A further look at quantitative trait loci affecting growth and fatness in a cross between Meishan and Large White pig populations

A detailed quantitative trait locus (QTL) analysis of growth and fatness data from a three generation experimental cross between Large White (LW) and Meishan (MS) pig breeds was carried out to search for sex × QTL interactions, imprinting effects and multiple linked QTLs. A total of 530 F2 males and 573 F2 females issued from 6 F1 boars and 23 F1 sows were typed for a total of 137 markers covering the entire porcine genome. Nine growth traits and three backfat thickness measurements were analysed. All analyses were performed using line cross regression procedures. A QTL with sex-specific expression was revealed in the proximal region of chromosome 8, although some confusion between herd and sex effects could not be discarded. This previously undetected QTL affected male growth during the fattening period, with a favourable additive effect of the LW allele. The analyses also revealed the presence of two linked QTLs segregating on chromosome 1, affecting growth traits during the post-weaning period. The first QTL, previously detected using a single QTL model, was located at the end of the q arm of chromosome 1 and had a favourable MS allele. The second QTL had a favourable LW allele and was located in the proximal extremity of the q arm of chromosome 1. Suggestive genomic imprinting was found in the distal region of chromosome 9 affecting growth during the fattening period

Social network analysis of agonistic behaviour and its association with economically important traits in pigs

Aggression behaviour has several negative consequences on the performance and welfare of pigs. Here, the Social Network Analysis (SNA) approach was employed to (1) identify individual traits that describe the role of each animal in the aggression; (2) investigate the association of these traits with performance and feeding behaviour traits. The study was conducted on 326 Duroc pigs reared in 29 pens. Several individual centrality traits were identified and used to calculate the Social Rank Index. The Dominant, Subordinate, and Isolated animals represented 21.1%, 57.5% and 21.4%, respectively. No significant correlations were observed between out-degree (number of initiated agonistic behaviours) and growth traits, indicating the similarity of growth patterns for dominant and non-dominant animals. Furthermore, out-degree was correlated positively with average daily occupation time (time at the feeder/day) and average daily feeding frequency (number of visits to the feeder/day) but negatively with average daily feeding rate (gr/min). This may indicate the ability of non-dominant pigs to modify their behaviour to obtain their requirements. The Hamming distances between networks showed that there is no common behaviour pattern between pens. In conclusion, SNA showed the potential for extracting behaviour traits that could be used to improve pig performance and welfare.info:eu-repo/semantics/publishedVersio

Muscle transcriptomic profiles in pigs with divergent phenotypes for fatness traits

Background: Selection for increasing intramuscular fat content would definitively improve the palatability and juiciness of pig meat as well as the sensorial and organoleptic properties of cured products. However, evidences obtained in human and model organisms suggest that high levels of intramuscular fat might alter muscle lipid and carbohydrate metabolism. We have analysed this issue by determining the transcriptomic profiles of Duroc pigs with divergent phenotypes for 13 fatness traits. The strong aptitude of Duroc pigs to have high levels of intramuscular fat makes them a valuable model to analyse the mechanisms that regulate muscle lipid metabolism, an issue with evident implications in the elucidation of the genetic basis of human metabolic diseases such as obesity and insulin resistance. Results: Muscle gene expression profiles of 68 Duroc pigs belonging to two groups (HIGH and LOW) with extreme phenotypes for lipid deposition and composition traits have been analysed. Microarray and quantitative PCR analysis showed that genes related to fatty acid uptake, lipogenesis and triacylglycerol synthesis were upregulated in the muscle tissue of HIGH pigs, which are fatter and have higher amounts of intramuscular fat than their LOW counterparts. Paradoxically, lipolytic genes also showed increased mRNA levels in the HIGH group suggesting the existence of a cycle where triacylglycerols are continuously synthesized and degraded. Several genes related to the insulin-signalling pathway, that is usually impaired in obese humans, were also upregulated. Finally, genes related to antigen-processing and presentation were downregulated in the HIGH group. Conclusion: Our data suggest that selection for increasing intramuscular fat content in pigs would lead to a shift but not a disruption of the metabolic homeostasis of muscle cells. Future studies on the post-translational changes affecting protein activity or expression as well as information about protein location within the cell would be needed to to elucidate the effects of lipid deposition on muscle metabolism in pigs

Modelo numérico para evaluar el comportamiento sísmico de una vivienda de adobe de dos pisos con refuerzo metálico

