Genomic analysis of mobility measures on 5-month-old gilts associated with structural soundness.

Sow lameness results in premature culling, causing economic loss and well-being issues. A study, utilizing a pressure-sensing mat (GAIT4) and video monitoring system (NUtrack), was conducted to identify objective measurements on gilts that are predictive of future lameness. Gilts (N = 3656) were categorized to describe their lifetime soundness: SOUND, retained for breeding with no detected mobility issues; LAME_SOW, retained for breeding and detected lame as a sow; CULL_STR, not retained due to poor leg structure; LAME_GILT, not retained due to visible signs of lameness; and CULL, not retained due to reasons other than leg structure.

State-of-the-art performance of deep learning methods for pre-operative radiologic staging of colorectal cancer lymph node metastasis: a scoping review.

Objectives: To assess the current state-of-the-art in deep learning methods applied to pre-operative radiologic staging of colorectal cancer lymph node metastasis. Specifically, by evaluating the data, methodology and validation of existing work, as well as the current use of explainable AI in this fast-moving domain.

Design: Scoping review.

Delayed endometrial preparation for the induction of luteolysis as a potential factor for improved reproductive performance in Angus beef heifers with high antral follicle counts.

Antral Follicle Count (AFC) and anti-Müllerian hormone (AMH) concentrations are reflective for ovarian reserve and have been associated with improved reproductive performance in cattle. Key events for regulation of uterine receptivity are orchestrated by progesterone. As progesterone concentrations are greater in animals with high than low AFC, we tested the hypothesis, if the resulting improved uterine environment will lead to improved conceptus elongation and endometrial response to interferon tau.

Online feeding behavior monitoring of individual group-housed grow-finish pigs using a low-frequency RFID electronic feeding system.

Early identification of animals in need of management intervention is critical to maximize animal health and welfare and minimize issues with productivity. Feeding behavior, captured by automated feeding systems, can be used to monitor the health and welfare status of individual pigs. Here, we present a framework for monitoring feeding behavior of grow-finish pigs in real time, using a low-frequency radio frequency identification (RFID) system.

Clustering of multi-tissue transcriptomes in gilts with normal cyclicity or delayed puberty reveals genes related to pubertal development†.

In gilts, puberty is marked by standing estrus in the presence of a boar. Delayed puberty (DP; failure to display pubertal estrus) is a major reason for gilt removal. To investigate the physiological determinants underlying DP in gilts, transcriptomic data from tissues relevant to estrus and puberty, such as mediobasal hypothalamus, anterior pituitary gland, ovarian cortex, olfactory bulb, amygdala, and hippocampus, were obtained from age-matched DP (n = 8) and cyclic control gilts at follicular phase (n = 8) and luteal phase (n = 8) of the estrous cycle.

Long-term alliance for pathology equipment and technology acquisition: a paradigm shift for improved quality and efficiency.

Objective: Personnel costs are the largest single budget item in the clinical laboratory, other major expenses being equipment, analyzers, blood and blood components, and cost of day-to-day consumables. This report describes our experience with developing a long-term relationship with a single major vendor as a paradigm shift from the traditional multiple vendors, multiple contracts, and recurrent extended negotiations. Our objective was to develop a long-term approach for replacement of effete equipment and upgrades to operations in a pathology and laboratory medicine department in collaboration with vendors providing equipment and services.

gBLUP-GWAS identifies candidate genes, signaling pathways, and putative functional polymorphisms for age at puberty in gilts.

Successful development of replacement gilts determines their reproductive longevity and lifetime productivity. Selection for reproductive longevity is challenging due to low heritability and expression late in life. In pigs, age at puberty is the earliest known indicator for reproductive longevity and gilts that reach puberty earlier have a greater probability of producing more lifetime litters.

Recent developments and future directions in meta-analysis of differential gene expression in livestock RNA-Seq.

Decreases in the costs of high-throughput sequencing technologies have led to continually increasing numbers of livestock RNA-Seq studies in the last decade. Although the number of studies has increased dramatically, most livestock RNA-Seq experiments are limited by cost to a small number of biological replicates. Meta-analysis procedures can be used to integrate and jointly analyze data from multiple independent studies.

Genes Involved in Feed Efficiency Identified in a Meta-Analysis of Rumen Tissue from Two Populations of Beef Steers.

In cattle, the rumen is an important site for the absorption of feed by-products released by bacterial fermentation, and variation in ruminal function plays a role in cattle feed efficiency. Studies evaluating gene expression in the rumen tissue have been performed prior to this. However, validating the expression of genes identified in additional cattle populations has been challenging.

Dam parity structure and body condition during lactation influence piglet growth and gilt sexual maturation through pre-finishing.

Energy demands during lactation greatly influence sow body condition and piglet performance. We hypothesized that primiparous sows or sows with reduced body condition would produce piglets with reduced growth and delayed sexual maturation. Eight weekly farrowing seasons were used to evaluate sow body condition (post-farrowing, PF and weaning, WN) and piglet growth from 157 dams.

Global analysis of differential gene expression within the porcine conceptus transcriptome as it transitions through spherical, ovoid, and tubular morphologies during the initiation of elongation.

This study aimed to identify transcriptome differences between distinct or transitional stage spherical, ovoid, and tubular porcine blastocysts throughout the initiation of elongation. We performed a global transcriptome analysis of differential gene expression using RNA-Seq with high temporal resolution between spherical, ovoid, and tubular stage blastocysts at specific sequential stages of development from litters containing conceptus populations of distinct or transitional blastocysts. After RNA-Seq analysis, significant differentially expressed genes (DEGs) and pathways were identified between distinct morphologies or sequential development stages.

