Genetic control of complex traits, with a focus on reproduction in pigs

Identification of Candidate Genes and eQTLs Related to Porcine Reproductive Function

Expression quantitative trait locus (eQTL) mapping is an effective tool for identifying genetic variations that regulate gene expression. An increasing number of studies suggested that SNPs associated with complex traits in farm animals are considered as expression quantitative trait loci. Identifying eQTLs associated with gene expression levels in the endometrium helps to unravel the regulatory mechanisms of genes related to reproductive functions in this tissue and provides molecular markers for the genetic improvement of high-fertility sow breeding. In this study, 218 RNA-seq data from pig endometrial tissue were used for eQTL analysis to identify genetic variants regulating gene expression. Additionally, weighted gene co-expression network analysis (WGCNA) was performed to identify hub genes involved in reproductive functions. The eQTL analysis identified 34,876 significant cis-eQTLs regulating the expression of 5632 genes (FDR ≤ 0.05), and 90 hub genes were identified by WGCNA analysis. By integrating eQTL and WGCNA results, 14 candidate genes and 16 fine-mapped cis-eQTLs were identified, including FRK, ARMC3, SLC35F3, TMEM72, FFAR4, SOWAHA, PSPH, FMO5, HPN, FUT2, RAP1GAP, C6orf52, SEL1L3, and CLGN, which were involved in the physiological processes of reproduction in sows through hormone regulation, cell adhesion, and amino acid and lipid metabolism. These eQTLs regulate the high expression of candidate genes in the endometrium, thereby affecting reproductive-related physiological functions. These findings enhance our understanding of the genetic basis of reproductive traits and provide valuable genetic markers for marker-assisted selection (MAS), which can be applied to improve sow fecundity and optimize breeding strategies for high reproductive performance.

Genetic strategies for enhancing litter size and birth weight uniformity in piglets

This study aimed to estimate the genetic parameters and develop selection indices for litter size and birth weight uniformity in piglets. These traits are crucial for improving productivity and profitability of swine production. Data were collected from 9,969 litters of 4,465 sows and 106,463 piglets of various breeds from a farm in Thailand. The analyzed traits included the total number born (TNB), number born alive (NBA), litter birth weight (LBW), mean birth weight, and individual birth weight. The assessed piglet uniformity traits included the difference between the maximum and minimum values (range), interquartile range of birth weight (IQRBW), variance in birth weight (VBW), standard deviation of birth weight (SDBW), and coefficient of variation of birth weight (CVBW). Variance components and genetic parameters were estimated using a multiple-trait animal model and the average information-restricted maximum likelihood method. The appropriate selection index (I) was determined based on heritability, genetic correlations between traits, and the economic significance of the traits. The results revealed that litter size traits (TNB and NBA) and piglet birth weight uniformity traits (Range, IQRBW, VBW, SDBW, and CVBW) exhibited low heritability (p < 0.1), suggesting that environmental factors have a substantial influence. In contrast, birth weight traits showed moderate heritability (approximately 0.2). Negative genetic correlations between litter size and birth weight traits were observed, indicating that increasing litter size might reduce piglet birth weight and uniformity, potentially affecting survival rate. A selection index combining NBA, LBW, and CVBW was constructed to optimize the selection process for productivity and uniformity. In conclusion, genetic improvement programs should prioritize litter size and birth weight uniformity to enhance productivity and uniformity on commercial pig farms. These findings can assist breeders in developing more effective selection strategies, ultimately resulting in larger, more uniform litters and improved overall farm efficiency.

Effect of heat stress on pig production and its mitigation strategies: a review

Heat stress (HS) poses a significant challenge to pig production worldwide, with far-reaching consequences for productivity, reproduction, and overall animal welfare. Stress, broadly defined as the nonspecific physiological response to environmental demands, disrupts homeostasis, leading to health imbalances, behavioral changes, and reduced productive efficiency. Pigs are particularly susceptible to HS due to their limited thermoregulatory capacity, influenced by a low density of functional sweat glands and a thick subcutaneous fat layer. Rising global temperatures have exacerbated HS-induced economic losses in the swine industry, manifesting as decreased growth rates, poor reproductive performance, reduced feed efficiency, increased morbidity, and mortality. HS impairs pig production by diminishing feed intake and nutrient availability, which leads to reduced growth, suboptimal carcass quality, and compromised reproduction. Sows experience increased anestrus, extended weaning-to-estrus intervals, and smaller litter sizes, while boars exhibit reduced semen quality and fertility. The genetic selection for higher productivity has inadvertently lowered heat tolerance, as metabolic heat production increases with improved production traits. Furthermore, inadequate environmental management in pig housing exacerbates the impact of HS. Variations in heat tolerance among pigs underscore the importance of understanding genetic, physiological, and environmental factors influencing their response to HS. Research reveals genetic differences in thermotolerance, offering potential avenues for selective breeding to improve resilience. Effective management strategies, including nutritional adjustments, environmental modifications, and genetic selection, are crucial for mitigating the negative effects of HS and enhancing pig productivity. This review highlights the multifaceted impacts of HS on swine production, explores the physiological and reproductive consequences, and discusses adaptive and ameliorative measures to address these challenges, with a focus on maintaining sustainable pig production in the face of climatic changes.

