at collection, year of collection, month of collection, number of collection per bull and day, interval between consecutive collections, semen collector, bull breed as well as a random additive genetic component and a permanent environmental effect. The same model without a fixed breed effect was used to estimate VC and repeatabilities separately for each of the breeds BS, HO, RH, SF and SI. Estimated heritabilities across all breeds were 0.42, 0.25 and 0.09 for ejaculate volume, sperm concentration and sperm motility, respectively. Different heritabilities were estimated for ejaculate volume (0.42; 0.45; 0.49; 0.40; 0.10), sperm concentration (0.34; 0.30; 0.20; 0.07; 0.23) and number of semen portions (0.18; 0.30; 0.04; 0.14; 0.04) in BS, HO, RH, SF and SI breed, respectively. The phenotypic and genetic correlations across all breeds between ejaculate volume and sperm concentration were negative (?0.28; ?0.56). The other correlations across all breeds were positive. The phenotypic and genetic correlations were 0.01 and 0.19 between sperm motility and ejaculate volume, respectively. Between sperm motility and sperm concentration, the phenotypic and genetic correlations were 0.20 and 0.36, respectively. The results are consistent with other analyses and show that genetic improvement through selection is possible in bull semen production traits.     

Power and robustness of three whole genome association mapping approaches in selected populations

Selection is known to influence the linkage disequilibrium (LD) pattern in livestock populations. Spurious LD may lead to a higher number of false-positive signals in whole genome association mapping experiments. We compared three approaches for whole genome association mapping in a simulation study: single marker regression (SMR), a two-step approach, which analyses residuals corrected for family effects with an SMR (GRAMMAR), and a combined linkage and LD approach, which applies the quantitative transmission disequilibrium test to the Mendelian sampling term (MTDT). Three different scenarios were simulated: idealized random mating, limited number of parents and directional selection. The number of false-positive associations increased when the number of parents was limited. Mapping accuracy was the worst in the scenario with directional selection for all approaches. As SMR produced a high number of false-positive signals in small populations, results of whole genome scans in livestock analysed with SMR should be considered with caution. GRAMMAR was the most accurate approach, but also the least powerful one. The Bonferroni-corrected significance threshold seemed to be too stringent for this approach. Results obtained with MTDT changed only slightly with selected populations. MTDT combined sufficient power with a manageable number of false-positive associations in all scenarios.     

LDSO: a program to simulate pedigrees and molecular information under various evolutionary forces

Simulations are a major tool to evaluate new statistical methods and optimize experimental designs in the genomic era. However, this can only be achieved when the simulations are close enough to reality, as well as diverse enough to be realistic. For mapping studies, it is thus critical to re-create as much as possible the forces generating linkage (mutation, random drift, changes in population sizes, selection and pedigree structure) and the mechanisms producing trait genetic architecture (additivity, dominance, epistasis). We present here a computer program (ldso) simulating these phenomena. Optional outputs provide statistics on the linkage disequilibrium (LD) structure and the identity by descent between chromosomal segments, facilitating further data analyses. Furthermore, ldso enables the simulation of genomic data in known pedigrees, which sticks as precisely as possible to recent population history and structures of the long-range LD, allowing optimization of fine-mapping strategies.     

Relationship Between Soft Wheat Flour Physicochemical Composition and Cookie‐Making Performance

