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Loin muscle area (LMA) and loin muscle depth (LMD) are important traits influencing the production performance of breeding pigs. However, the genetic architecture of these two traits is still poorly understood. To discern the genetic architecture of LMA and LMD, a material consisting of 6043 Duroc pigs belonging to two populations with different genetic backgrounds was collected and applied in genome-wide association studies (GWAS) with a genome-wide distributed panel of 50K single nucleotide polymorphisms (SNPs). To improve the power of detection for common SNPs, we conducted a meta-analysis in these two pig populations and uncovered additional significant SNPs. As a result, we identified 75 significant SNPs for LMA and LMD on SSC6, 7, 12, 16, and 18. Among them, 25 common SNPs were associated with LMA and LMD. One pleiotropic quantitative trait locus (QTL), which was located on SSC7 with a 283 kb interval, was identified to affect LMA and LMD. Marker ALGA0040260 is a key SNP for this QTL, explained 1.77% and 2.48% of the phenotypic variance for LMA and LMD, respectively. Another genetic region on SSC16 (709 kb) was detected and displayed prominent association with LMA and the peak SNP, WU_10.2_16_35829257, contributed 1.83% of the phenotypic variance for LMA. Further bioinformatics analysis determined eight promising candidate genes (GCLC, GPX8, DAXX, FGF21, TAF11, SPDEF, NUDT3, and PACSIN1) with functions in glutathione metabolism, adipose and muscle tissues development and lipid metabolism. This study provides the first GWAS for the LMA and LMD of Duroc breed to analyze the underlying genetic variants through a large sample size. The findings further advance our understanding and help elucidate the genetic architecture of LMA, LMD and growth-related traits in pigs.

An important economic reason for the loss of local breeds is that they tend to be less productive, and hence having less market value than commercial breeds. Nevertheless, local breeds often have irreplaceable values, genetically and sociologically. In the breeding programs with local breeds, it is crucial to balance the selection for genetic gain and the maintaining of genetic diversity. These two objectives are often conflicting, and finding the optimal point of the trade-off has been a challenge for breeders. Genomic selection (GS) provides a revolutionary tool for the genetic improvement of farm animals. At the same time, it can increase inbreeding and produce a more rapid depletion of genetic variability of the selected traits in future generations. Optimum-contribution selection (OCS) represents an approach to maximize genetic gain while constraining inbreeding within a targeted range. In the present study, 515 Ningxiang pigs were genotyped with the Illumina Porcine SNP60 array or the GeneSeek Genomic Profiler Porcine 50K array. The Ningxiang pigs were found to be highly inbred at the genomic level. Average locus-wise inbreeding coefficients were 0.41 and 0.37 for the two SNP arrays used, whereas genomic inbreeding coefficients based on runs of homozygosity were 0.24 and 0.25, respectively. Simulated phenotypic data were used to assess the utility of genomic OCS (GOCS) in comparison with GS without inbreeding control. GOCS was conducted under two scenarios, selecting sires only (GOCS_S) or selecting sires and dams (GOCS_SD), while kinships were constrained on selected parents. The genetic gain for average daily body weight gain (ADG) per generation was between 18.99 and 20.55 g with GOCS_S, and between 23.20 and 28.92 with GOCS_SD, and it varied from 25.38 to 48.38 g under GS without controlling inbreeding. While the rate of genetic gain per generation obtained using GS was substantially larger than that obtained by the two scenarios of genomic OCS in the beginning generations of selection, the difference in the genetic gain of ADG between GS and GOCS reduced quickly in latter generations. At generation ten, the difference in the realized rates of genetic gain between GS and GOCS_SD diminished and ended up with even a slightly higher genetic gain with GOCS_SD, due to the rapid loss of genetic variance with GS and fixation of causative genes. The rate of inbreeding was mostly maintained below 5% per generation with genomic OCS, whereas it increased to between 10.5% and 15.3% per generation with GS. Therefore, genomic OCS appears to be a sustainable strategy for the genetic improvement of local breeds such as Ningxiang pigs, but keeping mind that a variety of GOCS methods exist and the optimal forms remain to be exploited further.