Chromosome-Level Genome Assembly of the Meishan Pig and Insights into Its Domestication Mechanisms

Pigs are essential agricultural animals, and among the various breeds, the Meishan pig, a native breed of China, is renowned for its high reproductive performance. This breed has been introduced to many countries to enhance local pig breeding programs. However, there have been limited genomic and population genetics studies focusing on Meishan pigs. We created a chromosomal-level genomic assembly using high-depth PacBio sequencing and Illumina sequencing data collected from a Meishan pig. Additionally, we analyzed whole-genome sequencing (WGS) data from Chinese boars and Meishan pigs to identify domestication selection signals within the Meishan breed. The assembled genome of the Meishan pig (MSjxau) was found to be 2.45 Gb in size, with a scaffold length of 139.17 Mb. The quality value was 37.06, and the BUSCO score was 96.2%, indicating good completeness, continuity, and accuracy. We annotated transposable elements, segmental duplication, and genes in the MSjxau genome. By combining these data with 28 publicly available genomes, we provide a high-quality structural variants resource for pigs. Furthermore, we identified 716 selective sweep intervals between Chinese wild pigs and Meishan pigs, where the selected gene PGR may be linked to the high fertility observed in Meishan pigs. Our study offers valuable genomic and variation resources for pig breeding and identifies several genes associated with the domestication of the Meishan pig. This lays the groundwork for further investigation into the genetic mechanisms behind complex traits in pigs.

Comparison of Development and Antioxidative Ability in Fertilized Crossbred (Yorkshire × Landrace × Duroc) Oocytes Using Duroc and Landrace Sperm

Pig production through crossbreeding methods is a pillar of the swine industry; however, research on the fertilization ability of male pigs in crossbreeds is lacking. Therefore, this study investigated the effects of Duroc sperm (DS) and Landrace sperm (LS) on fertility in Yorkshire × Landrace × Duroc (YLD) oocytes. Sperm were collected from the Duroc and Landrace species, and sperm characteristics, viability, and acrosome reactions were analyzed using flow cytometry. Oocytes were collected from YLD ovaries, and the fertility of DS and LS was determined using in vitro fertilization (IVF). Reactive oxygen species (ROS) and antioxidative abilities were analyzed using H2DCFDA and a Cell Tracker Red assay. Pluripotency (OCT4, SOX2, and NANOG), antioxidative (SOD1, SOD2, CAT, and GPx1), apoptotic (Bax and Bcl-2), and cell cycle-related (Cdc2 and CCNB1) genes were detected using quantitative reverse transcription polymerase chain reaction (qRT-PCR) in oocytes fertilized with sperm. The results showed no significant difference in viability or acrosome reaction between DS and LS. ROS levels were significantly lower in the LS group than in the DS group, whereas glutathione (GSH) levels in the embryo did not significantly differ between the DS and LS groups. The OCT4, GPx1, and Cdc2 mRNA expression levels were significantly higher in the LS than DS groups. Blastocyst formation was significantly higher in the LS than DS groups. ROS levels were reduced, and blastocyte formation was increased in LS-obtained embryos. In conclusion, these results provide a fundamental understanding of using Landrace semen in the three-way crossbreeding of YLD pigs.

Importance and variability of the paternal component in sow reproductive traits

Reproductive traits are an integral part of the goals of the breeding programs that contribute to the economic success of production. Reproductive phenotypes such as litter size, number of piglets born alive, or litter weight at birth are mainly attributed to females. Thus, the maternal components can be found by default in quantitative genetics' animal models. Still, paternal contribution to variance components should not be discarded. In this review, we indicate the importance of paternal effects in pig breeding by describing both the biology and genetics of boars' traits, the use of (non-)genetic service sire effects in quantitative genetic models for traits measured on females, and genes involved in male reproduction. We start by describing the important biological traits of boars that have the most important effect on their reproductive abilities, i.e., sexual maturity, sperm quality, and testes parameters. Then we move to the possible environmental effects that could affect those traits of boars (e.g., feed, temperature). The main part of the review in detail describes the genetics of boars' reproductive traits (i.e., heritability) and their direct effect on reproductive traits of females (i.e., genetic correlations). We then move to the use of both genetic and non-genetic service sire effects in quantitative models estimated as their percentage in the total variance of traits, which vary depending on the breed from 1 to 4.5% or from 1 to 2%, respectively. Finally, we focus on the description of candidate genes and confirmed mutations affecting male reproduction success: IGF2, Tgm8, ESR1, ZSWIM7, and ELMO1. In conclusion, the observed variance of paternal effects in female reproduction traits might come from various attributes of boars including biological and genetic aspects. Those attributes of boars should not be neglected as they contribute to the success of female reproductive traits.

Comparative Study of Single-Trait and Multi-Trait Genomic Prediction Models

Conventional genomic selection models trait individually, neglecting complex trait interactions. Multi-trait models address this by considering genetic correlations, thus improving breeding value accuracy. Despite their theoretical benefits, quantifying these models' breeding advantages across genetic backgrounds is essential. This study evaluates the benefits of multi-trait models under varying population sizes and three levels of genetic correlations (low, medium, high) using simulations based on 50 K chip data from 5000 individuals. In equal heritability scenarios, the multi-trait GBLUP model consistently outperforms single-trait models, with breeding advantages increasing with heritability. For example, with a reference population of 4500, improvements range from 0.3% to 4.1%. Notably, trait combinations with low heritability are insensitive to changes in genetic correlation, with gains remaining ≤ 0.1% across different genetic correlations under low heritability conditions. In differing heritability scenarios, the multi-trait model's benefits vary, particularly enhancing low-heritability traits when paired with high-heritability ones. Additionally, modeling time increases as genetic correlation decreases. The results of this study indicate that multi-trait models improve breeding accuracy but require more modeling time and place higher demands on algorithms and software. We recommend breeding strategies tailored to different phenotypes and genetic backgrounds to balance efficiency and accuracy.

