The search for SNPs and genes associated with the feed conversion ratio using entropy analysis.

The aim of this study was to detect the chromosomal regions connected with feed conversion ratio and point out the respective genes in meat-type chicken. Analysis covered 862 genotyped commercial line of broiler using 60K Illumina iSelect chicken array and obtained information about 57636 SNPs. Feed conversion ratio between 39-46 days were registered. Finally, 42770 SNPs were analysed. The information theory is employed to detect the association between SNPs and recorded traits. The following parameters were estimated: entropy coefficient, conditional entropy, portion of information and mutual information. Important regions at chromosomes 1 and Z were identified. They are mainly located within genes determining the nervous system and expressed also in gastrointestinal tract

Analysis of meat quality traits and gene expression profiling of pigs divergent in residual feed intake

peer-reviewedResidual feed intake (RFI), the difference between actual feed intake and predicted feed requirements, is suggested to impact various aspects of meat quality. The objective of this study was to investigate the molecular mechanisms underpinning the relationship between RFI and meat quality. Technological, sensory and nutritional analysis as well as transcriptome profiling were carried out in Longissimus thoracis et lumborum muscle of pigs divergent in RFI (n = 20). Significant differences in sensory profile and texture suggest a minor impairment of meat quality in more efficient pigs. Low RFI animals had leaner carcasses, greater muscle content and altered fatty acid profiles compared to high RFI animals. Accordingly, differentially expressed genes were enriched in muscle growth and lipid & connective tissue metabolism. Differences in protein synthesis and degradation suggest a greater turnover of low RFI muscle, while divergence in connective tissue adhesion may impact tenderness. Fatty acid oxidation tending towards decrease could possibly contribute to reduced mitochondrial activity in low RFI muscle

Homer 1 genotype AA variant relates to congenital splay leg syndrome in piglets by repressing Pax7 in myogenic progenitors

IntroductionPorcine congenital splay leg syndrome (PCS) is a major birth defect in piglets, resulting in lameness and high mortality rates. The multifactorial pathogenesis of PSC is not well understood but includes a polygenic inheritance.MethodsHere, in addition to morphological investigations, we characterized the expression of myogenic genes and functional (proliferation and differentiation) properties of myogenic precursor/satellite cells (SATCs) in 1 day-old PCS piglets, non-affected littermates (LCs), and piglets from PCS-free healthy litters (HCs). In addition, PCS phenotypes were related to the SNP Homer1_rs325197091 within the Homer1 locus, which has been identified as a potential hereditary cause of PCS.Results and discussionSamples from musculus semitendinosus (ST) of PCS piglets had a higher proportion of type II fibers, reflecting myofiber immaturity. In addition, myofiber atrophy, a lower number of myonuclei per fiber (ST), and a higher apoptotic activity (in ST and longissimus dorsi muscle; LD) were found in the PCS group. A higher proportion of cycling committed myoblasts (Pax7+/Ki67+ cells) occurred in samples from PCS-affected piglets, and on the other hand, the mRNA expression of genes involved in differentiation (muscle differentiation 1; MyoD, myogenin; MyoG) was repressed compared with HCs. Cultured SATCs from PCS-affected animals showed a temporal shift in peak expression of Pax7, MyoD, and MyoG toward days 3 and 4 of their 7 days differentiation regime. In vitro experiments with isolated SATCs confirmed the lower differentiation potential and the delayed progression of the myogenic processes in cells from piglets with PCS phenotype. In addition, Pax7 and desmin were differently expressed in Homer1_rs325197091 genotype variants (GG, GA, and AA). Both genes showed the lowest expression in the homozygous AA-variant, which was most frequently found in PCS-affected animals. The homozygous AA-variant was also associated with lower expression of the truncated Homer1-subtype 205. Thus, we hypothesize that in PCS, the balance between Homer1 proteins and its signaling functions is changed in a way detrimental to the myogenic differentiation program. Our results demonstrated direct negative effects of the Homer1 AA genotype on Pax7 expression, but the exact mode of action still needs to be elucidated