El adobe es el material constructivo más usado por personas pobres en el Perú. Durante los últimos cincuenta años se han realizado numerosas investigaciones en la PUCP para conocer, predecir y evaluar el comportamiento de este material así como reducir su vulnerabilidad sísmica reforzándolo con diferentes sistemas y materiales constructivos de bajo costo y fácil instalación. Estos esfuerzos se han registrado en artículos científicos y manuales de construcción de viviendas de adobe que ha publicado la Universidad. El profesor Joseph Adell, plantea el empleo de una adaptación del sistema ALLWALL, consistente en cerchas tridimensionales para reforzar viviendas de adobe, con ello se genera una nueva investigación a través de un Proyecto UPM-PUCP, creándose un primer modelo experimental para una vivienda de dos pisos que se somete a ensayo de simulación sísmica en el Laboratorio de Estructuras de la Universidad. Durante el ensayo de simulación sísmica, se apreció que la estructura representa de manera realista su respuesta en el rango elástico, los adobes aportan principalmente masa y el Sistema de Albañilería Integral (en adelante SAI) incrementa su ductilidad. El trabajo de investigación presentado a continuación, procesa y determina las características dinámicas del modelo experimental, elabora un modelo analítico que represente su respuesta sísmica en el rango elástico utilizando el método de elementos finitos y compara el comportamiento de ambos, determina la efectividad del sistema de refuerzo y su factibilidad de aplicación. Queda pendiente el desarrollo de un modelo que prediga el comportamiento inelástico de estructuras de adobe, así como la representación precisa de la interacción entre muros de adobe y su refuerzo con el ALLWALL System que podrán ser abarcados como líneas futuras de investigación.Tesi

Discovery and annotation of novel microRNAs in the porcine genome by using a semi-supervised transductive learning approach

Despite the broad variety of available microRNA (miRNA) prediction tools, their application to the discovery and annotation of novel miRNA genes in domestic species is still limited. In this study we designed a comprehensive pipeline (eMIRNA) for miRNA identification in the yet poorly annotated porcine genome and demonstrated the usefulness of implementing a motif search positional refinement strategy for the accurate determination of precursor miRNA boundaries. The small RNA fraction from gluteus medius skeletal muscle of 48 Duroc gilts was sequenced and used for the prediction of novel miRNA loci. Additionally, we selected the human miRNA annotation for a homology-based search of porcine miRNAs with orthologous genes in the human genome. A total of 20 novel expressed miRNAs were identified in the porcine muscle transcriptome and 27 additional novel porcine miRNAs were also detected by homology-based search using the human miRNA annotation. The existence of three selected novel miRNAs (ssc-miR-483, ssc-miR484 and ssc-miR-200a) was further confirmed by reverse transcription quantitative real-time PCR analyses in the muscle and liver tissues of Göttingen minipigs. In summary, the eMIRNA pipeline presented in the current work allowed us to expand the catalogue of porcine miRNAs and showed better performance than other commonly used miRNA prediction approaches. More importantly, the flexibility of our pipeline makes possible its application in other yet poorly annotated non-model species.info:eu-repo/semantics/acceptedVersio

Identificação por "Multiplex PCR" do sorotipo monofásico e atípico Salmonella enterica subsp. enterica sorotipo 1,4,[5],12:i:-, no Estado de São Paulo, Brasil: freqüência e resistência antimicrobiana

Salmonella spp. are the etiologic agents of salmonellosis, a worldwide spread zoonoses causing foodborne outbreaks and clinical diseases. By serological identification, Salmonella enterica subsp. enterica serotype 1,4,[5],12:i:- accounted for 8.8% of human and 1.6% of nonhuman Salmonella strains isolated in São Paulo State, during 1991-2000. A total of 28.6% of them amplified a fragment corresponding to H:1,2 (flagellar phase two) through PCR analysis and were further assigned as S. Typhimurium. Antimicrobial resistance was detected in 36.3% of the 369 PCR-negative strains tested, including the multiresistance to ampicillin, chloramphenicol, sulfonamides, tetracycline, and streptomycin.Salmonella spp. é o agente etiológico da salmonelose, zoonose mundialmente distribuída e responsável por surtos de doenças transmitidas por alimentos e doenças clínicas. Sorologicamente, Salmonella enterica subsp. enterica sorotipo 1,4,[5],12:i:- correspondeu a 8,8% e 1,6% das cepas de Salmonella de origem humana e não-humana, respectivamente, isoladas no Estado de São Paulo, no decênio 1991-2000. Aproximadamente 28,6% destas cepas amplificaram o fragmento correspondente a H:1,2 (fase flagelar dois) em testes de PCR e foram, então, identificadas como S. Typhimurium. Das 369 cepas negativas em PCR, 36,3% apresentou resistência antimicrobiana, incluindo multirresistência a ampicilina, cloranfenicol, sulfonamidas, tetraciclina e estreptomicina

Genetic parameters and expected responses to selection for components of feed efficiency in a Duroc pig line

