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.

Analysis of polygenic selection in purebred and crossbred pig genomes using generation proxy selection mapping.

Background: Artificial selection on quantitative traits using breeding values and selection indices in commercial livestock breeding populations causes changes in allele frequency over time at hundreds or thousands of causal loci and the surrounding genomic regions. In population genetics, this type of selection is called polygenic selection. Researchers and managers of pig breeding programs are motivated to understand the genetic basis of phenotypic diversity across genetic lines, breeds, and populations using selection mapping analyses.

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.

Effect of rearing cross-fostered piglets in litters of differing size relative to sow functional teat number on preweaning growth and mortality.

Litter sizes of commercial sows have increased considerably over recent decades, and often exceed the number of functional teats on the sow. The objective of this study was to evaluate the effect of litter size after cross-fostering relative to sow functional teat number on piglet preweaning growth and mortality. A total of 39 litters (561 piglets) were used in a randomized complete block design; blocking factors were farrowing day and sow parity, body condition score, and functional teat number.

Effect of within-litter birth weight variation after cross-fostering on piglet preweaning growth and mortality.

Cross-fostering is commonly used in commercial swine production to equalize litter sizes and/or adjust piglet birth weights within litters. However, there is limited published information on optimum cross-fostering procedures. This study evaluated the effects of within-litter birth weight variation after cross-fostering (using litters of 14 piglets) on piglet preweaning mortality (PWM) and weaning weight (WW).

Microbial composition differs between production systems and is associated with growth performance and carcass quality in pigs.

Background: The role of the microbiome in livestock production has been highlighted in recent research. Currently, little is known about the microbiome's impact across different systems of production in swine, particularly between selection nucleus and commercial populations. In this paper, we investigated fecal microbial composition in nucleus versus commercial systems at different time points.

Effect of farrowing pen size on pre-weaning performance of piglets.

Litter sizes in commercial pig production have increased substantially over recent years; however, farrowing pen sizes have generally not changed over the same time period. The objective of this study was to evaluate the effect of farrowing pen size on piglet pre-weaning growth and mortality. Differences in pen size were created by varying the width of pens of the same length, increasing the creep area available to the piglets.

Effect of drying and/or warming piglets at birth under warm farrowing room temperatures on piglet rectal temperature over the first 24 h after birth.

Piglets experience a decline in body temperature immediately after birth, and both drying and warming piglets at birth reduce this. However, these interventions may be less effective at higher farrowing room temperatures. This study was carried out at a commercial facility to compare the effect of drying and/or warming piglets at birth on postnatal rectal temperature () under relatively warm farrowing room temperatures (26.

Effects of drying and providing supplemental oxygen to piglets at birth on rectal temperature over the first 24 h after birth.

Neonatal piglets can experience both a decrease in body temperature and hypoxia, increasing risks for pre-weaning mortality. This research evaluated the effects of drying and providing supplemental oxygen to newborn piglets on rectal temperature (RT) over the first 24 h after birth. The study used a CRD with three Intervention Treatments (IT; applied at birth): Control (no intervention), Drying (dried using a desiccant), Oxygen [dried using a desiccant and placed in a chamber (at 40% oxygen concentration) for 20 min].

Genetic Parameters for Tolerance to Heat Stress in Crossbred Swine Carcass Traits.

Data for loin and backfat depth, as well as carcass growth of 126,051 three-way crossbred pigs raised between 2015 and 2019, were combined with climate records of air temperature, relative humidity, and temperature-humidity index. Environmental covariates with the largest impact on the studied traits were incorporated in a random regression model that also included genomic information. Genetic control of tolerance to heat stress and the presence of genotype by environment interaction were detected.

Gut microbiome mediates host genomic effects on phenotypes: a case study with fat deposition in pigs.

A large number of studies have highlighted the importance of gut microbiome composition in shaping fat deposition in mammals. Several studies have also highlighted how host genome controls the abundance of certain species that make up the gut microbiota. We propose a systematic approach to infer how the host genome can control the gut microbiome, which in turn contributes to the host phenotype determination.

