Accuracy of genomic prediction using imputed whole‐genome sequence data in white layers

There is an increasing interest in using whole‐genome sequence data in genomic selection breeding programmes. Prediction of breeding values is expected to be more accurate when whole‐genome sequence is used, because the causal mutations are assumed to be in the data. We performed genomic prediction for the number of eggs in white layers using imputed whole‐genome resequence data including ~4.6 million SNPs. The prediction accuracies based on sequence data were compared with the accuracies from the 60 K SNP panel. Predictions were based on genomic best linear unbiased prediction (GBLUP) as well as a Bayesian variable selection model (BayesC). Moreover, the prediction accuracy from using different types of variants (synonymous, non‐synonymous and non‐coding SNPs) was evaluated. Genomic prediction using the 60 K SNP panel resulted in a prediction accuracy of 0.74 when GBLUP was applied. With sequence data, there was a small increase (~1%) in prediction accuracy over the 60 K genotypes. With both 60 K SNP panel and sequence data, GBLUP slightly outperformed BayesC in predicting the breeding values. Selection of SNPs more likely to affect the phenotype (i.e. non‐synonymous SNPs) did not improve the accuracy of genomic prediction. The fact that sequence data were based on imputation from a small number of sequenced animals may have limited the potential to improve the prediction accuracy. A small reference population (n = 1004) and possible exclusion of many causal SNPs during quality control can be other possible reasons for limited benefit of sequence data. We expect, however, that the limited improvement is because the 60 K SNP panel was already sufficiently dense to accurately determine the relationships between animals in our data.     

The effect of adipocyte and heart fatty acid-binding protein genes on intramuscular fat and backfat content in Meishan crossbred pigs

Effects of genetic variation in porcine adipocyte and heart fatty acid-binding protein genes, A-FABP and H-FABP, respectively, on intramuscular fat (IMF) content and backfat thickness (BFT) were examined in F2 crossbreds of Meishan and Western pigs. The involvement of each FABP gene in IMF accretion was studied to confirm previous results for Duroc pigs. The F2 crossbred pigs were genotyped for various markers including microsatellite sequences situated within both FABP genes. Linkage analysis assigned the A-FABP and H-FABP genes to marker intervals S0001-S0217 (20 cM) on SSC4 and Sw316-S0003 (16.6 cM) on SSC6, respectively, refining previous chromosomal assignments. Next, the role of both chromosome regions/genes on genetic variation in IMF content and BFT was studied by 1) screening SSC4 and SSC6 for QTL affecting both traits by performing a line-cross analysis and 2) estimation of the effect of individual A-FABP and H-FABP alleles on both traits. In the first analysis, suggestive and chromosome-wise significant evidence for a QTL affecting IMF was detected on SSC6. The H-FABP gene is a candidate gene for this effect because it resides within the large region containing this putative QTL. The second analysis showed a considerable but nonsignificant effect of H-FABP microsatellite alleles on IMF content. Suggestive evidence for a QTL affecting BFT was found on SSC6, but H-FABP was excluded as a candidate gene. In conclusion, present and previous results support involvement of H-FABP gene polymorphisms in IMF accretion independently from BFT in pigs. Therefore, implementation of these polymorphisms in marker-assisted selection to control IMF content independently from BFT may be considered. In contrast to previous findings for Duroc pigs, no evidence was found for an effect of the A-FABP gene on IMF or BFT in this population.     

Composition of seminal plasma and ovarian fluid in Ide Leuciscus idus and Northern pike Esox lucius

Seminal plasma (SP) and ovarian fluid (OF) plays an important role as storage media to prevent the activation of gametes both in vivo and under artificial conditions. The objectives of this study were to quantify gamete biochemistry and explore correlations among quantitative characteristics of SP, OF and sperm performance traits of Ide Leuciscus idus and Northern pike Esox lucius. Generally, Na⁺, K⁺ and Cl^? were found to be the most dominating ions, although concentrations of K⁺ were higher in SP, while Na⁺ and Cl^? concentrations were higher in OF for both species. Several significant correlations among the biochemical properties such as total protein, glucose, osmolality, cholesterol, K⁺, Ca²⁺, Cl^? and Mg²⁺ were observed for SP and OF. Total protein content of Ide SP was positively correlated with sperm activity traits (r ≥ .89, p ≤ .05), while K⁺ concentration was negatively correlated with sperm traits (r ≥ ?.89, p ≤ .05). Moreover, Ca²⁺ concentration in Northern pike SP was positively correlated with the percentage of sperm motility (r = . 98, p < .01). In conclusion, these results can be used to better understand the biochemistry of SP and OF, improve methods for short‐ and long‐term storage of gametes and standardize fertilization protocols.     

Detection and characterization of quantitative trait loci for meat quality traits in pigs.

In an experimental cross between Meishan and Dutch Large White and Landrace lines, 785 F2 animals with carcass information and their parents were typed for molecular markers covering the entire porcine genome. Linkage was studied between these markers and eight meat quality traits. Quantitative trait locus analyses were performed using interval mapping by regression under two genetic models: 1) the line-cross approach, where the founder lines were assumed to be fixed for different QTL alleles and 2) a half-sib model where a unique allele substitution effect was fitted within each of the 38 half-sib families. The line-cross approach included tests for genomic imprinting and sex-specific QTL effects. In total, three genome-wide significant and 26 suggestive QTL were detected. The significant QTL on chromosomes 3, 4, and 13, affecting meat color, were only detected under the half-sib model. Failure of the line-cross approach to detect the meat color QTL suggests that the founder lines have similar allele frequencies for these QTL. This study provides information on new QTL affecting meat quality traits. It also shows the benefit of analyzing experimental data under different genetic and statistical models.     