Effects of parity, season of birth, and sex on within-litter variation and pre-weaning performance of F1 Large White × Landrace pigs

Background and Aim

A piglet's pre-weaning performance significantly influences both animal welfare and profitability in pig production. Understanding piglet pre-weaning performance influencing factors is key to enhancing animal welfare, reducing losses, and boosting profitability. The study aimed to evaluate the impact of parity, season of birth, and sex on within-litter variation and pre-weaning performance of F1 Large White × Landrace pigs.

Materials and Methods

Information regarding total litter size, number of born alive, number of stillbirths, piglet weight at birth, mortality, and count of weaned F1 Large White × Landrace piglets was acquired from the farm database (April 2022-February 2023). 2602 females and 2882 males, a total of 5484 piglets were utilized, with records from 360 sows. The coefficient of variation (CV) of birth weights among piglets within a litter was calculated. The general linear model analysis in MiniTab 17 was used to evaluate the data, with Fisher's least significant difference test (p < 0.05) used for mean separation and Pearson's moment correlation coefficient calculated to assess relationships between survival rates, mortality rates, litter size, birth weight, and birth weight CV.

Results

Parity had a statistically significant impact on litter size, birth weight, and survival rate (p < 0.05). The sow's parity did not significantly (p > 0.05) impact the number of piglets born alive or weaned. Multiparous sows had a significantly larger litter size (p < 0.05) than primiparous sows at birth. The litter weights for parities 2, 4, and 5 did not significantly differ (p > 0.05), with averages of 20.95, 20.74, and 20.03 kg, respectively. About 91.29% was the highest survival rate recorded in parity 2 (p < 0.05). The 1st week of life recorded an 8.02% mortality rate. The mortality rate in parity 3-5 group was significantly (p < 0.05) higher (11.90%) in week 1 than in the other groups (parity 1: 6.79%, parity 2: 5.74%, parity 3-5: 8.54 and 9.21%). The litter sizes in autumn (17.34) and spring (17.72) were significantly larger (p < 0.05) than those in summer (16.47) and winter (16.83). In autumn and spring, the survival rate (83.15 and 85.84%, respectively) was significantly lower (p < 0.05) compared to summer (88.40%) and winter (89.07%). In all seasons, the litter weights did not significantly differ (p > 0.05). The birth weight CV was significantly (p < 0.05) lower during summer (20.11%) than during spring (22.43%), autumn (23.71%), and winter (21.69%). The season of birth had no significant effect (p > 0.05) on the number of live piglets. Males (1.34 kg) were heavier (p < 0.05) than females (1.30 kg) at birth. Notably, the birth weight CV was similar between males (22.43%) and females (22.52%). Litter size was positively correlated with average litter weight (rp = 0.576, p < 0.001), birth weight CV (rp = 0.244, p < 0.001), and mortality rate (rp = 0.378, p < 0.001). An insignificant relationship was observed between average litter weight and birth weight CV (rp = -0.028, p > 0.05) and survival rate (rp = -0.032, p > 0.05).

Conclusion

In F1 Large White × Landrace pigs, birth uniformity among piglets declines as litter size grows larger. In parity 3-5, multiparous sows yield litters with reduced uniformity. With an increase in litter size, uniformity among piglets at birth worsens. A larger litter size and greater piglet birth weight variation are linked to a higher pre-weaning mortality rate. Producers need a balanced selection approach to boost litter size and must cull aging sows carefully to introduce younger, more productive females.

An Integrative ATAC-Seq and RNA-Seq Analysis of the Endometrial Tissues of Meishan and Duroc Pigs

Meishan pigs are a well-known indigenous pig breed in China characterized by a high fertility. Notably, the number of endometrial grands is significantly higher in Meishan pigs than Duroc pigs. The characteristics of the endometrial tissue are related to litter size. Therefore, we used the assay for transposase-accessible chromatin with sequencing (ATAC-seq) and RNA-sequencing (RNA-seq) to analyze the mechanisms underlying the differences in fecundity between the breeds. We detected the key transcription factors, including Double homeobox (Dux), Ladybird-like homeobox gene 2 (LBX2), and LIM homeobox 8 (Lhx8), with potentially pivotal roles in the regulation of the genes related to endometrial development. We identified the differentially expressed genes between the breeds, including SOX17, ANXA4, DLX3, DMRT1, FLNB, IRF6, CBFA2T2, TFCP2L1, EFNA5, SLIT2, and CYFIP2, with roles in epithelial cell differentiation, fertility, and ovulation. Interestingly, ANXA4, CBFA2T2, and TFCP2L1, which were upregulated in the Meishan pigs in the RNA-seq analysis, were identified again by the integration of the ATAC-seq and RNA-seq data. Moreover, we identified genes in the cancer or immune pathways, FoxO signaling, Wnt signaling, and phospholipase D signaling pathways. These ATAC-seq and RNA-seq analyses revealed the accessible chromatin and potential mechanisms underlying the differences in the endometrial tissues between the two types of pigs.

Physiology and management of the peri-parturient sow in the context of changing production conditions

Genetic selection has resulted in a considerable increase in litter size, paralleled by an increase in farrowing duration and perinatal mortality. This paper describes some of the physiological changes around farrowing, and how genetic trends and sow management interact with these. Compromised farrowing can be related to nutritional management, or to housing conditions and handling of periparturient sows. Transition diets, for example, can be formulated to support calcium homeostasis and alleviate constipation. The opportunity to express natural behaviours and minimize stress around farrowing can further optimize farrowing conditions and reduce piglet mortality. Loose farrowing systems are part of the answer to the challenges around farrowing; however, current systems do not perform consistently. In conclusion, increased farrowing duration and increased perinatal mortality may to some extent be inevitably related to trends in pig production; however, they can be improved by nutritional measures, housing conditions and farrowing management.