Background For genomic selection in populations with a small reference population, combining populations of the same breed or populations of related breeds is an effective way to increase the size of the reference population. However, genomic predictions based on single nucleotide polymorphism (SNP)-chip genotype data using combined populations with different genetic backgrounds or from different breeds have not shown a clear advantage over using within-population or within-breed predictions. The increasing availability of whole-genome sequencing (WGS) data provides new opportunities for combined population genomic prediction. Our objective was to investigate the accuracy of genomic prediction using imputation-based WGS data from combined populations in pigs. Using 80K SNP panel genotypes, WGS genotypes, or genotypes on WGS variants that were pruned based on linkage disequilibrium (LD), three methods [genomic best linear unbiased prediction (GBLUP), single-step (ss)GBLUP, and genomic feature (GF)BLUP] were implemented with different prior information to identify the best method to improve the accuracy of genomic prediction for combined populations in pigs. Results In total, 2089 and 2043 individuals with production and reproduction phenotypes, respectively, from three Yorkshire populations with different genetic backgrounds were genotyped with the PorcineSNP80 panel. Imputation accuracy from 80K to WGS variants reached 92%. The results showed that use of the WGS data compared to the 80K SNP panel did not increase the accuracy of genomic prediction in a single population, but using WGS data with LD pruning and GFBLUP with prior information did yield higher accuracy than the 80K SNP panel. For the 80K SNP panel genotypes, using the combined population resulted in a slight improvement, no change, or even a slight decrease in accuracy in comparison with the single population for GBLUP and ssGBLUP, while accuracy increased by 1 to 2.4% when using WGS data. Notably, the GFBLUP method did not perform well for both the combined population and the single populations. Conclusions The use of WGS data was beneficial for combined population genomic prediction. Simply increasing the number of SNPs to the WGS level did not increase accuracy for a single population, while using pruned WGS data based on LD and GFBLUP with prior information could yield higher accuracy than the 80K SNP panel.

Field studies on Salmonella infection in suckling piglets are scarce due to the intrinsic difficulties of collecting proper samples (i.e. tonsils or mesenteric lymph nodes), and most of them rely on the analysis of rectal swabs that limit their accuracy. We used 495 slaughtered 4-weeks-old male piglets intended for human consumption from 5 Salmonella -seropositive breeding farms to collect gastrointestinal packages and perform a thorough detection of Salmonella on mesenteric lymph nodes and intestinal content. The overall prevalence of both infection and shedding was high (≈ 36%) indicating that piglets played an active role in Salmonella maintenance in the farms. Major serotypes found in piglets included 4,[5],12:i: (35.4%), Rissen (17.1%), Derby (10.9%) and Bovismorbificans (10.3%). In most of the infected animals (72.8%) the same serotype was found in mesenteric lymph nodes and feces. Significant higher ELISA OD% values were found in meat juice samples from non-infected piglets compared to infected ones (median OD% of 12.0 and 17.3, respectively; P  = 0.002) suggesting some protective effect of sow’s colostrum. Salmonella was also isolated from feces from weaned sows contemporary of the slaughtered piglets, and 89% of the serotypes identified in sows were also detected in piglets. Pulsed field gel electrophoresis analyses showed that 75% of the piglet isolates that were compared to those of sows were related to them, suggesting the circulation of Salmonella strains between sows and piglets. It appears that improving piglet colostrum intake along with the reduction of the shedding in sows may favor the control of Salmonella infection in breeding farms.