Host-Microbiota Interactions in Ileum and Caecum of Pigs Divergent in Feed Efficiency Contribute to Nutrient Utilization

peer-reviewedThe composition of the intestinal microbiota plays an important role in the digestion and utilization of nutrients and for gut health. Low-fiber diets stimulate digestion and absorption processes, predominantly in the upper region of the gastrointestinal tract, thereby increasing the conversion of feed into body weight. As a consequence, the chemical composition of digesta after duodenal and jejunal absorption processes and passage has a limited complexity affecting colonization and molecular profiles of enterocytes in the hind gut. To decipher ileal and caecal microbial ecosystems and host transcriptional profiles that are beneficial for effective use of the remaining nutrients, pigs differing in feeding efficiency were studied. Biological functions that were consistently enriched at both the gene and microbiota levels comprise immunity-related processes, which ensure the integrity of the gastrointestinal tract. In addition, the differential abundance of certain genera, including Rothia, Subdoligranulu, Leeia and Cellulosilyticum, reflects the establishment of a microbial profile that supports the digestion of endogenously indigestible dietary components in highly feed-efficient pigs. Overall, the results indicate the potential to promote these beneficial functions and further improve feed efficiency through manipulation of dietary and probiotic strategies

Detection of SNP effects on feed conversion ratio in pigs based on entropy approach.

The objectives of the study were to classify SNPs according to their contribution to the feed conversion ratio and to indicate interactions between the most informative SNPs using entropy analysis. The records of 1296 pigs were included. Two selection criteria for molecular data were applied: call rate 0.95 and minor allele frequency 0.05. After this, 50 951 SNPs were included into the entropy analysis. For each SNP entropy and conditional entropy were estimated. For interaction analyses the most informative SNPs were selected. For each pair of SNPs, the mutual information was assessed. A majority of the loci studied showed relatively small contributions. The most informative SNPs are mainly located on chromosomes: 1, 4, 7, 9 and 14. Whereas important interactions between SNP pairs were detected on chromosomes: 1, 14, 15 and 16. High mutual information was registered for SNPs located nearby.

Strategies towards Improved Feed Efficiency in Pigs Comprise Molecular Shifts in Hepatic Lipid and Carbohydrate Metabolism

Publication history: Accepted - 28 July 2017; Published online - 1 August 2017Due to the central role of liver tissue in partitioning and metabolizing of nutrients, molecular liver-specific alterations are of considerable interest to characterize an efficient conversion and usage of feed in livestock. To deduce tissue-specific and systemic effects on nutrient metabolism and feed efficiency (FE) twenty-four animals with extreme phenotypes regarding residual feed intake (RFI) were analyzed. Transcriptome and fatty acid profiles of liver tissue were complemented with measurements on blood parameters and thyroid hormone levels. Based on 803 differentially-abundant probe sets between low- and high-FE animals, canonical pathways like integrin signaling and lipid and carbohydrate metabolism, were shown to be affected. Molecular alterations of lipid metabolism show a pattern of a reduced hepatic usage of fatty acids in high-FE animals. Complementary analyses at the systemic level exclusively pointed to increased circulating triglycerides which were, however, accompanied by considerably lower concentrations of saturated and polyunsaturated fatty acids in the liver of high-FE pigs. These results are in accordance with altered muscle-to-fat ratios usually ascribed to FE animals. It is concluded that strategies to improve FE might favor a metabolic shift from energy storage towards energy utilization and mobilization.This work was funded by the European Union Seventh Framework Programme (FP7/2007–2013) as part of the ECO-FCE project under grant agreement No. 311794. The Leibniz Institute for Farm Animal Biology provided its own matched fundin

Elevated haplotypes frequencies reveal similarities for selection signatures in Western and Russian Simmental populations

This paper shows a straightforward, but surprisingly effective approach to detect genomic regions of importance, illustrated on two Simmental cattle populations. Medium density genomic data of 42 German/Austrian (denoted as “Western“) and 38 Russian Simmental cattle were used to identify the most frequent haplotypes within the two populations. The haplotypes were defined as non-overlapping segments of ten single nucleotide ploymorphisms (SNP). The phasing was done with the SHAPEIT software, with a follow up analysis of haplotypes using the GHap package. Despite the low sample size a number of high frequency haplotypes could be identified across the whole genome. The identified genes residing directly in these high frequency haplotypes were extremely relevant for the dual purpose Simmental cattle. A large part of these genes influenced growth rate and carcass traits, others were relevant for the milk production. A smaller proportion was connected to the reproduction, immune system and cellular processes, with indirect influence on production traits