Functional genomics of reproduction in pigs: Are we there yet?

Reproductive failure is the main reason for culling females in swine herds and is both a financial and sustainability issue. Because reproductive traits are complex and lowly to moderately heritable, genomic selection within populations can achieve substantial genetic gain in reproductive efficiency. A better understanding of the physiological components affecting the expression of these traits will facilitate greater understanding of the genes affecting reproductive traits and is necessary to improve and optimize management strategies to maximize reproductive success of gilts and sows. Large-scale genotyping with single-nucleotide polymorphism (SNP) arrays are used for genome-wide association studies (GWAS) and have facilitated identification of positional candidate genes. Transcriptomic data can be used to weight SNP for GWAS and could lead to previously unidentified candidate genes. Resequencing and fine mapping of candidate genes are necessary to identify putative functional variants and some of these have been incorporated into new genotyping arrays. Sequence imputation and genotype by sequence are newer strategies that could reveal novel functional mutations. In this study, these approaches are discussed. Advantages and limitations are highlighted where additional research is needed.

Cluster analysis and potential influencing factors of boars with different fertility

The fertility of boars is intimately tied to the pig farm's economic benefits. This study aimed to rapidly categorize boars of different fertility and investigate the factors influencing the categorization using the production data in a large pig farm in northern China, including 11,163 semen collection records of Yorkshire boars (215), 11,163 breeding records and 8770 records of farrowing performance of Yorkshire sows (4505), as well as 4720 records of selection indices (sire line index and dam line index) for boars and sows (215 and 4505) between 2017 and 2020. The boar population was classified by two-step cluster analysis, followed by factor analysis to minimize the dimensionality of data variables and eliminate multicollinearity, and then using ordinal logistic regression model to investigate the risk variables impacting boar fertility categorization. Results showed that the two-step clustering divided the 215 boars into three subgroups: high-fertility (n = 61, 28.4%), medium-fertility (n = 127, 59.1%) and low-fertility (n = 27, 12.6%). The high-fertility boars were shown to be substantially greater than the medium-fertility or low-fertility boars (p < 0.05) in average total litter size, number of born alive, and number of healthy piglets of mated sows. Compared with low-fertility boars, the high-fertility boars were also significantly higher (p < 0.05) in the pregnancy rate and farrowing rate of mated sows. However, the three boar subgroups showed no difference (p > 0.05) in semen quality information (average sperm motility, average sperm density, and average sperm volume). Collinearity diagnosis indicated severe multicollinearity among the 20 data variables, which were reduced to 8 factor variables (factors 1-8) by factor analysis, and further collinearity diagnosis exhibited no multicollinearity among the 8 factor variables. Ordered logistic regression analysis revealed a significant and positive correlation (p < 0.05) of boar fertility with factor 2 (average total litter size, number of born alive, number of healthy piglets), factor 4 (average number of weak piglets and average weak piglet rate), factor 6 (sire line index of boars and dam line index of boars), factor 8 (pregnancy rate and farrowing rate), highlighting factor 2 as the most important factor influencing the classification of boar fertility. Our results indicate that the two-step cluster analysis can be used as a simple and effective method to screen boars with different fertility and that farm producers should pay attention to the recording of the reproductive performance of the mated sows due to its role as the risk factor for classification of boar fertility.

Genome wide association study of thyroid hormone levels following challenge with porcine reproductive and respiratory syndrome virus

Introduction: Porcine reproductive and respiratory syndrome virus (PRRSV) causes respiratory disease in piglets and reproductive disease in sows. Piglet and fetal serum thyroid hormone (i.e., T3 and T4) levels decrease rapidly in response to Porcine reproductive and respiratory syndrome virus infection. However, the genetic control of T3 and T4 levels during infection is not completely understood. Our objective was to estimate genetic parameters and identify quantitative trait loci (QTL) for absolute T3 and/or T4 levels of piglets and fetuses challenged with Porcine reproductive and respiratory syndrome virus. Methods: Sera from 5-week-old pigs (N = 1792) at 11 days post inoculation (DPI) with Porcine reproductive and respiratory syndrome virus were assayed for T3 levels (piglet_T3). Sera from fetuses (N = 1,267) at 12 or 21 days post maternal inoculation (DPMI) with Porcine reproductive and respiratory syndrome virus of sows (N = 145) in late gestation were assayed for T3 (fetal_T3) and T4 (fetal_T4) levels. Animals were genotyped using 60 K Illumina or 650 K Affymetrix single nucleotide polymorphism (SNP) panels. Heritabilities, phenotypic correlations, and genetic correlations were estimated using ASREML; genome wide association studies were performed for each trait separately using Julia for Whole-genome Analysis Software (JWAS). Results: All three traits were low to moderately heritable (10%-16%). Phenotypic and genetic correlations of piglet_T3 levels with weight gain (0-42 DPI) were 0.26 ± 0.03 and 0.67 ± 0.14, respectively. Nine significant quantitative trait loci were identified for piglet_T3, on Sus scrofa chromosomes (SSC) 3, 4, 5, 6, 7, 14, 15, and 17, and collectively explaining 30% of the genetic variation (GV), with the largest quantitative trait loci identified on SSC5, explaining 15% of the genetic variation. Three significant quantitative trait loci were identified for fetal_T3 on SSC1 and SSC4, which collectively explained 10% of the genetic variation. Five significant quantitative trait loci were identified for fetal_T4 on SSC1, 6, 10, 13, and 15, which collectively explained 14% of the genetic variation. Several putative immune-related candidate genes were identified, including CD247, IRF8, and MAPK8. Discussion: Thyroid hormone levels following Porcine reproductive and respiratory syndrome virus infection were heritable and had positive genetic correlations with growth rate. Multiple quantitative trait loci with moderate effects were identified for T3 and T4 levels during challenge with Porcine reproductive and respiratory syndrome virus and candidate genes were identified, including several immune-related genes. These results advance our understanding of growth effects of both piglet and fetal response to Porcine reproductive and respiratory syndrome virus infection, revealing factors associated with genomic control of host resilience.

