Identification of candidate genes for congenital splay leg in piglets by alternative analysis of DNA microarray data

The congenital splay leg syndrome in piglets is characterized by a temporarily impaired functionality of the hind leg muscles immediately after birth. Etiology and pathogenetic mechanisms for the disease are still not well understood. We compared genome wide gene expression of three hind leg muscles (M. adductores, M. gracilis and M. sartorius) between affected piglets and their healthy littermates with the GeneChip® Porcine Genome Array (Affymetrix) in order to identify candidate genes for the disease. Data analysis with standard algorithms revealed no significant differences between both groups. By application of an alternative approach, we identified 63 transcripts with differences in two muscles and 5 genes differing between the groups in three muscles. The expression of six selected genes (SQSTM1, SSRP1, DDIT4, ENAH, MAF, and PDK4) was investigated with SYBRGreen RT - Real time PCR. The differences obtained with the microarray analysis could be confirmed and demonstrate the validity of the alternative approach to microarray data analysis. Four genes with different expression levels in at least two muscles (SQSTM1, SSRP1, DDIT4, and MAF) are assigned to transcriptional cascades related to cell death and may thus indicate pathways for further investigations on congenital splay leg in piglets

A short critical history of the application of genomics to animal breeding

[EN] Two scientific schools have been in coexistence from the beginning of genetics, one of them searching for factors of inheritance and the other one applying biometrical models to study the relationships between relatives. With the development of molecular genetics, the possibilities of detecting genes having a noticeable effect in traits augmented. Some genes with large or medium effects were localized in animals, although the most common result was to detect markers linked to these genes, allowing the possibility of assisting selection programs with markers. When a large amount of simple and inexpensive markers were available, the SNPs, new possibilities were opened since they did not need the presence of genes of large or medium effect controlling a trait, because the whole genome was scanned. Using a large amount of SNPs permits having a prediction of the breeding value at birth accurate enough to be used in some cases, like dairy cattle, to halve its generation interval. In other animal breeding programs, the implementation of genomic selection is less clear and the way in which it can be useful should be carefully studied. The need for large populations for associating phenotypic data and markers, plus the need for repeating the process continuously, complicates its application in some cases. The implementation of the information provided by the SNPs in current genetic programs has led to the development of complex statistical tools, joining the efforts of the two schools, factorial and biometrical, that nowadays work closely related. (C) 2014 Elsevier B.V. All rights reserved.This work was partially funded by the Ministerio de Economia y Competitividad, Spain (Projects AGL2011-29831-C03-01 and CGL2012-39861-C02-02). We are grateful to Dr. Saif Agha for his useful comments.Blasco Mateu, A.; Toro, MA. (2014). A short critical history of the application of genomics to animal breeding. Livestock Science. 166:4-9. doi:10.1016/j.livsci.2014.03.015S4916

Occurrence of Nine Pyrrolizidine Alkaloids in Senecio vulgaris L. Depending on Developmental Stage and Season

The contamination of phytopharmaceuticals and herbal teas with toxic plants is an increasing problem. Senecio vulgaris L. is a particularly noxious weed in agricultural and horticultural crops due to its content of toxic pyrrolizidine alkaloids (PAs). Since some of these compounds are carcinogenic, the distribution of this plant should be monitored. The amount of PAs in S. vulgaris is affected by various factors. Therefore, we investigated the occurrence of PAs depending on the developmental stage and season. A systematic study using field-plot experiments (four seasons, five developmental stages of the plants: S1 to S5) was performed and the PA concentration was determined via LC-MS/MS analysis. The total amount of PAs in the plant increased with the plant development, however, the total PA concentrations in µg/g dry matter remained nearly unchanged, whilst trends for specific PAs were observed. The concentrations of PA-N-oxides (PANOs) were much higher than that of tertiary PAs. Maximal amounts of the PA total were 54.16 ± 4.38 mg/plant (spring, S5). The total amount of PAs increased strongly until later developmental stages. Therefore, even small numbers of S. vulgaris may become sufficient for relevant contaminations set out by the maximal permitted daily intake levels recommended by the European Food Safety Authority (EFSA)

Enlarging a training set for genomic selction by imputation of un-genotyped animals in populations of varying genetic architecture

