Energy metabolism disorders during in vitro maturation of bovine cumulus-oocyte complexes interfere with blastocyst quality and metabolism.

Glucose and fatty acids (FA) metabolism disturbances during oocyte in vitro maturation (IVM) affect their metabolism and surrounding cumulus cells, but only inhibition of glucose metabolism decreases embryo culture efficiency. Therefore, the present experiment aimed to reveal if glucose or FA metabolism inhibition leads to the disruption of embryo developmental potential, and to characterize the metabolic landscape of embryos reaching the blastocyst stage. Inhibitors of glucose (IO + DHEA) or FA (ETOMOXIR) metabolism were applied during IVM, and the control group was matured under standard conditions. Blastocysts obtained from experimental and control groups were analyzed with regard to lipidome and metabolome (mass spectrometry), transcriptome (RNA-Seq) and fluorescence lipid droplets staining (BODIPY). We showed that inhibition of glucose and fatty acid metabolism leads to cellular stress response compromising the quality of preimplantation embryos. The inhibition of energy metabolism affects membrane fluidity as well as downregulates fatty acids biosynthesis and gene expression of trophectoderm cell line markers. Therefore, we conclude that oocyte maturation environment exerts a substantial effect on preimplantation development programming at cellular and molecular levels.

Husbandry practices associated with extensification in European pig production and their effects on pork quality.

This review has been developed as part of the mEATquality project with the main objective to examine the types of extensification practices used in European pig husbandry and their effect on intrinsic meat quality. Literature search has resulted in 679 references in total, from which 53 showed a strict compliance with the goals of this review: 1) the use of local European breeds and their crossbreds (22 papers); 2) addition of forage to diet (9 papers); 3) increased space allowance (3 papers); 4) enrichment of environment (19 papers). The evaluation of selected extensification factors showed that not all of them have a clear impact on meat quality, and are often confounded. The most clear differences were observed when comparing autochthonous with commercial breeds, and systems with access to pastures or woodlands vs. indoor housing. Despite many studies focusing on the extensification of husbandry practices, some of the factors cannot be confirmed to have a direct effect on pork intrinsic quality.

Effect of mastitis incidence on litter size, litter weight, and milk composition of rabbit does.

This study aimed to examine the effect of mastitis incidence on the litter size, litter birth weight, and milk composition of Hycole does on a commercial rabbit farm during their third and fourth parity. At third parity does were assigned to the "No mastitis" (n = 30) and "Mastitis" (n = 28) groups on the basis of visible abscesses in the mammary gland area. The microbiological analysis revealed the presence of different pathogenic bacteria. At third parity, "Mastitis" females had fewer kits than the "No mastitis" group, and the average birth weight was lower. On day 2 of the third lactation, "Mastitis" does produced significantly less milk daily compared with the "No mastitis" group. A significant effect on the incidence of mastitis on the litter size and litter weight during the growth of kits up to the 35th day was also observed. The effect of the incidence of mastitis on milk chemical composition was limited. At the fourth parity, the litter characteristics and daily milk yield were leveled in "Mastitis" and "No mastitis" females. To conclude, our study showed that mastitis negatively affects litter size, birth weight, and daily milk yield in the current parity. However, early detection and proper treatment allowed to obtain good reproductive results and healthy kits in the next parity.

Meta-Analysis of SNPs Determining Litter Traits in Pigs.

Nearly 2000 SNPs associated with pig litter size traits have been reported based on genome-wide association studies (GWASs). The aims of this study were to gather and integrate previously reported associations between SNPs and five litter traits: total number born (TNB), number born alive (NBA), number of stillborn (SB), litter birth weight (LWT), and corpus luteum number (CLN), in order to evaluate their common genetic background and to perform a meta-analysis (MA) of GWASs for total number born (TNB) recorded for animals from five pig populations. In this study, the genes with the largest number of associations with evaluated litter traits were GABRG3, RBP7, PRKD1, and STXBP6. Only 21 genes out of 233 associated with the evaluated litter traits were reported in more than one population or for more than one trait. Based on this evaluation, the most interesting candidate gene is PRKD1, which has an association with SB and TNB traits. Based on GO term analysis, PRKD1 was shown to be involved in angiogenesis as well. As a result of the MA, two new genomic regions, which have not been previously reported, were found to be associated with the TNB trait. One SNP was located on Sus scrofa chromosome (SSC) 14 in the intron of the FAM13C gene. The second SNP was located on SSC9 within the intron of the AGMO gene. Functional analysis revealed a strong candidate causal gene underlying the QTL on SSC9. The third best hit and the most promising candidate gene for litter size was found within the SOSTDC1 gene, associated with lower male fertility in rats. We showed that litter traits studied across pig populations have only a few genomic regions in common based on candidate gene comparison. PRKD1 could be an interesting candidate gene with a wider association with fertility. The MA identified new genomic regions on SSC9 and SSC14 associated with TNB. Further functional analysis indicated the most promising gene was SOSTDC1, which was confirmed to affect male fertility in other mammals. This is an important finding, as litter traits are by default linked with females rather than males.