Effects of nursing a large litter and ovarian response to gonadotropins at weaning on subsequent fertility in first parity sows

Post-weaning fertility failures occur more often in parity 1 (P1) sows due to high metabolic demands for lactation and their inability to meet energy requirements for maintenance, growth, and reproduction. We hypothesized that body condition loss occurs more frequently in P1 sows nursing a large litter, resulting in impairment of ovarian follicle development during lactation and post-weaning, which can negatively impact estrus and subsequent fertility. At 24 h post-farrowing, P1 sows (n = 123) were assigned to treatment (TRT) based on sow weight and the number of functional teats to receive a high number (HN, 15 to 16) or low number (LN, 12) of nursing piglets. At weaning, sows in each TRT were assigned to receive PG600 or None (Control). During lactation, sow body measures were obtained and ovarian follicles were assessed in mid-lactation and post-weaning. Lactation data were analyzed for the effects of TRT, and fertility data after weaning were assessed for TRT x PG600, but there were no interactions (P > 0.10). During lactation, 22.2 % of HN sows lost ≥ 4 piglets due to death or removal, and so these sows were excluded from further analysis. The HN sows were lighter (-6.2 kg), had less backfat (-1.0 mm), had lower body condition score (-0.4), and lost more nursing piglets (-1.2) than LN sows (P < 0.05). However, HN sows weaned more pigs (14.0) than LN sows (11.0). There was no effect of TRT on wean to estrus interval (4.2 d), but the interval was 0.5 days shorter for PG600 (P = 0.004) than control. There were no effects of TRT or PG600 on estrus within seven days after weaning (87.3 %), but PG600 induced smaller (P = 0.002) follicles at estrus (6.7 mm) than control (7.3 mm). In the subsequent parity, there were no effects of TRT or PG600 on farrowing rate (93.9%) and total born (13.2). Overall, HN sows lost more piglets and body condition but still weaned more pigs without any detrimental effects on subsequent reproductive performance.

Utility of multi-omics data to inform genomic prediction of heifer fertility traits

Biologically informed single nucleotide polymorphisms (SNPs) impact genomic prediction accuracy of the target traits. Our previous genomics, proteomics, and transcriptomics work identified candidate genes related to puberty and fertility in Brahman heifers. We aimed to test this biological information for capturing heritability and predicting heifer fertility traits in another breed i.e., Tropical Composite. The SNP from the identified genes including 10 kilobases (kb) region on either side were selected as biologically informed SNP set. The SNP from the rest of the Bos taurus genes including 10-kb region on either side were selected as biologically uninformed SNP set. Bovine high-density (HD) complete SNP set (628,323 SNP) was used as a control. Two populations-Tropical Composites (N = 1331) and Brahman (N = 2310)-had records for three traits: pregnancy after first mating season (PREG1, binary), first conception score (FCS, score 1 to 3), and rebreeding score (REB, score 1 to 3.5). Using the best linear unbiased prediction method, effectiveness of each SNP set to predict the traits was tested in two scenarios: a 5-fold cross-validation within Tropical Composites using biological information from Brahman studies, and application of prediction equations from one breed to the other. The accuracy of prediction was calculated as the correlation between genomic estimated breeding values and adjusted phenotypes. Results show that biologically informed SNP set estimated heritabilities not significantly better than the control HD complete SNP set in Tropical Composites; however, it captured all the observed genetic variance in PREG1 and FCS when modeled together with the biologically uninformed SNP set. In 5-fold cross-validation within Tropical Composites, the biologically informed SNP set performed marginally better (statistically insignificant) in terms of prediction accuracies (PREG1: 0.20, FCS: 0.13, and REB: 0.12) as compared to HD complete SNP set (PREG1: 0.17, FCS: 0.10, and REB: 0.11), and biologically uninformed SNP set (PREG1: 0.16, FCS: 0.10, and REB: 0.11). Across-breed use of prediction equations still remained a challenge: accuracies by all SNP sets dropped to around zero for all traits. The performance of biologically informed SNP was not significantly better than other sets in Tropical Composites. However, results indicate that biological information obtained from Brahman was successful to predict the fertility traits in Tropical Composite population.

Traits Defining Sow Lifetime Maternal Performance

Declining sow performance with increasing parity or an increase in the number of poor- quality pigs potentially impacts on farm productivity. This study investigated the phenotypic and genetic background of the sow's influence on (i) the number of pigs not meeting the industry standards (tail-enders) and (ii) changes in performance with parity. Data were available for 3592 sows and their litters (13,976 litters) from a pig production system in NSW, Australia. The mean, standard deviation (SD), and slope for trait values over time were estimated for the sow characteristic traits: number of born-alive (NBA) and stillborn (SB) piglets and body condition of sow recorded with a caliper (CAL), along with maternal effects on piglet performance, represented by: average piglet birth weight (APBW), number of weaned piglets (WEAN), and tail-enders (TEND). Traits were analyzed in ASReml 4.2, by using an animal model. The number of tail-enders produced by a sow is a heritable trait, with a heritability estimate of 0.14 ± 0.04. Sow characteristics and maternal effects on piglet performance expressed by mean and slope had similar heritability estimates, ranging from 0.10 ± 0.03 to 0.38 ± 0.05, whereas estimates for SD traits were generally not different from zero. The latter suggests individual variability in sow characteristics or maternal performance between parities is largely not genetic in origin. This study demonstrated that more attention is required to identify contributions to the problem of tail-enders, and that slope traits could potentially be useful in the breeding program to maximize lifetime performance.