Nowadays in Argentina, cookies, crackers, and cakes are made of flour obtained from bread wheat with additives or enzymes that decrease the gluten strength but increase production costs. The present research work aims to study the relationship between flour physicochemical composition (particle size average [PSA], protein, damaged starch [DS], water soluble pentosans [WSP], total pentosans [TP], and gluten), alkaline water retention capacities behavior, solvent retention capacities profile (SRC) and cookie‐making performance in a set of 51 adapted soft wheat lines with diverse origin to identify better flour parameters for predicting cookie quality. Cookie factor (CF) values were 5.06–7.56. High and significant negative correlations between sucrose SRC (–0.68), water SRC (–0.65), carbonate SRC (–0.59), and CF were found, followed by lactic SRC that presented a low negative but significant correlation (r = –0.35). The flour components DS (r = –0.67), WSP (r = –0.49), and TP (r = –0.4) were negatively associated to CF. PSA showed a negative correlation with CF (r = –0.43). Protein and gluten were the flour components that affected cookie hardness, but no significant correlation were found with pentosan or DS content. A prediction equation for CF was developed. Sucrose SRC, PSA, and DS could be used to predict 68% of the variation in cookie diameter. The cluster analysis was conducted to assess differences in flour quality parameters among genotypes based on CF. Clusters 1 and 4 were typified by lower CF (5.70 and 5.23, respectively), higher DS, pentosan content, and SRC values. Cluster 2 with a relative good CF (6.47) and Cluster 3 with the best cookie quality, high CF (7.32) and low firmness, and the lowest DS, TP, WSP content, and sucrose SRC values.     

A gamma‐ray spectrometry approach to field separation of illuviation‐type WRB reference soil groups in northern Thailand

According to the World Reference Base for Soil Resources (IUSS Working Group WRB, 2006), the differentiation of Acrisols and Alisols is based on the cation‐exchange capacity of clay, which cannot be directly determined in the field, but needs expensive and time‐consuming soil‐chemical analyses. This is an unsatisfactory situation for pedologists, who urgently require a rapid field method to distinguish illuviation‐type reference soil groups (Alisols, Acrisols, Luvisols, Lixisols). In this study, we tested the ability of gamma‐ray spectrometry to separate major WRB reference soil groups in the field. The underlying hypothesis is that Alisols and Acrisols are distinguished by their clay mineral composition, which should be reflected by geochemistry and consequently gamma‐ray radiation (i.e., K‐containing illite vs. K‐free kaolinite). Highly significant differences in their gamma‐ray spectrum for K, Th, and U were found for limestone and its soils. Especially the K and Th signatures allowed a clear separation of Acrisols and Alisols. In general, the surface radiation was sufficient to separate these soils. Best results were revealed considering parent rock and the whole soil profile. This means by using a portable radiometer and a pH meter, all illuviation‐type reference soil groups could be distinguished in this case. If applicable at other sites, this approach could enormously reduce expenditures for soil‐chemical analysis needed to assist soil classification.     

Interplay between heritability,genetic correlation and economic weighting in a selection index with and without genomic information

The availability of genomic information demands proper evaluation on how the kind (phenotypic versus genomic) and the amount of information influences the interplay of heritability (h²), genetic correlation () and economic weighting of traits with regard to the standard deviation of the index (σ_I). As σ_I is directly proportional to response to selection, it was the chosen parameter for comparing the indices. Three selection indices incorporating conventional and genomic information for a two trait (i and j) breeding goal were compared. Information sources were chosen corresponding to pig breeding applications. Index I incorporating an own performance in trait j served as reference scenario. In index II, additional information in both traits was contributed by a varying number of full‐sibs (2, 7, 50). In index III, the conventional own performance in trait j was combined with genomic information for both traits. The number of animals in the reference population (N_P = 1000, 5000, 10 000) and thus the accuracy of GBVs were varied. With more information included in the index, σ_I became more independent of , and relative economic weighting. This applied for index II (more full‐sibs) and for index III (more accurate GBVs). Standard deviations of index II with seven full‐sibs and index III with N_P = 1000 were similar when both traits had the same heritability. If the heritability of trait j was reduced ( = 0.1), σ_I of index III with N_P = 1000 was clearly higher than for index II with seven full‐sibs. When enhancing the relative economic weight of trait j, the decrease in σ_I of the conventional full‐sib index was much stronger than for index III. Our results imply that N_P = 1000 can be considered a minimum size for a reference population in pig breeding. These conclusions also hold for comparing the accuracies of the indices.     

