Tailoring Genomic Selection for : A Comprehensive Review of SNP Arrays and Reference Genomes.

Background: Advances in SNP arrays and reference genome assemblies have significantly transformed cattle genomics, particularly for (Zebu cattle). Many commercial SNP arrays were originally designed for , leading to ascertainment bias and the exclusion of crucial SNPs specific to Zebu populations. This review assesses progress in SNP array and reference genome development, with a focus on efforts tailored to Zebu populations and their impact on genomic selection and breeding efficiency.

The effect of electronic cooling pads and Moringa oleifera supplementation from late gestation to weaning on sow production performance under heat stress conditions.

Lactating sows and their litters are particularly vulnerable to heat stress (HS). HS decreases fertility, feed intake, milk production, and litter growth of sows. Approaches are needed to mitigate the negative effects of HS on animal welfare and oxidative damage to tissues.

Deciphering Estrus Expression in Gilts: The Role of Alternative Polyadenylation and LincRNAs in Reproductive Transcriptomics.

The fertility rate and litter size of female pigs are critically affected by the expression of estrus. The objective of this study was to elucidate the regulatory mechanisms of estrus expression by analyzing the differential expression of genes and long intergenic non-coding RNAs (lincRNA), as well as the utilization of alternative polyadenylation (APA) sites, in the vulva and vagina during the estrus and diestrus stages of Large White and indigenous Chinese Mi gilts. Our study revealed that the number of differentially expressed genes (DEG) in the vulva was less than that in the vagina, and the DEGs in the vulva were enriched in pathways such as "neural" pathways and steroid hormone responses, including the "Calcium signaling pathway" and "Oxytocin signaling pathway".

A Functional Single Nucleotide Polymorphism in the 3' Untranslated Region of the Porcine JARID2 Gene Is Associated with Aggressive Behavior of Weaned Pigs after Mixing.

In pig production, pigs often show more aggressive behavior after mixing, which adversely affects animal welfare and growth performance. The Jumonji and structural domain-rich AT interaction domain 2 (JARID2) gene plays an important role in neurodevelopment in mice and various psychiatric disorders in humans. The JARID2 gene may impact the aggressive behavior of pigs.

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.

Production and meat quality traits of genetically lean immunocastrated pigs naturally divergent for loin tenderness.

Warner-Bratzler Shear Force (WBSF) is a quantitative measurement of meat toughness that has great impact on the consumer acceptability of meat. This study was conducted to evaluate growth performance, carcass and meat quality characteristics, and fatty acids profile of longissimus lumborum (LL) intramuscular fat (IMF) of pigs that are genetically divergent for WBSF. Based on WBSF values of the LL from a previous study, 12 immunocastrated male pigs selected from 96 pigs were divided into two groups with high WBSF (53.

Characterization and analysis of transcriptomes of multiple tissues from estrus and diestrus in pigs.

A comprehensive understanding of the complex regulatory mechanisms governing estrus and ovulation across multiple tissues in mammals is imperative to improve the reproductive performance of livestock and mitigate ovulation-related disorders in humans. To comprehensively elucidate the regulatory landscape, we analyzed the transcriptome of protein-coding genes and long intergenic non-coding RNAs (lincRNAs) in 58 samples (including the hypothalamus, pituitary, ovary, vagina, and vulva) derived from European Large White gilts and Chinese Mi gilts during estrus and diestrus. We constructed an intricate regulatory network encompassing 358 hub genes across the five examined tissues.

Genomic background of biotypes related to growth, carcass and meat quality traits in Duroc pigs based on principal component analysis.

As the swine industry continues to explore pork quality traits alongside growth, feed efficiency and carcass leanness traits, it becomes imperative to understand their underlying genetic relationships. Due to this increase in the number of desirable traits, animal breeders must also consider methods to efficiently perform direct genetic changes for each trait and evaluate alternative selection indexes with different sets of phenotypic measurements. Principal component analysis (PCA) and genome-wide association studies (GWAS) can be combined to understand the genetic architecture and biological mechanisms by defining biological types (biotypes) that relate these valuable traits.

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).

Postmortem Metabolism and Pork Quality Development Are Affected by Electrical Stimulation across Three Genetic Lines.

Variations in postmortem metabolism in muscle impact pork quality development. Curiously, some genetic lines are more refractile to adverse pork quality development than others and may regulate energy metabolism differently. The aim of this study was to challenge pork carcasses from different genetic populations with electrical stimulation (ES) to determine how postmortem metabolism varies with genetic line and explore control points that reside in glycolysis in dying muscle.

Feeding a whole-cell inactivated yeast to gestating and lactating sows in a commercial production system.