Determination of puberty in gilts: contrast of diagnostic methods

BACKGROUND

Early onset of a gilt´s puberty is needed for adequate economic performance in farms, because it indicates her reproductive performance and longevity. Therefore, an effective diagnosis is needed. Our purpose was to compare different procedures (external characteristics, blood progesterone analysis and ultrasonography diagnosis) to detect puberty in 70 gilts (Topigs TN70; 240 days old) on farm conditions. Postmortem examination was the standard reference. Multiple logistic regression analysis was used to identify which combination of independent variables (predictors) best predicts the status of gilts.

RESULTS

Puberty (46/70 gilts; 65.71%) was characterized by the presence of follicles larger than 6 mm, corpus albicans, corpus rubrum, and corpus luteum (postmortem examination). Vaginal length, body condition, backfat, carcass weight and progesterone blood concentration were significantly higher in pubertal than prepubertal gilts (P < 0.05). Two types of ultrasonography equipment (DELTA and W3) were compared and performed by the same senior technician (V1). The results obtained by two technicians with different levels of experience (V1 and V2, a junior technician) using W3 were also compared. Ultrasonography provided better results than other diagnostic techniques, although the effectiveness of the ultrasonography changed with technological improvements and with increased expertise of technicians. The most accurate results were found by V1/DELTA (Nagelkerke´s R² = 0.846; Sensitivity = 0.956; Specificity = 0.958; Positive predictive value = 0.978; Negative predictive value = 0.920; Area under ROC curve = 0.957). Results using the W3 equipment could be improved when used in conjunction with vaginal length (V1; Nagelkerke´s R² = 0.834; Sensitivity = 0.933; Specificity = 0.958; Positive predictive value = 0.977; Negative predictive value = 0.885; Area under ROC curve = 0.972) or progesterone concentration (V2; Nagelkerke´s R² = 0.780; Sensitivity = 0.955; Specificity = 0.826; Positive predictive value = 0.915; Negative predictive value = 0.905; Area under ROC curve = 0.970).

CONCLUSIONS

Ultrasonography provided better results than other diagnostic techniques. The effectiveness of the ultrasonography changes with technological improvements and with increased expertise of technicians. Results using the W3 equipment could be improved when used along with vaginal length (V1) or progesterone concentration (V2). Accuracy parameters are a guide to choose puberty diagnosis, but the farms must also evaluate effect on gilts, ease and cost of administration.

Genetic aspects of piglet survival and related traits: a review

In livestock, mortality in general, and mortality of the young, is societal worries and is economically relevant for farm efficiency. Genetic change is cumulative; if it exists for survival of the young and genetic merit can be estimated with sufficient accuracy, it can help alleviate the pressure of mortality. Lack of survival is a moving target; livestock production is in continuous change and labor shortage is a given. There is now ample evidence of clear genetic variance and of models able to provide genomic predictions with enough accuracy for selection response. Underlying traits such as birth weight, uniformity in birth weight, gestation length, number of teats, and farrowing duration all show genetic variation and support selection for survival or, alternatively, be selected for on their own merit.

Heritability and genetic correlation estimates of semen production traits with litter traits and pork production traits in purebred Duroc pigs

We estimated heritabilities of semen production traits and their genetic correlations with litter traits and pork production traits in purebred Duroc pigs. Semen production traits were semen volume, sperm concentration, proportion of morphologically normal sperms, total number of sperm, and total number of morphologically normal sperm. Litter traits at farrowing were total number born, number born alive, number stillborn, total litter weight at birth, mean litter weight at birth, and piglet survival rate at birth. Litter traits at weaning were litter size at weaning, total litter weight at weaning, mean litter weight at weaning, and piglet survival rate from birth to weaning. Pork production traits were average daily gain, backfat thickness, and loin muscle area. We analyzed 45,913 semen collection records of 896 boars, 6,950 farrowing performance records of 1,400 sows, 2,237 weaning performance records of 586 sows, and individual growth performance records of 9,550 animals measured at approximately 5 mo of age. Heritabilities were estimated using a single-trait animal model. Genetic correlations were estimated using a 2-trait animal model. Estimated heritabilities of semen production traits ranged from 0.20 for sperm concentration to 0.29 for semen volume and were equal to or higher than those of litter traits, ranging from 0.06 for number stillborn and piglet survival rate at birth to 0.25 for mean litter weight at birth, but lower than those of pork production traits, ranging from 0.50 for average daily gain to 0.63 for backfat thickness. In many cases, the absolute values of estimated genetic correlations between semen production traits and other traits were smaller than 0.3. These estimated genetic parameters provide useful information for establishing a comprehensive pig breeding scheme.

Genetic parameters of 5 semen production traits, 10 litter traits, and 3 pork production traits in purebred Duroc pigs was estimated. Heritabilities of semen production traits ranged from 0.20 for sperm concentration to 0.29 for semen volume and were equal to or higher than those of litter traits, ranging from 0.06 for number stillborn and piglet survival rate at birth to 0.25 for mean litter weight at birth, but lower than those of pork production traits, ranging from 0.50 for average daily gain to 0.63 for backfat thickness. In many cases, the absolute values of genetic correlations between semen production traits and other traits were smaller than 0.3. These estimated genetic parameters provide useful information for establishing a comprehensive pig breeding scheme.