BACKGROUND: The most common application of imputation is to infer genotypes of a high-density panel of markers on animals that are genotyped for a low-density panel. However, the increase in accuracy of genomic predictions resulting from an increase in the number of markers tends to reach a plateau beyond a certain density. Another application of imputation is to increase the size of the training set with un-genotyped animals. This strategy can be particularly successful when a set of closely related individuals are genotyped. METHODS: Imputation on completely un-genotyped dams was performed using known genotypes from the sire of each dam, one offspring and the offspring’s sire. Two methods were applied based on either allele or haplotype frequencies to infer genotypes at ambiguous loci. Results of these methods and of two available software packages were compared. Quality of imputation under different population structures was assessed. The impact of using imputed dams to enlarge training sets on the accuracy of genomic predictions was evaluated for different populations, heritabilities and sizes of training sets. RESULTS: Imputation accuracy ranged from 0.52 to 0.93 depending on the population structure and the method used. The method that used allele frequencies performed better than the method based on haplotype frequencies. Accuracy of imputation was higher for populations with higher levels of linkage disequilibrium and with larger proportions of markers with more extreme allele frequencies. Inclusion of imputed dams in the training set increased the accuracy of genomic predictions. Gains in accuracy ranged from close to zero to 37.14%, depending on the simulated scenario. Generally, the larger the accuracy already obtained with the genotyped training set, the lower the increase in accuracy achieved by adding imputed dams. CONCLUSIONS: Whenever a reference population resembling the family configuration considered here is available, imputation can be used to achieve an extra increase in accuracy of genomic predictions by enlarging the training set with completely un-genotyped dams. This strategy was shown to be particularly useful for populations with lower levels of linkage disequilibrium, for genomic selection on traits with low heritability, and for species or breeds for which the size of the reference population is limited

Assessing the impact of natural service bulls and genotype by environment interactions on genetic gain and inbreeding in organic dairy cattle genomic breeding programs.

The objective of the present study was to compare genetic gain and inbreeding coefficients of dairy cattle in organic breeding program designs by applying stochastic simulations. Evaluated breeding strategies were: (i) selecting bulls from conventional breeding programs, and taking into account genotype by environment (G×E) interactions, (ii) selecting genotyped bulls within the organic environment for artificial insemination (AI) programs and (iii) selecting genotyped natural service bulls within organic herds. The simulated conventional population comprised 148 800 cows from 2976 herds with an average herd size of 50 cows per herd, and 1200 cows were assigned to 60 organic herds. In a young bull program, selection criteria of young bulls in both production systems (conventional and organic) were either 'conventional' estimated breeding values (EBV) or genomic estimated breeding values (GEBV) for two traits with low (h 2=0.05) and moderate heritability (h 2=0.30). GEBV were calculated for different accuracies (r mg), and G×E interactions were considered by modifying originally simulated true breeding values in the range from r g=0.5 to 1.0. For both traits (h 2=0.05 and 0.30) and r mg⩾0.8, genomic selection of bulls directly in the organic population and using selected bulls via AI revealed higher genetic gain than selecting young bulls in the larger conventional population based on EBV; also without the existence of G×E interactions. Only for pronounced G×E interactions (r g=0.5), and for highly accurate GEBV for natural service bulls (r mg>0.9), results suggests the use of genotyped organic natural service bulls instead of implementing an AI program. Inbreeding coefficients of selected bulls and their offspring were generally lower when basing selection decisions for young bulls on GEBV compared with selection strategies based on pedigree indices.peerReviewe

Lying, Feeding and Activity Preference of Weaned Piglets for LED-Illuminated vs. Dark Pen Compartments

Little is known on the effect of light on pig behaviour. The choice behaviour of weaned piglets kept under two different light-emitting diode (LED) illuminance levels was investigated: 32 piglets (in two batches) were housed in a preference test room composed of two identical double pen units. One side of the pen unit was permanently illuminated with 600 lux, while the other was darkened to almost 0 lux (~0 lx); by using a passageway, piglets could move between the two sides. The “lying”, “eating” and “activity” behaviours were evaluated during three days in the first, third and fifth experimental week based on video recordings and a 5-min time sampling method. At first, piglets preferred to stay in the 600 lux illuminated compartments. Then, this preference decreased for the “eating” and “activity” behaviours and reversed for the “lying” behaviour, with the darkened compartments being preferred. The results also show that pen soiling was higher under 600 lux, but feed consumption was not affected by the illuminance. Since pigs choose between the two illuminance levels to perform specific behaviours, illuminance could be used to divide the pens into functional areas and, thus, help in meeting pigs’ behavioural needs