Hypothermic storage of boar semen provides the possibility to omit antibiotics from semen extenders so long as sperm quality is maintained and bacterial growth prevented. The objective of this study was to determine an optimal cooling-rate frame for boar semen preserved at 5˚C in an antibiotic-free extender. Semen from eight boars extended in AndroStar® Premium was cooled from 30˚C to 5˚C using seven different cooling rates, ranging initially from 0.01 to 0.36˚C min–1 and reaching 5˚C between 2 h and 24 h after dilution. Sperm motility, membrane integrity, membrane fluidity, mitochondrial membrane potential and the response to the capacitation stimulus bicarbonate remained at a high level for 144 h at 5˚C when the semen was initially cooled in a cooling-rate frame ranging from 0.01 to 0.09˚C min-1 in the temperature zone from 30 to 25˚C, followed by 0.02 to 0.06˚C min–1 to 10˚C and 0.01 to 0.02˚C min-1 to the final storage temperature. A cooling rate of 0.07˚C min–1 in the temperature zone from 30 to 10˚C led to a reduced response to bicarbonate (P < 0.01) and fast cooling to 5˚C within 1 h with a cooling rate of 0.31˚C min–1 resulted in lower values (P > 0.05) of all sperm parameters. In a further experiment, slow cooling with a holding time of 6 h at 22˚C induced after 6 h storage a temporary increase in Escherichia coli of 0.5 × 103 to 2.4 × 103 CFU mL–1 in the sperm-free inoculated extender. Overall, the load of mesophilic bacteria in the stored semen was below 6 × 103 CFU mL–1, a level that is not regarded as critical for sperm quality. In conclusion, appropriate cooling protocols were established for the antibiotic-free storage of boar semen at 5˚C, allowing the application of hypothermic preservation in research and in artificial insemination.

Background The pig breeding industry has undergone a large number of mergers in the past decades. Various commercial lines were merged or discontinued, which is expected to reduce the genetic diversity of the pig species. The objective of the current study was to investigate the genetic diversity of different former Dutch Landrace breeding lines and quantify their relationship with the current Dutch Landrace breed that originated from these lines. Results Principal component analysis clearly divided the former Landrace lines into two main clusters, which are represented by Norwegian/Finnish Landrace lines and Dutch Landrace lines. Structure analysis revealed that each of the lines that are present in the Dutch Gene bank has a unique genetic identity. The current Dutch Landrace breed shows a high level of admixture and is closely related to the six former lines. The Dumeco N-line, which is conserved in the Dutch Gene bank, is poorly represented in the current Dutch Landrace. All seven lines (the six former and the current line) contribute almost equally to the genetic diversity of the Dutch Landrace breed. As expected, the current Dutch Landrace breed comprises only a small proportion of unique genetic diversity that was not present in the other lines. The genetic diversity level, as measured by Eding’s core set method, was equal to 0.89 for the current Dutch Landrace breed, whereas total genetic diversity across the seven lines, measured by the same method, was equal to 0.99. Conclusions The current Dutch Landrace breed shows a high level of admixture and is closely related to the six former Dutch Landrace lines. Merging of commercial Landrace lines has reduced the genetic diversity of the Landrace population in the Netherlands, although a large proportion of the original variation is maintained. Thus, our recommendation is to conserve breeding lines in a gene bank before they are merged.

Live pig trade patterns, drivers and characteristics, particularly in backyard predominant systems, remain largely unexplored despite their important contribution to the spread of infectious diseases in the swine industry. A better understanding of the pig trade dynamics can inform the implementation of risk-based and more cost-effective prevention and control programs for swine diseases. In this study, a semi-structured questionnaire elaborated by FAO and implemented to 487 farmers was used to collect data regarding basic characteristics about pig demographics and live-pig trade among villages in the country of Georgia, where very scarce information is available. Social network analysis and exponential random graph models were used to better understand the structure, contact patterns and main drivers for pig trade in the country. Results indicate relatively infrequent (a total of 599 shipments in one year) and geographically localized (median Euclidean distance between shipments = 6.08 km; IQR = 0-13.88 km) pig movements in the studied regions. The main factors contributing to live-pig trade movements among villages were being from the same region (i.e., local trade), usage of a middleman or a live animal market to trade live pigs by at least one farmer in the village, and having a large number of pig farmers in the village. The identified villages' characteristics and structural network properties could be used to inform the design of more cost-effective surveillance systems in a country which pig industry was recently devastated by African swine fever epidemics and where backyard production systems are predominant.