Polymorphism of OPN and AREG Genes in Relation to Transcript Expression of a Panel of 12 Genes Controlling Reproduction Processes and Litter Size in Pigs

The aim of this study was to define the transcript expression of 12 genes, identify new polymorphisms in selected 2 genes and to estimate the association between the level of expression, gene polymorphism and litter size in sows. Two groups of sows were selected: 71 crossbred sows and 328 purebred sows. For transcript analysis endometrial tissue samples were collected, while blood was sampled for the purpose of DNA polymorphism analysis. For all animals data on litter size and weaned piglets were obtained. Transcript analysis of 12 genes was performed in the uterine endometrium of sows in the luteal and follicular phases. Eight out of 12 genes showed higher mRNA expression levels during the luteal phase (AREG, FABP3, IL1A, ITGAV, ITGB3, NMB, OPN, RBP4). In turn, higher expression levels in the follicular phase were observed for 4 genes (IL1B, PPARG, S100A8, SELL). Analysis of six new polymorphic sites within the OPN and AREG genes revealed the highest heterozygosity for OPNe6_Knoll, OPNp3_617 and AREGe2_317 polymorphisms and the lowest heterozygosity in the AREGe3_561 locus. Association analyses concerning transcript expression levels of the 12 genes and the OPN and AREG genotypes in the two groups of sows showed a significant relationship between the IL1A, ITGB3 transcript expression and the OPNe7_603 genotype also between OPNp3_617 genotype and ITGB3 transcript expression. With regard to the litter size and the number of weaned piglets a significant relation with the OPNp3_617, OPNe6_462 and AREGe2_317 genotypes was observed only in the purebred sows. Transcript expression of the genes encoding osteopontin and amphiregulin in the uterus of the sows affect reproductive traits by preparing the uterus for embryo reception.

Selection for litter size and litter birthweight in Large White pigs: Maximum, mean and variability of reproduction traits

Gradually increasing trend of litter size poses a challenge to pig farmers in terms of managing larger litters. Therefore, it seems that a balanced approach that optimises litter size, litter birthweight, and uniformity of those traits is needed in order to address animal welfare and farm management concerns. This study aimed to investigate this issue by defining several traits for total number born (TNB), number born alive (NBA) and litter birthweight (LW). First, the highest value from at least five records per sow was selected as maximum (max) value for each reproduction trait. Second, a mean (mean) for each reproduction trait was calculated per sow. Last, the variability of reproduction traits between parities of the sow was calculated as log-transformed variance of residuals of all observations per sow for each reproduction trait (LnVar). In total, 23 193 Large White sows from Topigs Norsvin with 152 282 litter records were used for analysis in ASReml 4.1. Also, a simulation of breeding schemes was performed with the use of SelAction 2.1 and estimates from genetic analysis. Maximum value of reproductive traits had a much higher heritability than repeated observations or mean of reproduction traits, e.g., 0.31 for maxTNB vs. 0.12 for TNB and 0.07 for meanTNB, which allows for a faster response under selection. The maximum value traits, however, were found to carry more risks, i.e. higher ratio of stillborn (not for maxNBA) and increased variability of traits. Thus, using them in breeding programme should be carefully considered. The genetic coefficient of variation on SD level estimated to indicate the genetic magnitude for variability phenotypes indicated a maximum change of 6-9% in genetic SD of TNB, NBA and LW. The genetic correlations between mean and corresponding variability traits varied from 0.66 to 0.74, whereas the correlation between other mean and variability traits ranged from 0.33 to 0.99. The simulation indicated that even with selection targeted against the variability of reproduction traits, a very limited change should be expected due to a complex genetic and phenotypic relationship between the traits. In the scenarios with selection against LnVarTNB and LnVarLW, this was a decrease of 0.1-0.6% per year, whereas in scenario with selection against LnVarNBA, the range was 0.6-1.1% per year. It is still possible to increase litter size and birthweight further, however, a balance between mean and variability of reproduction traits is required, which can be obtained only by a very well designed breeding programme.

Complete Chromatin Decondensation of Pig Sperm Is Required to Analyze Sperm DNA Breaks With the Comet Assay

Sperm quality is usually evaluated prior to artificial insemination in farm animals. In addition to conventional semen analysis, other biomarkers, such as mitochondrial activity, integrity and lipid disorder of plasma membrane, generation of reactive oxygen species (ROS) and sperm DNA integrity, have been found to be related to fertility rates in different species. While mounting evidence indicates that the Comet assay is a sensitive method for the detection of DNA breaks, complete sperm chromatin decondensation is required in order to properly analyze the presence of single- and double-strand DNA breaks. In this sense, a previous study showed that longer lysis treatment with proteinase K is needed to achieve complete chromatin decondensation. The current work sought to determine which specific lysis treatment leads to complete chromatin decondensation in pig sperm, as this is needed for the measurement of DNA damage in this species. With this purpose, incubation with a lysis solution containing proteinase K for 0, 30, and 180 min was added to the conventional protocol. The impact of the DNA damage induced by hydrogen peroxide (H₂O₂; 0.01 and 0.1%) and DNAse I (1U and 4U) was also evaluated. Complete chromatin decondensation was only achieved when a long additional lysis treatment (180 min) was included. Furthermore, olive tail moment (OTM) and percentage of tail DNA (TD) indicated that a higher amount of DNA breaks was detected when hydrogen peroxide and DNAse I treatments were applied (P < 0.05). The comparison of treated and control sperm allowed defining the thresholds for OTM; these thresholds revealed that the percentage of sperm with fragmented DNA determined by the alkaline Comet does not depend on chromatin decondensation (P > 0.05). In conclusion, complete chromatin decondensation prior to alkaline and neutral Comet assays is needed to analyze DNA breaks in pig sperm.

