Maternal Supplementation of Dietary Choline and Docosahexaenoic Acid during Gestational Nutrition Restriction Alters Hepatic mRNA and miRNA Expression Patterns in Full-Term Fetal Pigs.

Background: Supplementing choline and docosahexaenoic acid (DHA) to pregnant gilts modified fetal pig hepatic global DNA methylation induced by gestational malnutrition, suggesting that gene expression and regulation and its associated metabolic pathways are affected in the liver of offspring during growth and development.

Objective: To investigate the effect of maternal supplementation of choline, DHA and their interaction on hepatic mRNA expression, miRNA regulation and metabolic pathways in the fetal pigs born to malnourished mothers.

Methods: The abundance of mRNA and miRNA was profiled in fetal liver from sows with undernutrition supplemented with choline and DHA in a 2 × 2 factorial design.

Optimizing genetic diversity in Australian Holsteins and Jerseys: A comparative analysis of whole-genome and regional inbreeding depression effects.

Homozygosity, which can arise from several genetic mechanisms including inbreeding, is frequently observed in the offspring of related parents. This inbreeding can lead to a reduced performance, due to a phenomenon known as inbreeding depression. This study assessed inbreeding depression using whole genome and regional approaches in first-lactation Australian Holsteins and Jerseys, involving approximately 33,000 Holstein and 7,000 Jersey cows born between 2000 and 2017.

Capturing resilience from phenotypic deviations: a case study using feed consumption and whole genome data in pigs.

Background: In recent years, interest has grown in quantifying resilience in livestock by examining deviations in target phenotypes. This method is based on the idea that variability in these phenotypes reflects an animal's ability to adapt to external factors. By utilizing routinely collected time-series feed intake data in pigs, researchers can obtain a broad measure of resilience.

Effects of germplasm exchange strategies on genetic gain, homozygosity, and genetic diversity in dairy stud populations: A simulation study.

Although genomic selection has led to considerable improvements in genetic gain, it has also seemingly led to increased rates of inbreeding and homozygosity, which can negatively affect genetic diversity and the long-term sustainability of dairy populations. Using genotypes from US Holstein animals from 3 distinct stud populations, we performed a simulation study consisting of 10 rounds of selection, with each breeding population composed of 200 males and 2,000 females. The investigated selection strategies consisted of selection using true breeding values, EBV, EBV penalized for the average future genomic inbreeding of progeny (PEN-EBV), or random selection (RAND).

Detection and evaluation of parameters influencing the identification of heterozygous-enriched regions in Holstein cattle based on SNP chip or whole-genome sequence data.

Background: A heterozygous-enriched region (HER) is a genomic region with high variability generated by factors such as balancing selection, introgression, and admixture processes. In this study, we evaluated the genomic background of HERs and the impact of different parameters (i.e.

Multiple-trait genomic prediction for swine meat quality traits using gut microbiome features as a correlated trait.

Traits such as meat quality and composition are becoming valuable in modern pork production; however, they are difficult to include in genetic evaluations because of the high phenotyping costs. Combining genomic information with multiple-trait indirect selection with cheaper indicator traits is an alternative for continued cost-effective genetic improvement. Additionally, gut microbiome information is becoming more affordable to measure using targeted rRNA sequencing, and its applications in animal breeding are becoming relevant.

Investigation of cosmopolitan and local Italian beef cattle breeds uncover common patterns of heterozygosity.

The analysis of livestock heterozygosity is less common compared to the study of homozygous patterns. Heterozygous-Rich Regions (HRRs) may harbor significant loci for functional traits such as immune response, survival rate, and fertility. For this reason, this study was conducted to investigate and characterize the heterozygosity patterns of four beef cattle breeds, which included two cosmopolitan breeds (Limousine and Charolaise) and two local breeds (Sarda and Sardo Bruna).

A first characterization of the microbiota-resilience link in swine.

Background: The gut microbiome plays a crucial role in understanding complex biological mechanisms, including host resilience to stressors. Investigating the microbiota-resilience link in animals and plants holds relevance in addressing challenges like adaptation of agricultural species to a warming environment. This study aims to characterize the microbiota-resilience connection in swine.

The potential of microbiota information to better predict efficiency traits in growing pigs fed a conventional and a high-fiber diet.

Background: Improving pigs' ability to digest diets with an increased dietary fiber content is a lever to improve feed efficiency and limit feed costs in pig production. The aim of this study was to determine whether information on the gut microbiota and host genetics can contribute to predict digestive efficiency (DE, i.e.

Longitudinal genomic analyses of automatically-recorded vaginal temperature in lactating sows under heat stress conditions based on random regression models.

Background: Automatic and continuous recording of vaginal temperature (T) using wearable sensors causes minimal disruptions to animal behavior and can generate data that enable the evaluation of temporal body temperature variation under heat stress (HS) conditions. However, the genetic basis of T in lactating sows from a longitudinal perspective is still unknown. The objectives of this study were to define statistical models and estimate genetic parameters for T in lactating sows using random regression models, and identify genomic regions and candidate genes associated with HS indicators derived from automatically-recorded T.

Inbreeding depression for producer-recorded udder, metabolic, and reproductive diseases in US dairy cattle.