Occurrence and Characteristics of CS31A Antigen‐Producing Escherichia coli in Calves with Diarrhoea and Septicaemia in Argentina

CS31A is a K88‐related non‐fimbrial adhesin first described on Escherichia coli strains isolated from diarrhoeic and septicaemic calves. In this report, CS31A antigen was screened by immunological methods and confirmed by PCR among bovine E. coli isolates. In addition, CS31A‐producing strains were characterized with respect to different fimbrial antigens, O‐serogroup and other properties related to virulence. Faecal or tissue specimens of 100 diarrhoeic or septicaemic calves and 27 older cattle with different pathologies from 71 outbreaks or individual cases that occurred in Buenos Aires province, Argentina, were examined. CS31A+ E. coli strains were isolated from 21 (21.0%) calves from 16 outbreaks or individual cases. No CS31A+ E. coli was detected in samples from cattle more than 1 year old. Fimbriae F5, F41, F17a and F17b were not detected among the CS31A‐producing strains. Three (14.3%) of the CS31A+ E. coli strains expressed the F17c fimbria. All of the 21 isolates exhibited at least one property of septicaemic strains (resistance to serum, production of aerobactin or colicins) but none of them demonstrated heat‐stable enterotoxigenic activity. CS31A+ E. coli isolates belonged to 10 serogroups, more commonly O8, O7, O17 and O21. The results obtained here confirm the worldwide distribution of CS31A antigen in bovine E. coli strains. However, CS31A+ or CS31A+/F17c+ E. coli were less frequently isolated than they were in North hemisphere countries.     

Genetic variability of Appaloosa horses: a study of a closed breeding population from Argentina

The genetic diversity and structure of 72 Appaloosa horses belonging to a closed breeding population from an ecological reserve in Buenos Aires, Argentina, was investigated using eight microsatellite markers from the International Society for Animal Genetics panel. Our data showed that this Appaloosa horse population had an elevated degree of genetic diversity (He= 0.746) and did not present a significant increase of homozygous individuals (F_IS~0). However, the short tandem repeats, AHT5, ASB2, HTG10 and VHL20, were not in Hardy–Weinberg equilibrium (P-value<0.05). Genetic relationships between this population and other well known horse breeds showed that Appaloosa horses from Argentina could have had their origin in the horses of the Nez Perce’s people in Idaho while other Appaloosa horses may have had influences from Andalusian and Lusitano breeds. This closed breeding population conserves an important degree of Appaloosa genetic diversity and notwithstanding its particular breeding characteristics, represents a valuable genetic resource for conservation.     

1,25(OH)D vitamin D promotes NOS2 expression in response to bacterial and viral PAMPs in primary bovine salivary gland fibroblasts

Veterinary Research Communications - The faecal-oral route is a predominant mode of infectious disease transmission and yet the immunology of the bovine oral cavity is poorly understood. The...     

New data about home range and movements of Oligoryzomys flavescens (Rodentia: Cricetidae) help to understand the spread and transmission of Andes virus that causes Hantavirus Pulmonary Syndrome

Hantavirus pulmonary syndrome is an emerging infectious disease caused by viruses of the genus Orthohantavirus. The rodent Oligoryzomys flavescens is distributed along four countries of South America. In Argentina, O. flavescens acts as a reservoir of three genotypes of ANDV orthohantavirus. The aims of this work were to estimate home range size and movements—with spool‐and‐line and radiotelemetry—of infected and non‐infected O. flavescens in order to understand the spread and transmission of the virus. O. flavescens use a wide area to satisfice its requirements, reaching a home range of 1.82 ha during spring. Orthohantavirus infection did not change the behaviour of individuals. We observed a great overlapping in the home range of infected and non‐infected individuals resulting in a high probability of virus dispersion on rodent population. These results show that human health risks could be high on island environments and knowledge about the movement ecology of O. flavescens provides useful information on prevention.