Background: Improving feed efficiency (FE) is a key factor for any pig breeding company. Although this can be achieved by selection on an index of multi-trait best linear unbiased prediction of breeding values with optimal economic weights, considering deviations of feed intake from actual needs (RFI) should be of value for further research on biological aspects of FE. Here, we present a random regression model that extends the classical definition of RFI by including animal-specific needs in the model. Using this model, we explore the genetic determinism of several FE components: use of feed for growth (WG), use of feed for backfat deposition (FG), use of feed for maintenance (MW), and unspecific efficiency in the use of feed (RFI). Expected response to alternative selection indexes involving different components is also studied. Results: Based on goodness-of-fit to the available feed intake (FI) data, the model that assumes individual (genetic and permanent) variation in the use of feed for maintenance, WG and FG showed the best performance. Joint individual variation in feed allocation to maintenance, growth and backfat deposition comprised 37% of the individual variation of FI. The estimated heritabilities of RFI using the model that accounts for animal-specific needs and the traditional RFI model were 0.12 and 0.18, respectively. The estimated heritabilities for the regression coefficients were 0.44, 0.39 and 0.55 for MW, WG and FG, respectively. Estimates of genetic correlations of RFI were positive with amount of feed used for WG and FG but negative for MW. Expected response in overall efficiency, reducing FI without altering performance, was 2.5% higher when the model assumed animal-specific needs than when the traditional definition of RFI was considered. Conclusions: Expected response in overall efficiency, by reducing FI without altering performance, is slightly better with a model that assumes animal-specific needs instead of batch-specific needs to correct FI. The relatively small difference between the traditional RFI model and our model is due to random intercepts (unspecific use of feed) accounting for the majority of variability in FI. Overall, a model that accounts for animal-specific needs for MW, WG and FG is statistically superior and allows for the possibility to act differentially on FE components

Detection of homozygous genotypes for a putatively lethal recessive mutation in the porcine argininosuccinate synthase 1 (ASS1) gene

The sequencing of the pig genome revealed the existence of homozygous individuals for a nonsense mutation in the argininosuccinate synthase 1 (ASS1) gene (rs81212146, c.944T>A, L315X). Paradoxically, an AA homozygous genotype for this polymorphism is expected to abolish the function of the ASS1 enzyme that participates in the urea cycle, leading to citrullinemia, hyperammonemia, coma and death. Sequencing of five Duroc boars that sired a population of 350 Duroc barrows revealed the segregation of the c.944T>A polymorphism, so we aimed to investigate its phenotypic consequences. Genotyping of this mutation in the 350 Duroc barrows revealed the existence of seven individuals homozygous (AA) for the nonsense mutation. These AA pigs had a normal weight despite the fact that mild citrullinemia often involves impaired growth. Sequencing of the region surrounding the mutation in TT, TA and AA individuals revealed that the A substitution in the second position of the codon (c.944T>A) is in complete linkage disequilibrium with a C replacement (c.943T>C) in the first position of the codon. This second mutation would compensate for the potentially damaging effect of the c.944T>A replacement. In fact, this is the most probable reason why pigs with homozygous AA genotypes at the 944 site of the ASS1 coding region are alive. Our results illustrate the complexities of predicting the consequences of nonsense mutations on gene function and phenotypes, not only because of annotation issues but also owing to the existence of genetic mechanisms that sometimes limit the penetrance of highly harmful mutations

Pedigree analysis of eight Spanish beef cattle breeds

The genetic structure of eight Spanish autochthonous populations (breeds) of beef cattle were studied from pedigree records. The populations studied were: Alistana and Sayaguesa (minority breeds), Avileña – Negra Ibérica and Morucha ("dehesa" breeds, with a scarce incidence of artificial insemination), and mountain breeds, including Asturiana de los Valles, Asturiana de la Montaña and Pirenaica, with extensive use of AI. The Bruna dels Pirineus breed possesses characteristics which make its classification into one of the former groups difficult. There was a large variation between breeds both in the census and the number of herds. Generation intervals ranged from 3.7 to 5.5 years, tending to be longer as the population size was larger. The effective numbers of herds suggest that a small number of herds behaves as a selection nucleus for the rest of the breed. The complete generation equivalent has also been greatly variable, although in general scarce, with the exception of the Pirenaica breed, with a mean of 3.8. Inbreeding effective population sizes were actually small (21 to 127), especially in the mountain-type breeds. However, the average relatedness computed for these breeds suggests that a slight exchange of animals between herds will lead to a much more favourable evolution of inbreeding. The effective number of founders and ancestors were also variable among breeds, although in general the breeds behaved as if they were founded by a small number of animals (25 to 163)