The metabolic profile of bovine blastocysts is affected by in vitro culture system and the pattern of first zygotic cleavage.

Time lapse monitoring (TLM) is a commercial system of individual embryo culture based on the well-of-the-well system. It allows for collecting a panel of intrinsic parameters of special importance to non-invasive quality assessment. Besides, a combined analysis of TLM and metabolome data provides a deeper insight into the embryo quality. Two questions have been addressed by this study: (i) whether embryo culture in the Primo Vision affects embryo development and quality compared to the classical system and (ii) whether the first zygotic cleavage (FZC) dysmorphisms affect metabolomic profile of blastocysts. Presumptive zygotes from IVM/IVF oocytes were cultured either in classical drops (pools of 30 embryos, control group) or on Primo Vision plates (16 embryos in separate wells, sharing culture medium, Primo Vision group). The two categories of blastocysts were analysed for relative transcript abundance of five genes (real time PCR; FASN, Hsp70, PLIN2, Bax, Slc2a1) and for metabolite profile (mass spectrometry). Besides, basing on retrospective analysis of the TLM files, the Primo Vision blastocysts were allocated into one of two groups depending on the FZC pattern (normal NC or direct cleavage DC) and analysed for metabolite profiles. The Primo Vision embryos showed higher cleavage rate (p < 0.01) but reduced blastocyst rate (p < 0.05) when compared to the control group. Although the culture system (Primo Vision vs classical) did not affect the relative transcript abundance, the metabolomic analysis revealed different activity of five pathways. Two of them, related to beta-oxidation of fatty acids were up-regulated, whereas the remaining three corresponding to ubiquinone synthesis, metabolism of phenyloalanine and tyrosine as well as vitamin B6 metabolism were down-regulated. The metabolite profiles were however particularly affected by the FZC pattern. The NC and DC blastocysts differed significantly in the activity of 16 metabolic pathways which mainly involved pyruvic acid. The DC embryos displayed a higher level of pyruvic acid (p < 0.05) which may imply disturbances in the switch from lipid to glucose metabolism. Besides, in our opinion, embryos cultured in separate wells in the Primo Vision may face increased ROS level which reduces their developmental potential. Summarizing we underline application of metabolome analysis to embryo quality assessment due to providing a wider insight into embryo response to environmental factors.

Evaluation of the phenotypic and genomic background of variability based on litter size of Large White pigs.

BACKGROUND: The genetic background of trait variability has captured the interest of ecologists and animal breeders because the genes that control it could be involved in buffering various environmental effects. Phenotypic variability of a given trait can be assessed by studying the heterogeneity of the residual variance, and the quantitative trait loci (QTL) that are involved in the control of this variability are described as variance QTL (vQTL). This study focuses on litter size (total number born, TNB) and its variability in a Large White pig population. The variability of TNB was evaluated either using a simple method, i.e. analysis of the log-transformed variance of residuals (LnVar), or the more complex double hierarchical generalized linear model (DHGLM). We also performed a single-SNP (single nucleotide polymorphism) genome-wide association study (GWAS). To our knowledge, this is only the second study that reports vQTL for litter size in pigs and the first one that shows GWAS results when using two methods to evaluate variability of TNB: LnVar and DHGLM. RESULTS: Based on LnVar, three candidate vQTL regions were detected, on Sus scrofa chromosomes (SSC) 1, 7, and 18, which comprised 18 SNPs. Based on the DHGLM, three candidate vQTL regions were detected, i.e. two on SSC7 and one on SSC11, which comprised 32 SNPs. Only one candidate vQTL region overlapped between the two methods, on SSC7, which also contained the most significant SNP. Within this vQTL region, two candidate genes were identified, ADGRF1, which is involved in neurodevelopment of the brain, and ADGRF5, which is involved in the function of the respiratory system and in vascularization. The correlation between estimated breeding values based on the two methods was 0.86. Three-fold cross-validation indicated that DHGLM yielded EBV that were much more accurate and had better prediction of missing observations than LnVar. CONCLUSIONS: The results indicated that the LnVar and DHGLM methods resulted in genetically different traits. Based on their validation, we recommend the use of DHGLM over the simpler method of log-transformed variance of residuals. These conclusions can be useful for future studies on the evaluation of the variability of any trait in any species.