Uterine Responses to Exogenous Oxytocin Before and After Pre-partum Luteolysis in the Cow

The aim of this study was to test the functional status of uterine oxytocin receptors in cows in vivo around parturition. The animals received consecutive, intra‐arterial injections of 800, 1600 and 3200 mU of oxytocin at three different stages: during late gestation (days 260–274), at 12 h and at 24 h after intramuscular injection of a prostaglandin F_2α analogue at day 275 to induce parturition. Cows (n=6) had been provided with myometrial electrodes and a catheter had been installed in the aorta and in a branch of the uterine vein (UV). Regular blood samples were obtained from the UV from 5 min before until 45 min after each oxytocin injection to measure plasma levels of prostaglandin F_2α (PGF_2α) and oxytocin. Uterine electromyographic (EMG) activity was registered continuously during each experiment. The increase of oxytocin levels in UV plasma after intra‐arterial injections was dose dependent (p < 0.02). Pre‐ and post treatment oxytocin levels at 24 h after induction of parturition were significantly increased (p=0.0313). Both during late pregnancy and at 12 h after induction of parturition, oxytocin caused a significant increase in EMG activity (p=0.022). After the 3200 mU dose the increase was significantly higher than with the other 2 doses (p=0.004). After each dose, EMG activity returned to baseline levels within some 15 min. At 24 h after induction of parturition, the pre‐treatment level of EMG activity had increased. Doses of 800 mU and 1600 mU of oxytocin produced a significant (p=0.022) increment of EMG activity, which was of the same magnitude as during the preceding stages; after 3200 mU of oxytocin the response was significantly higher than before (p=0.008). No significant increases of PGF_2α levels in UV plasma could be measured after oxytocin injections at any of the three stages. It is concluded that the myometrium of the pregnant cow responds in vivo to physiological doses of oxytocin. At 24 h after induction of parturition, when luteolysis has occurred and a parturient pattern of parturient myometrial activity has already started to develop, the response is enhanced. Physiological doses of oxytocin did not evoke a spurt release of PGF_2α in uterine venous blood during the peripartal period.     

Smooth Muscle Cells of the Bovine Cervical Stroma may have a Secretory, rather than a Contractile Function during Parturition

The bovine cervix contains a large amount of smooth muscle cells distributed over an outer muscular layer and within a stromal layer. The stromal layer exhibits no electromyographic (EMG) activity at parturition. This leads to the question whether the stromal smooth muscle cells of the bovine cervix are prepared to contract with parturition, or whether they have another function. To this end, cervical biopsies were repeatedly taken from 10 pregnant cows at day-185 and -275 of gestation, at spontaneous, uncomplicated calving and at 30 days after calving. The smooth muscle bundles of the stroma were immunohistochemically analysed (n = 5) with regard to their integrity and cellular density, and the degree of staining for connexin-43, smooth muscle actin α (SMA), desmin and vimentin. Additionally, the mRNA expression for connexin-43, SMA, desmin and vimentin was determined with RT-PCR (n = 5). The smooth muscle tissue was arranged in bundles, also at parturition. However, the cellular density of these bundles and the SMA mRNA expression were decreased at parturition. Additionally, the SMA staining and connexin-43 expression and staining remained constant during pregnancy and at parturition. This might indicate that stromal smooth muscle cells are not prepared to contract with parturition, in contrast to the myometrial smooth muscle cells. The smooth muscle cells, stained for SMA, also expressed vimentin, and the proportion of co-expression was increased at day-275 of pregnancy. This suggests that the stromal smooth muscle cells predominantly have a secretory function in cows.     

Cervical Ripening and Parturition in Cows are Driven by a Cascade of Pro-Inflammatory Cytokines

The final stages of cervical ripening and parturition resemble an inflammatory process. Although the role of cytokines in both spontaneous and experimentally induced parturitions has been described in several small laboratory animals and humans, the involvement of pro‐inflammatory and regulatory cytokines in physiologic parturition in cows has not been determined. In this study, the cytokine expression profiles were assessed in bovine cervical tissue at several stages of pregnancy and at parturition. Serial biopsy samples of the cervix were obtained from 10 cows on day 185 and day 275 of pregnancy (which was on average 5.4 days before parturition) and at parturition. Messenger RNA expression levels of interleukin (IL)‐1β, IL‐6, IL‐8, IL‐10 and tumour necrosis factor (TNF)α were determined using real‐time polymerase chain reaction and the number of neutrophils and eosinophils was estimated by Luna and Sirius Red staining. At parturition, IL‐8 expression had increased 430‐fold (p < 0.001) when compared with that of the day 185 of pregnancy, large numbers of neutrophils had invaded the cervix while eosinophils remained scarce, IL‐1β had increased eightfold (p < 0.05) and IL‐6 had not changed significantly. Additionally, IL‐10 was increased by 10‐fold (p < 0.001) and TNFα decreased by 57% (p < 0.05) when compared with that of the day 185 of pregnancy. The large increase in expression of IL‐8, enabling the influx of neutrophils, is indicative of its important role in the final stage of cervical ripening and at parturition. As previous studies have shown that neutrophils excrete matrix metalloproteinases (MMP), this might contribute to softening of the cervix. In contrast, the only slightly increased levels of IL‐1, steady concentrations of IL‐6 and decreased TNFα, the potential consequences of increased IL‐10 expression, indicate that final cervical of cows in ripening at term parturition is an inflammatory process influenced by regulatory cytokines.