Effect of Hay Steaming on the Estimated Precaecal Digestibility of Crude Protein and Selected Amino Acids in Horses

Steaming hay is increasingly used to treat low-quality forage because it was proven to reduce inhalable allergens such as mould spores, bacteria, and airborne dust particles. Preliminary results have shown a substantial loss of precaecal (pc) digestibility (D) of crude protein (CP) and amino acids (AA). For this purpose, six different batches of hay from central Germany were divided into four subsamples, and each one was individually steamed. Native hay and four replicates of each steamed subsample were analysed for CP, AA, neutral detergent insoluble crude protein (NDICP), neutral detergent soluble crude protein (NDSCP) as well as pepsin insoluble CP (piCP). Based on the analytical parameters, pcD of CP, protein solubility (PS), piCP (% CP) and precaecal digestible (pcd) CP and pcdAA contents were calculated. Selected Maillard reaction products (MRP), namely furosine and carboxymethyllysine (CML), were also analysed. Steaming did not affect CP content (native = 69, steamed = 67 g/kg dry matter, DM; p > 0.05), but it had an impact on the insoluble part of CP. Thus, NDICP increased by 57% (native = 27, steamed = 42 g/kg DM; p < 0.05) and piCP by 15% overall (native = 40, steamed = 46% of CP; p < 0.05). This could be a consequence of the heat damage and the associated increase in MRP. The content of furosine rose by 67% (native = 17.6, steamed = 29.4 mg/100 g DM; p < 0.05). The content of CML increased by 120% (native = 5.1, steamed = 11.3 mg/100 g DM; p < 0.05). We chose to analyse these two MRPs because they represent the reaction products with the limiting AA lysine. In contrast, the soluble fractions of CP declined, while PS as a percentage of CP decreased by 38% as a result of the treatment, and NDSCP was reduced by as much as 41% (p < 0.05). In line with this, the steaming process decreased the pcD of CP (native = 56%, steamed = 35%; p < 0.05) and pcdCP (native = 37.9, steamed = 22.5 g/kg DM; p < 0.05), respectively. The same effects were shown for selected AA; e.g., sulphuric AA pcd methionine plus pcd cysteine decreased by 45%, pcd threonine decreased by 41%, and the limited AA pcd lysine decreased by more than 50% (p < 0.05). In conclusion, the high temperatures generated during steaming lead to protein damage and consequently to a reduction in the pcD of CP and essential AA. Nevertheless, steaming successfully reduces viable microorganisms and binds dust particles. Therefore, steamed hay is still a proper and sometimes the only possible roughage for horses suffering from respiratory diseases such as equine asthma. Essentially, horse diets based on steamed hay should be balanced accordingly

Feed Intake Patterns and Immediate Glycaemic and Insulinaemic Responses of Horses Following Ingestion of Different Quantities of Starch From Oat, Barley and Grains

BACKGROUND: Relevant literature indicate that more than 0.8 g starch/kg body weight from compounded feed composed of different starch sources induces disproportionate glycaemic and insulinaemic responses in horses. OBJECTIVE: It should be investigated whether crushed oats, barley and maize also cause a disproportionate increase in plasma glucose and insulin when fed as the only concentrate in quantities equal to and above 0.8 g starch/kg body weight. METHOD: Four mares received hay plus oats, barley and maize, respectively, in quantities equal to 0.8, 1.0 and 2.0 g starch/kg body weight. At the test days, chewing parameters were detected and blood sampled before and 30, 60, 90 and 120 min after the concentrate meal. Plasma glucose and insulin were measured and areas under the curve were calculated. RESULTS: Maize was ingested particularly slowly (dry matter basis; P < 0.05), but glycaemic and insulinaemic responses were particularly low (starch basis; P < 0.05). In general, the glycaemic responses were highest with 1 g starch/kg body weight (P < 0.05). The quantity of starch had no effect on the insulinaemic response (P > 0.05). A defined increase in plasma glucose induced the highest insulinaemic response with oat grains. CONCLUSION: Oats and barley are ingested faster and induce higher glycaemic and insulinaemic responses than maize. Until 120 min postprandial, elevated quantities of starch from these grains seem to induce no disproportionate or at least linear increase of plasma glucose and insulin. The insulinaemic response to a defined increase of plasma glucose is particularly pronounced with oats