Reproductive Performance of Hycole Rabbit Does, Growth of Kits and Milk Chemical Composition during Nine Consecutive Lactations under Extensive Rhythm.

The goal of this study was to analyze the reproductive performance of does, growth of their kits, and chemical composition of their milk over nine consecutive parities in order to indicate the boundary of female reproductive profitability. The novelty of this study results from the combinations of three factors: extensive reproductive rhythm, commercial farming conditions, and a period of nine consecutive parities, showing the actual lifespan of a rabbit doe on commercial farms. The data was collected on 60 Hycole females kept at a commercial rabbit farm. Throughout the study, 32 does were excluded due to different reasons (e.g., excluded by means of selection-43.8% and mortalities-25.0%). The does were first inseminated at 28 weeks of age. Following artificial inseminations were conducted 14-15 days after each parturition. All kits were weaned at the age of 35 days. The following characteristics were analysed: body weight of rabbit does at artificial insemination, milk production per lactation, litter size, litter weight, average kit weight, and milk chemical composition. Rabbit does had a significant decrease in kindling rate between the eighth and the ninth parity (by 10.0 percentage points; p = 0.039). The litter size at weaning in the ninth parity was significantly lower to litters weaned at other analysed parities. The amount of milk produced per lactation was affected by the parity order (6.31-6.76 kg; p = 0.042). The litter weights on day 21 and 35 were the lowest at ninth parity. The content of total solids (TS), solids-not-fat, and fat was affected by the parity order on both analysed lactation days. The content of TS and fat in rabbit milk was characterized with a decreasing trend over the analysed period, on both lactation days. The results clearly indicate that rabbit does under extensive reproductive cycles characterize with a very good reproductive performance and can be successfully used for reproduction even up to the eighth parity. However, further research is needed if keeping them longer will not be profitable.

Selection for litter size and litter birthweight in Large White pigs: Maximum, mean and variability of reproduction traits.

Gradually increasing trend of litter size poses a challenge to pig farmers in terms of managing larger litters. Therefore, it seems that a balanced approach that optimises litter size, litter birthweight, and uniformity of those traits is needed in order to address animal welfare and farm management concerns. This study aimed to investigate this issue by defining several traits for total number born (TNB), number born alive (NBA) and litter birthweight (LW). First, the highest value from at least five records per sow was selected as maximum (max) value for each reproduction trait. Second, a mean (mean) for each reproduction trait was calculated per sow. Last, the variability of reproduction traits between parities of the sow was calculated as log-transformed variance of residuals of all observations per sow for each reproduction trait (LnVar). In total, 23 193 Large White sows from Topigs Norsvin with 152 282 litter records were used for analysis in ASReml 4.1. Also, a simulation of breeding schemes was performed with the use of SelAction 2.1 and estimates from genetic analysis. Maximum value of reproductive traits had a much higher heritability than repeated observations or mean of reproduction traits, e.g., 0.31 for maxTNB vs. 0.12 for TNB and 0.07 for meanTNB, which allows for a faster response under selection. The maximum value traits, however, were found to carry more risks, i.e. higher ratio of stillborn (not for maxNBA) and increased variability of traits. Thus, using them in breeding programme should be carefully considered. The genetic coefficient of variation on SD level estimated to indicate the genetic magnitude for variability phenotypes indicated a maximum change of 6-9% in genetic SD of TNB, NBA and LW. The genetic correlations between mean and corresponding variability traits varied from 0.66 to 0.74, whereas the correlation between other mean and variability traits ranged from 0.33 to 0.99. The simulation indicated that even with selection targeted against the variability of reproduction traits, a very limited change should be expected due to a complex genetic and phenotypic relationship between the traits. In the scenarios with selection against LnVarTNB and LnVarLW, this was a decrease of 0.1-0.6% per year, whereas in scenario with selection against LnVarNBA, the range was 0.6-1.1% per year. It is still possible to increase litter size and birthweight further, however, a balance between mean and variability of reproduction traits is required, which can be obtained only by a very well designed breeding programme.

Response of Bovine Cumulus-Oocytes Complexes to Energy Pathway Inhibition during In Vitro Maturation.