Fecal Microbiota Transplantation in Gestating Sows and Neonatal Offspring Alters Lifetime Intestinal Microbiota and Growth in Offspring

Previous studies suggest a link between intestinal microbiota and porcine feed efficiency (FE). Therefore, we investigated whether fecal microbiota transplantation (FMT) in sows and/or neonatal offspring, using inocula derived from highly feed-efficient pigs, could improve offspring FE. Pregnant sows were assigned to control or FMT treatments and the subsequent offspring to control treatment, FMT once (at birth), or FMT four times (between birth and weaning). FMT altered sow fecal and colostrum microbiota compositions and resulted in lighter offspring body weight at 70 and 155 days of age when administered to sows and/or offspring. This was accompanied by FMT-associated changes within the offspring?s intestinal microbiota, mostly in the ileum. These included transiently higher fecal bacterial diversity and load and numerous compositional differences at the phylum and genus levels (e.g., Spirochaetes and Bacteroidetes at high relative abundances and mostly members of Clostridia, respectively), as well as differences in the abundances of predicted bacterial pathways. In addition, intestinal morphology was negatively impacted, duodenal gene expression altered, and serum protein and cholesterol concentrations reduced due to FMT in sows and/or offspring. Taken together, the results suggest poorer absorptive capacity and intestinal health, most likely explaining the reduced body weight. An additive effect of FMT in sows and offspring also occurred for some parameters. Although these findings have negative implications for the practical use of the FMT regime used here for improving FE in pigs, they nonetheless demonstrate the enormous impact of early-life intestinal microbiota on the host phenotype.publishersversionPeer reviewe

Population structure and genetic diversity of 25 Russian sheep breeds based on whole-genome genotyping

Background: Russia has a diverse variety of native and locally developed sheep breeds with coarse, fine, and semi-fine wool, which inhabit different climate zones and landscapes that range from hot deserts to harsh northern areas. To date, no genome-wide information has been used to investigate the history and genetic characteristics of the extant local Russian sheep populations. To infer the population structure and genome-wide diversity of Russian sheep, 25 local breeds were genotyped with the OvineSNP50 BeadChip. Furthermore, to evaluate admixture contributions from foreign breeds in Russian sheep, a set of 58 worldwide breeds from publicly available genotypes was added to our data. Results: We recorded similar observed heterozygosity (0.354-0.395) and allelic richness (1.890-1.955) levels across the analyzed breeds and they are comparable with those observed in the worldwide breeds. Recent effective population sizes estimated from linkage disequilibrium five generations ago ranged from 65 to 543. Multi-dimensional scaling, admixture, and neighbor-net analyses consistently identified a two-step subdivision of the Russian local sheep breeds. A first split clustered the Russian sheep populations according to their wool type (fine wool, semi-fine wool and coarse wool). The Dagestan Mountain and Baikal fine-fleeced breeds differ from the other Merino-derived local breeds. The semi-fine wool cluster combined a breed of Romanian origin, Tsigai, with its derivative Altai Mountain, the two Romney-introgressed breeds Kuibyshev and North Caucasian, and the Lincoln-introgressed Russian longhaired breed. The coarse-wool group comprised the Nordic short-tailed Romanov, the long-fat-tailed outlier Kuchugur and two clusters of fat-tailed sheep: the Caucasian Mountain breeds and the Buubei, Karakul, Edilbai, Kalmyk and Tuva breeds. The Russian fat-tailed breeds shared co-ancestry with sheep from China and Southwestern Asia (Iran). Conclusions: In this study, we derived the genetic characteristics of the major Russian local sheep breeds, which are moderately diverse and have a strong population structure. Pooling our data with a worldwide genotyping set gave deeper insight into the history and origin of the Russian sheep populations