Gene expression in the amygdala and hippocampus of cyclic and acyclic gilts.

Age at first estrus is the earliest phenotypic indicator of future reproductive success of gilts. Prebreeding anestrus is a major reason for reproductive failure leading to culling of replacement gilts. The two types of prebreeding anestrus are delay in attaining puberty (prepubertal anestrus, PPA) and silent ovulation (behavioral anestrus, BA).

Hematology parameters as potential indicators of feed efficiency in pigs.

The identification of an inexpensive, indirect measure of feed efficiency in swine could be a useful tool to help identify animals with improved phenotypes to supplement expensive phenotypes including individual feed intakes. The purpose of this study was to determine whether hematology parameters in pigs at the beginning and end of a feed efficiency study, or changes in those values over the study, were associated with average daily gain (ADG), average daily feed intake (ADFI), or gain-to-feed (G:F). Whole blood samples were taken at days 0 and 42 from pigs ( = 178) that were monitored for individual feed intakes and body weight gain during a 6-week study.

Characterization and comparative analysis of transcriptional profiles of porcine colostrum and mature milk at different parities.

Background: Porcine milk is a complex fluid, containing a myriad of immunological, biochemical, and cellular components, made to satisfy the nutritional requirements of the neonate. Whole milk contains many different cell types, including mammary epithelial cells, neutrophils, macrophages, and lymphocytes, as well nanoparticles, such as milk exosomes. To-date, only a limited number of livestock transcriptomic studies have reported sequencing of milk.

Rumen epithelial transcriptome and microbiome profiles of rumen epithelium and contents of beef cattle with and without liver abscesses.

Abscess is the highest cause of liver condemnation and is estimated to cost the beef industry US$64 million annually. Fusobacterium necrophorum, commonly found in the bovine rumen, is the primary bacteria associated with liver abscess in cattle. Theoretically, damage to the rumen wall allows F.

Assessment of Imputation from Low-Pass Sequencing to Predict Merit of Beef Steers.

Decreasing costs are making low coverage sequencing with imputation to a comprehensive reference panel an attractive alternative to obtain functional variant genotypes that can increase the accuracy of genomic prediction. To assess the potential of low-pass sequencing, genomic sequence of 77 steers sequenced to >10X coverage was downsampled to 1X and imputed to a reference of 946 cattle representing multiple and -influenced breeds. Genotypes for nearly 60 million variants detected in the reference were imputed from the downsampled sequence.

Feeding behavior of grow-finish swine and the impacts of heat stress.

Heat stress has negative impacts on pork production, particularly in the grow-finish phase. During heat stress events, the feeding behavior of pigs is altered to reduce heat production. Several different systems have been developed to study feeding behavior.

Using SNP Weights Derived From Gene Expression Modules to Improve GWAS Power for Feed Efficiency in Pigs.

The "large small " problem has posed a significant challenge in the analysis and interpretation of genome-wide association studies (GWAS). The use of prior information to rank genomic regions and perform SNP selection could increase the power of GWAS. In this study, we propose the use of gene expression data from RNA-Seq of multiple tissues as prior information to assign weights to SNP, select SNP based on a weight threshold, and utilize weighted hypothesis testing to conduct a GWAS.

Genes associated with body weight gain and feed intake identified by meta-analysis of the mesenteric fat from crossbred beef steers.

Mesenteric fat is a visceral fat depot that increases with cattle maturity and can be influenced by diet. There may be a relationship between the accumulation of mesenteric fat and feed efficiency in beef cattle. The purpose of this study was to identify genes that may be differentially expressed in steers with high and low BW gain and feed intake.

A Survey of Copy Number Variation in the Porcine Genome Detected From Whole-Genome Sequence.

Copy number variations (CNVs) are gains and losses of large regions of genomic sequence between individuals of a species. Although CNVs have been associated with various phenotypic traits in humans and other species, the extent to which CNVs impact phenotypic variation remains unclear. In swine, as well as many other species, relatively little is understood about the frequency of CNV in the genome, sizes, locations, and other chromosomal properties.

Evaluation of genotype quality parameters for SowPro90, a new genotyping array for swine1.

Understanding early predictors of sow fertility has the potential to improve genomic predictions. A custom SNP array (SowPro90 produced by Affymetrix) was developed to include genetic variants overlapping quantitative trait loci for age at puberty, one of the earliest indicators of sow fertility, as well as variants related to innate and adaptive immunity. The polymorphisms included in the custom genotyping array were identified using multiple genomic approaches including deep genomic and transcriptomic sequencing and genome-wide associations.

Porcine single nucleotide polymorphisms and their functional effect: an update.

Objective: To aid in the development of a comprehensive list of functional variants in the swine genome, single nucleotide polymorphisms (SNP) were identified from whole genome sequence of 240 pigs. Interim data from 72 animals in this study was published in 2017. This communication extends our previous work not only by utilizing genomic sequence from additional animals, but also by the use of the newly released Sscrofa 11.

Neonatal lactocrine deficiency affects the adult porcine endometrial transcriptome at pregnancy day 13.

Reproductive performance of female pigs that do not receive sufficient colostrum from birth is permanently impaired. Whether lactocrine deficiency, reflected by low serum immunoglobulin immunocrit (iCrit), affects patterns of endometrial gene expression during the periattachment period of early pregnancy is unknown. Here, objectives were to determine effects of low iCrit at birth on the adult endometrial transcriptome on pregnancy day (PxD) 13.