Effect of drying and/or warming piglets at birth on rectal temperature over the first 24 h after birth.

Piglets experience a rapid decrease in body temperature immediately after birth, increasing the risk of mortality. The objective of this study was to determine the effect of drying and/or warming piglets at birth on rectal temperature over the first 24 h after birth. The study was carried out at a commercial sow facility using a completely randomized design with four treatments (applied to piglets at birth): Control (no drying or warming), Desiccant (dried using a desiccant), Warming Box (placed in a box under a heat lamp for 30 min), and Desiccant + Warming Box (both dried and warmed as above).

Effect of method of drying piglets at birth on rectal temperature over the first 24 h after birth.

Piglets are born wet, and evaporation of that moisture decreases body temperature, increasing the risk of mortality. The objective of this study was to compare the effect of two commercially applicable methods for drying piglets at birth on piglet rectal temperature over 24 h after birth. The study was carried out in standard commercial farrowing facilities with 52 litters, using a completely randomized design with three Drying Treatments: Control (not dried); Desiccant (dried at birth using a cellulose-based desiccant); Paper Towel (dried at birth using paper towels).

Heritability and genome-wide association of swine gut microbiome features with growth and fatness parameters.

Despite recent efforts to characterize longitudinal variation in the swine gut microbiome, the extent to which a host's genome impacts the composition of its gut microbiome is not yet well understood in pigs. The objectives of this study were: i) to identify pig gut microbiome features associated with growth and fatness, ii) to estimate the heritability of those features, and, iii) to conduct a genome-wide association study exploring the relationship between those features and single nucleotide polymorphisms (SNP) in the pig genome. A total of 1,028 pigs were characterized.

Increasing the ratio of SID lysine to metabolizable energy improves pig performance during a viral challenge.

Porcine reproductive and respiratory syndrome virus (PRRSV) compromises pig performance. However, increasing standardized ileal digestible Lys per Mcal metabolizable energy (SID Lys:ME) above requirement has been shown to mitigate reduced performance seen during a porcine reproductive and respiratory syndrome (PRRS) virus challenge. The objective of this study was to evaluate the effects of increasing the dietary SID Lys:ME from 100% National Research Council (NRC) requirement to 120% of the requirement in vaccinated (vac+; modified live vaccine Ingelvac PRRS) and non-vaccinated (vac-; no PRRS vaccine) grower pigs subjected to a PRRSV challenge.

Predicting Growth and Carcass Traits in Swine Using Microbiome Data and Machine Learning Algorithms.

In this paper, we evaluated the power of microbiome measures taken at three time points over the growth test period (weaning, 15 and 22 weeks) to foretell growth and carcass traits in 1039 individuals of a line of crossbred pigs. We measured prediction accuracy as the correlation between actual and predicted phenotypes in a five-fold cross-validation setting. Phenotypic traits measured included live weight measures and carcass composition obtained during the trial as well as at slaughter.

Increased lysine: metabolizable energy ratio improves grower pig performance during a porcine reproductive and respiratory syndrome virus challenge.

Porcine reproductive and respiratory syndrome virus (PRRSV) reduces grower pig performance. The amino acid (AA) requirements and lysine:metabolizable energy ratio (Lys:ME) of health-challenged pigs for optimum performance are poorly understood. Two experiments were conducted to evaluate the effect of increasing standardized ileal digestible (SID) Lys:ME (g SID Lys per Mcal ME) on growth performance during a PRRSV challenge.

Host contributes to longitudinal diversity of fecal microbiota in swine selected for lean growth.

Background: In pigs, gut bacteria have been shown to play important roles in nutritional, physiological, and immunological processes in the host. However, the contribution of their metagenomes or part of them, which are normally reflected by fragments of 16S rRNA-encoding genes, has yet to be fully investigated.

Results: Fecal samples, collected from a population of crossbred pigs at three time points, including weaning, week 15 post weaning (hereafter "week 15"), and end-of-feeding test (hereafter "off-test"), were used to evaluate changes in the composition of the fecal microbiome of each animal over time.