A total of 606 sows (PIC 1050) and their progeny (PIC 1050 × 280) were used to determine if feeding gestating and lactating sows a proprietary strain of as a whole-cell inactivated yeast product (; CitriStim, ADM Animal Nutrition, Quincy, IL) improves sow and litter performance in a commercial production system. Once confirmed pregnant at d 35 post-breeding pregnancy check, sows were fed a basal gestation control () diet (0.55% SID lysine) or the control diet fortified with 0.

A behavior and physiology-based decision support tool to predict thermal comfort and stress in non-pregnant, mid-gestation, and late-gestation sows.

Background: Although thermal indices have been proposed for swine, none to our knowledge differentiate by reproductive stage or predict thermal comfort using behavioral and physiological data. The study objective was to develop a behavior and physiology-based decision support tool to predict thermal comfort and stress in multiparous (3.28 ± 0.

Development of a Swine Production Cost Calculation Model.

This paper aims to present a tool that offers pig producers a standard method to calculate and control their production costs and, consequently, provides the necessary information to guide strategic decision-making. Following these premises, a mathematical model to estimate swine production costs were developed using Microsoft Excel software (version 2207). Case studies were used to assist in the characterization and construction of the model.

Genome-Wide Detection of Copy Number Variations and Evaluation of Candidate Copy Number Polymorphism Genes Associated With Complex Traits of Pigs.

Copy number variation (CNV) has been considered to be an important source of genetic variation for important phenotypic traits of livestock. In this study, we performed whole-genome CNV detection on Suhuai (SH) ( = 23), Chinese Min Zhu (MZ) ( = 11), and Large White (LW) ( = 12) pigs based on next-generation sequencing data. The copy number variation regions (CNVRs) were annotated and analyzed, and 10,885, 10,836, and 10,917 CNVRs were detected in LW, MZ, and SH pigs, respectively.

The importance of optimal body condition to maximise reproductive health and perinatal outcomes in pigs.

Overnutrition or undernutrition during all or part of the reproductive cycle predisposes sows to metabolic consequences and poor reproductive health which contributes to a decrease in sow longevity and an increase in perinatal mortality. This represents not only an economic problem for the pig industry but also results in poor animal welfare. To maximise profitability and increase sustainability in pig production, it is pivotal to provide researchers and practitioners with synthesised information about the repercussions of maternal obesity or malnutrition on reproductive health and perinatal outcomes, and to pinpoint currently available nutritional managements to keep sows' body condition in an optimal range.

A Single-Nucleotide Polymorphism in the Promoter of Porcine Gene Regulates Aggressive Behavior of Weaned Pigs After Mixing by Affecting the Binding of Transcription Factor p53.

Pigs are important biomedical model animals for the study of human neurological diseases. Similar to human aggressive behavior in children and adolescents, weaned pigs also show more aggressive behavior after mixing, which has negative effects on animal welfare and growth performance. The identification of functional single-nucleotide polymorphisms (SNPs) related to the aggressive behavior of pigs would provide valuable molecular markers of the aggressive behavioral trait for genetic improvement program.

Identification of functional single nucleotide polymorphisms in the porcine SLC6A4 gene associated with aggressive behavior in weaned pigs after mixing.

Variation in genes of the serotonergic system influences aggressive behavior by affecting serotonin levels in the central and cortical nervous system. SLC6A4 (serotonin transporter) is a master regulator of 5-HT signaling and involved in the regulation of aggressive behavior in humans and rodents. To identify potential functional single nucleotide polymorphisms (SNPs) for the porcine SLC6A4 gene associated with aggressive behavior, a total of 500 pigs (268 barrows and 232 gilts) were selected and mixed in 51 pens.

Functionally Antagonistic Transcription Factors IRF1 and IRF2 Regulate the Transcription of the Dopamine Receptor D2 Gene Associated with Aggressive Behavior of Weaned Pigs.

Aggressive behavior has negative effects on animal welfare and growth performance in pigs. The dopamine receptor D2 (DRD2) has a critical neuromodulator role in the dopamine signal pathway within the brain to control behavior. A functional single-nucleotide polymorphism (SNP), rs1110730503, in the promoter region of the porcine DRD2 gene was identified, which affects aggressive behavior in pigs.

Characterizing the effect of incrementally increasing dry bulb temperature on linear and nonlinear measures of heart rate variability in nonpregnant, mid-gestation, and late-gestation sows.

Characterizing the sow physiological response to an increased heat load is essential for effective heat stress mitigation. The study objective was to characterize the effects of a 400-min heating episode on sow heart rate variability (HRV) at different reproductive stages. HRV is a commonly used noninvasive proxy measure of autonomic function.