Glucose or fatty acids (FAs) metabolisms may alter the ovarian follicle environment and thus determine oocyte and the nascent embryo quality. The aim of the experiment was to investigate the effect of selective inhibition of glucose (iodoacetate + DHEA) or FA (etomoxir) metabolism on in vitro maturation (IVM) of bovine COCs (cumulus-oocyte complexes) to investigate oocyte's development, quality, and energy metabolism. After in vitro fertilization, embryos were cultured to the blastocyst stage. Lipid droplets, metabolome, and lipidome were analyzed in oocytes and cumulus cells. mRNA expression of the selected genes was measured in the cumulus cells. ATP and glutathione relative levels were measured in oocytes. Changes in FA content in the maturation medium were evaluated by mass spectrometry. Our results indicate that only glucose metabolism is substantial to the oocyte during IVM since only glucose inhibition decreased embryo culture efficiency. The most noteworthy differences in the reaction to the applied inhibition systems were observed in cumulus cells. The upregulation of ketone body metabolism in the cumulus cells of the glucose inhibition group suggest possibly failed attempts of cells to switch into lipid consumption. On the contrary, etomoxir treatment of the oocytes did not affect embryo development, probably due to undisturbed metabolism in cumulus cells. Therefore, we suggest that the energy pathways analyzed in this experiment are not interchangeable alternatives in bovine COCs.

Unraveling the actual background of second litter syndrome in pigs: based on Large White data.

Second litter syndrome (SLS) in sows is when fertility performance is lower in the second parity than in the first parity. The causes of SLS have been associated with lactation weight loss, premature first insemination, short lactation length, short weaning to insemination interval, season, and farm of farrowing. There is little known about the genetic background of SLS or if it is a real biological problem or just a statistical issue. Thus, we aimed to evaluate risk factors, investigate genetic background of SLS, and estimate the probability of SLS existing due to the statistical properties of the trait. The records of 246 799 litters (total number born, TNB) from 46 218 Large White sows were used. A total of 15 398 sows had SLS. Two traits were defined: first a binominal trait if a sow had SLS or not (biSLS) and second a continuous trait (Range) created by subtracting the total number of piglets born in the first parity (TNB1) from the piglets born in the second parity (TNB2). Lactation length, farm, and season of the farrowing had significant effects on SLS traits when tested as fixed effects in the genetic model. These effects are farm management-related factors. The age at first insemination and weaning to insemination interval were significant only for other reproduction traits (e.g., TNB1, TNB2, litter weight in parity 1 and 2). The heritability of biSLS was 0.05 (on observed scale), whereas heritability of Range was 0.03. To verify the existence of SLS data with records of 50 000 sows and 9 parities was simulated. The simulations showed that the average expected frequency of SLS across all the parities was 0.49 (±0.05) while the observed frequency in the actual data was 0.46 (±0.04). We compared this to SLS frequencies in 67 farms and only 2 farms had more piglets born in the first parity compared to the second. Therefore, on the individual sow level SLS is likely due to statistical properties of the trait, whereas on the farm level SLS is likely due to farm management. Thus, SLS should not be considered an abnormality nor a syndrome if on average the herd litter size in parity 2 is larger than in parity 1.

Estimation of litter size variability phenotypes in Large White sows.

The objective of this study was to obtain new phenotypes of phenotypic variability for the total number born (TNB) in pigs using the residual variance of TNB. The analysis was based on 246,799 Large White litter observations provided by Topigs Norsvin. Three animal models were used to obtain estimates of residual variance for TNB: the basic model (BM) containing fixed effects of farm-year and season and random effects of animal and permanent environmental sow, the basic model with an additional fixed effect of parity (BMP) and a random regression model (RRM). The within-individual variance of the residuals was calculated and log-transformed to obtain three new variability traits: LnVarBM, LnVarBMP and LnVarRRM. Then, (co)variance components, heritability, the genetic coefficient of variation at the standard deviation level (GCVSDe ) and genetic correlations between the three LnVar's and between the LnVar's and mean total number born (mTNB) were estimated with uni-, bi- and trivariate models. Results indicated that genetically LnVar's are the same trait and are positively correlated with the mTNB (~0.60). Thus, both traits should be included in breeding programmes to avoid an increase in TNB variability while selecting for increased TNB. Heritability of the LnVar's was estimated at 0.021. The GCVSDe for LnVar's showed that a change of 8% in residual standard deviation of TNB could be obtained per generation. Those results indicate that phenotypic variability of litter size is under genetic control, thus it may be improved by selection.

Selecting for changes in average "parity curve" pattern of litter size in Large White pigs.