Background Emergence and re-emergence of porcine epidemic diarrhea virus (PEDV) in North America, Asia and Europe has caused severe economic loss to the global swine industry. However, the virome of PEDV infected pigs and its effect on disease severity remains unknown. The advancements of sequencing technology have made it possible to characterize the entire microbiome of different body sites for any host. Methods The objective of this study was to characterize the RNA virome in PEDV-positive pigs using the hypothesis-free metagenomics approach based on next-generation sequencing. Specifically, 217 PEDV-positive swine fecal swab samples collected from diarrheic piglets over 17 US states during 2015–2016 were analyzed. Results A Kraken algorithm-based bioinformatics analysis revealed the presence of up to 9 different RNA genera besides PEDV ( Alphacoronavirus genus), including Mamastrovirus (52%, 113/217), Enterovirus (39%, 85/217), Sapelovirus (31%, 67/217), Posavirus (30%, 66/217), Kobuvirus (23%, 49/217), Sapovirus (13%, 28/217), Teschovirus (10%, 22/217), Pasivirus (9%, 20/217), and Deltacoronavirus (3%, 6/217). There were 58 out of 217 piglets (27%) have PEDV infection alone whereas the remaining 159 (73%) shed 2 up to 9 different viruses. Conclusion These findings demonstrated that PEDV infected diarrheic pigs had an extensive RNA viral flora consisting of four different families: Astroviridae, Picornaviridae, Caliciviridae , and Coronaviridae .

A partir da vigência do Protocolo de Kyoto houve um interesse renovado pela tecnologia dos biodigestores. Como eles permitem uma redução na emissão de gases do efeito estufa, em relação a outros métodos de tratamento de dejetos, a sua implantação pode permitir a comercialização de créditos de carbono, resultando em valores monetários. O presente trabalho tem como objetivo analisar o processo de disseminação desta tecnologia na Microrregião de Santa Rosa, situada na Mesorregião do Noroeste riograndense, impulsionada, especialmente, por empresas privadas. O presente estudo revelou que 33,33% dos equipamentos instalados encontram-se desativados. Estudou-se o perfil das propriedades que possuem estes equipamentos instalados, além de uma análise das possíveis dificuldades encontradas pelos proprietários rurais, no sentido de implantação e utilização dessa tecnologia, verificando-se a contribuição dos biodigestores, referente à questão energética e minimização da poluição do meio ambiente nessas áreas. Através da revisão da literatura existente e aplicação de questionários, foram levantadas diversas informações acerca da instalação de biodigestores, observando se contribuem como alternativa de agregação de valor às propriedades criadoras e como alternativa viável para a solução dos problemas ambientais envolvidos no processo.

Pigs have played a major role in the economic, social and symbolic systems of China since the Early Neolithic more than 8,000 years ago. However, the interaction between the history of pig domestication and transformations in Chinese society since then, have not been fully explored. In this paper, we investigated the co-evolution from the earliest farming communities through to the new political and economic models of state-like societies, up to the Chinese Empire, using 5,000 years of archaeological records from the Xiawanggang (XWG) and Xinzhai (XZ) sites (Henan Province). To trace the changes of pig populations against husbandry practices, we combined the geometric morphometric analysis of dental traits with a study of the stable carbon and nitrogen isotope ratios from bone collagen. The domestication process intensified during the Neolithic Yangshao, prompted by greater selective pressure and/or better herd control against wild introgression. After that, pig farming, in XWG, relied on local livestock and a gradual change of husbandry practices overtime. This was characterized by a gentle increase in millet foddering and animal protein intake, until a complete change over to household management during the Han dynasty. The only rupture in this steady trend of husbandry occurred during the Longshan period, with the appearance of small sized and idiosyncratic pigs with specific feeding practices (relying on millet and household scraps). From three exploratory hypothesis, we explored the possibility of anti-elite pig production in XWG during the Longshan period, as a means to resist incorporation into a new economic model promoting intensified domestic production. This exploratory hypothesis is the most suitable to our dataset; however, numerous areas need to be explored further in order to adequately document the role of pigs in the rise of China's complex societies.