This study leveraged a growing dataset of producer-recorded phenotypes for mastitis, reproductive diseases (metritis and retained placenta), and metabolic diseases (ketosis, milk fever, and displaced abomasum) to investigate the potential presence of inbreeding depression for these disease traits. Phenotypic, pedigree, and genomic information were obtained for 354,043 and 68,292 US Holstein and Jersey cows, respectively. Total inbreeding coefficients were calculated using both pedigree and genomic information; the latter included inbreeding estimates obtained using a genomic relationship matrix and runs of homozygosity.

Domestication shapes the pig gut microbiome and immune traits from the scale of lineage to population.

Animal ecology and evolution have long been known to shape host physiology, but more recently, the gut microbiome has been identified as a mediator between animal ecology and evolution and health. The gut microbiome has been shown to differ between wild and domestic animals, but the role of these differences for domestic animal evolution remains unknown. Gut microbiome responses to new animal genotypes and local environmental change during domestication may promote specific host phenotypes that are adaptive (or not) to the domestic environment.

Genetic parameters for automatically-measured vaginal temperature, respiration efficiency, and other thermotolerance indicators measured on lactating sows under heat stress conditions.

Background: Genetic selection based on direct indicators of heat stress could capture additional mechanisms that are involved in heat stress response and enable more accurate selection for more heat-tolerant individuals. Therefore, the main objectives of this study were to estimate genetic parameters for various heat stress indicators in a commercial population of Landrace × Large White lactating sows measured under heat stress conditions. The main indicators evaluated were: skin surface temperatures (SST), automatically-recorded vaginal temperature (T), respiration rate (RR), panting score (PS), body condition score (BCS), hair density (HD), body size (BS), ear size, and respiration efficiency (R).

Imputation accuracy from low- to medium-density SNP chips for US crossbred dairy cattle.

This study aimed at evaluating the quality of imputation accuracy (IA) by marker (IA) and by individual (IA) in US crossbred dairy cattle. Holstein × Jersey crossbreds were used to evaluate IA from a low- (7K) to a medium-density (50K) SNP chip. Crossbred animals, as well as their sires (53), dams (77), and maternal grandsires (63), were all genotyped with a 78K SNP chip.

Dietary Prebiotic Oligosaccharides and Arachidonate Alter the Fecal Microbiota and Mucosal Lipid Composition of Suckling Pigs.

Background: Early intestinal development is important to infant vitality, and optimal formula composition can promote gut health.

Objectives: The objectives were to evaluate the effects of arachidonate (ARA) and/or prebiotic oligosaccharide (PRE) supplementation in formula on the development of the microbial ecosystem and colonic health parameters.

Methods: Newborn piglets were fed 4 formulas containing ARA [0.

SLEMM: million-scale genomic predictions with window-based SNP weighting.

Motivation: The amount of genomic data is increasing exponentially. Using many genotyped and phenotyped individuals for genomic prediction is appealing yet challenging.

Results: We present SLEMM (short for Stochastic-Lanczos-Expedited Mixed Models), a new software tool, to address the computational challenge.

MicroRNA and mRNA sequencing analyses reveal key hepatic metabolic and signaling pathways responsive to maternal undernutrition in full-term fetal pigs.

Maternal undernutrition is highly prevalent in developing countries, leading to severe fetus/infant mortality, intrauterine growth restriction, stunting, and severe wasting. However, the potential impairments of maternal undernutrition to metabolic pathways in offspring are not defined completely. In this study, 2 groups of pregnant domestic pigs received nutritionally balanced gestation diets with or without 50% feed intake restriction from 0 to 35 gestation days and 70% from 35 to 114 gestation days.

Genomic characterization of autozygosity and recent inbreeding trends in all major breeds of US dairy cattle.

Maintaining a genetically diverse dairy cattle population is critical to preserving adaptability to future breeding goals and avoiding declines in fitness. This study characterized the genomic landscape of autozygosity and assessed trends in genetic diversity in 5 breeds of US dairy cattle. We analyzed a sizable genomic data set containing 4,173,679 pedigreed and genotyped animals of the Ayrshire, Brown Swiss, Guernsey, Holstein, and Jersey breeds.

Gut microbiota and host genetics contribute to the phenotypic variation of digestive and feed efficiency traits in growing pigs fed a conventional and a high fiber diet.

Background: Breeding pigs that can efficiently digest alternative diets with increased fiber content is a viable strategy to mitigate the feed cost in pig production. This study aimed at determining the contribution of the gut microbiota and host genetics to the phenotypic variability of digestive efficiency (DE) traits, such as digestibility coefficients of energy, organic matter and nitrogen, feed efficiency (FE) traits (feed conversion ratio and residual feed intake) and growth traits (average daily gain and daily feed intake). Data were available for 791 pigs fed a conventional diet and 735 of their full-sibs fed a high-fiber diet.

Genotyping and phenotyping strategies for genetic improvement of meat quality and carcass composition in swine.

Background: Meat quality and composition traits have become valuable in modern pork production; however, genetic improvement has been slow due to high phenotyping costs. Combining genomic information with multi-trait indirect selection based on cheaper indicator traits is an alternative for continued cost-effective genetic improvement.

Methods: Data from an ongoing breeding program were used in this study.