This study aimed to analyse genetic background of variation in reproductive performance between parities of a sow and to investigate selection strategies to change the "parity curve". Total number born (TNB) recorded in Large White sows was provided by Topigs Norsvin. Analysis with basic (BM) and random regression (RRM) models was done in ASReml 4.1. The BM included only a fixed "parity curve", while RRM included 3rd order polynomials for additive genetic and permanent sow effects. Parameters from RRM were used in simulations in SelAction 2.1. Based on Akaike information criterion, RRM was a better model for TNB data. Genetic variance and heritability estimates of TNB from BM and RRM were increasing with parity from parity 2. Genetically, parity 1 is the most different from parities 7 to 10, whereas most similar to parities 2 and 3. This indicates presence of genetic variation to change the "parity curve". Based on simulations, the selection to increase litter size in parity 1 only increases TNB in all parities, but does not change the observed shape of "parity curve", whereas selection for increased TNB in parity 1 and reduced TNB in parity 5 decreases differences between parities, but also reduces overall TNB in all parities. Changing the "parity curve" will be difficult as the genetic and phenotypic relationships between the parities are hard to overcome even when selecting for one parity.

Challenges in inbreeding estimation of large populations based on Polish Holstein-Friesian cattle pedigree.

The aim of this study was to evaluate observed and future inbreeding level in Polish Holstein-Friesian cattle population. In total, over 9.8 mln animals were used in the analysis coming from the pedigree of Polish Federation of Cattle Breeders and Dairy Farmers. Inbreeding level, as an average per birth year, was estimated with the method accounting for missing parent information with the assumption of year 1950 as the base year of the population. If an animal had no ancestral records, an average inbreeding level from its birth year was assigned. Twice the average inbreeding level served as relatedness of the animal to the population, which enabled estimation of inbreeding in its offspring. The future inbreeding of potential offspring was estimated as an average of animals (bulls and cows) available for mating in a certain year. It was observed that 30-50% of animals born between 1985 and 2015 had no relevant ancestral information, which is caused by a high number of new animals and/or entire farms entering the national milk recordings. For the year 2015, the observed inbreeding level was 3.30%, which was more than twice the inbreeding with the classical approach (without missing parent information) and higher by 0.4% than the future inbreeding. The average increase of inbreeding in years 2010-2015 was 0.10%, which is similar to other countries monitored by World Holstein-Friesian Federation. However, the values might be underestimated due to low pedigree completeness. The estimates of future inbreeding suggested that observed inbreeding could be even lower and also increase slower, which indicates a constant need to monitor rate of increase in inbreeding over time. The most important aspect of presented results is the necessity to advise individual farmers to keep precise recordings of the matings on their farm in order to improve the pedigree completeness of Polish Holstein-Friesian and to use suitable mating programs to avoid too rapid growth of inbreeding.

Genetic aspects of feed efficiency and reduction of environmental footprint in broilers: a review.

Currently, optimization of feed efficiency is one of the main challenges in improvement programs of livestock and poultry genetics. The objective of this review is to present the genetic aspects of feed efficiency related traits in meat-type chicken and possible ways to reduce the environmental impact of poultry meat production with effective breeding. Basic measures of feed efficiency are defined and the genetic background of these traits, including a review of heritabilities is described. Moreover, a number of genomic regions and candidate genes determining feed efficiency traits of broilers that were detected over the past decades are described. Classical and genomic selection strategies for feed efficiency in the context of its relationships with other performance traits are discussed as well. Finally, future strategies to improve feed digestibility are described as it is expected that they will decrease wastes and greenhouse gas emission. Further genetic improvement of feed efficiency, should be examined jointly with appropriate feeding strategies in broilers.

The prospects of selection for social genetic effects to improve welfare and productivity in livestock.

Social interactions between individuals living in a group can have both positive and negative effects on welfare, productivity, and health of these individuals. Negative effects of social interactions in livestock are easier to observe than positive effects. For example, laying hens may develop feather pecking, which can cause mortality due to cannibalism, and pigs may develop tail biting or excessive aggression. Several studies have shown that social interactions affect the genetic variation in a trait. Genetic improvement of socially-affected traits, however, has proven to be difficult until relatively recently. The use of classical selection methods, like individual selection, may result in selection responses opposite to expected, because these methods neglect the effect of an individual on its group mates (social genetic effects). It has become clear that improvement of socially-affected traits requires selection methods that take into account not only the direct effect of an individual on its own phenotype but also the social genetic effects, also known as indirect genetic effects, of an individual on the phenotypes of its group mates. Here, we review the theoretical and empirical work on social genetic effects, with a focus on livestock. First, we present the theory of social genetic effects. Subsequently, we evaluate the evidence for social genetic effects in livestock and other species, by reviewing estimates of genetic parameters for direct and social genetic effects. Then we describe the results of different selection experiments. Finally, we discuss issues concerning the implementation of social genetic effects in livestock breeding programs. This review demonstrates that selection for socially-affected traits, using methods that target both the direct and social genetic effects, is a promising, but sometimes difficult to use in practice, tool to simultaneously improve production and welfare in livestock.