Analysis of differentially abundant proteins related to boar fertility in seminal plasma using iTRAQ-based quantitative proteomics

Animal fertility is one of the most important characteristics for the livestock breeding industry. Conventional semen analysis provides basic information on sperm quality, but the predictive value of such analysis with regard to fertility remains questionable. Therefore, it is important to determine and predict male fertility more accurately in the clinic. To identify seminal plasma proteins involved in fertility, isobaric tags for relative and absolute quantitation (iTRAQ) and liquid chromatography with tandem mass spectrometry (quantitative proteomic analysis) were used to identify differentially abundant proteins (DAPs) in seminal plasma between high- and low-reproductive-efficiency Landrace boars. A total of 141 DAPs were identified, of which 125 upregulated and 16 downregulated proteins were subjected to bioinformatics analysis. These DAPs were found to be mainly involved in proteolysis, ATP binding, and energy metabolism. We investigated the relevance of three DAPs-ceruloplasmin, carboxypeptidase E (CPE), and serpin family A member 12 (SERPINA12)-in an in vitro fertility assay. This assay revealed that the inhibition of these proteins with antibodies can reduce or increase the fertilization rate. These results indicate possible biomarkers for the selection of high-fertility boars and provide a theoretical basis for the use of protein biomarkers in the livestock breeding industry. SIGNIFICANCE: Our study identified differentially abundant proteins in the seminal plasma of high-reproductive-efficiency and low-reproductive-efficiency Landrace boars. These proteins may be used as biomarkers to screen out high-fertility boars. The study can provide not only a new method for improving the effects of artificial insemination and reproductive efficiency of boars but also an important reference for boar breeding. Meanwhile, because pigs and humans have similar physiological parameters and organ sizes, our findings can also serve as a reference for human reproduction research.

IGF-1 concentrations after weaning in young sows fed different pre-mating diets are positively associated with piglet mean birth weight at subsequent farrowing

Pre-mating diets can influence piglet birth weight and within-litter birth weight variation and thereby piglet survival and development. The major objective of this study was to evaluate the litter characteristics of young sows whose pre-mating diets received different supplementation. The supplements included a top-dressing of 200 g, consisting of either wheat (CON) or wheat plus microfibrillated cellulose, _L-carnitine or _L-arginine at one of two supplementation levels (low and high) in late lactation and during the weaning-to-oestrus interval (WEI). The second objective was to investigate the role of body condition loss and IGF-1 concentration during the WEI for subsequent litter characteristics. In total, sows after their first (N =41) and second (N =15) lactation were used. One week before weaning, the sows were allocated to the seven treatments based on the number of piglets and BW loss from farrowing until 1 week before weaning. Pre-mating diets did not affect litter characteristics at subsequent farrowing. However, at subsequent farrowing, sows after their first lactation had a lower total number of piglets born per litter (18.3 v. 20.3), higher mean piglet birth weight (1365 v. 1253 g), lower CV of birth weight (20.0 v. 26.1%) and lower percentage of piglets <1000 g (11.5 v. 24.4%) than sows after their second lactation. Litter weight at second parturition was positively related to IGF-1 during the WEI after first lactation (P <0.04). Within parity, piglet mean birth weight was positively related to IGF-1 at oestrus (P <0.02). Surprisingly, within parity, a higher relative loin muscle depth loss during previous lactation was related to lower CV and SD of birth weight (P <0.05, for both). In conclusion, pre-mating diets did not affect litter characteristics at subsequent birth. However, a higher IGF-1 concentration during the WEI was positively associated with subsequent litter weight and piglet mean birth weight. Further studies should elucidate the role of IGF-1 during the WEI for subsequent litter characteristics and dietary interventions to stimulate IGF-1.

Phenotypic and genomic relationships between vulva score categories and reproductive performance in first-parity sows

Background

One of the biggest challenges in the swine industry is to increase female reproductive efficiency. Recently, vulva score categories (VSC), assessed prior to puberty, has been proposed as an indicator trait of efficient reproductive performance in sows. The objective of this study was to validate the use of VSC as an indicator trait for reproductive performance, and to perform genetic and genomic analyses for VSC.

Methods

The phenotypic relationship of VSC, using a three-point scale: small (VSC-S), medium (VSC-M), and large (VSC-L), on reproductive performance was evaluated on three farms. VSC was measured at 15 weeks of age, for farms 1 and 2, and at 14 weeks of age for farm 3 on 3981 Yorkshire gilts, in which 1083 had genotypes (~ 50 K SNPs). Genetic parameters for VSC with reproductive traits were estimated using ssGBLUP. A Genome-wide association study (GWAS) for VSC was performed using BayesB.

Results

For the phenotypic analysis of VSC across datasets, differences in performance were identified there was a significant effect (P ≤ 0.05) for the interaction between Farm and VSC for total number dead (TND), and a trend (P < 0.10) for total number born (TNB). There were significant (P ≤ 0.05) pre-defined contrasts of VSC-S versus VSC-M + L on TNB, number born alive (NBA), TND, number of stillborn (NSB), and number of mummies (MUM). Heritability estimates for VSC as a categorical trait (VSCc) and a quantitative trait (VSCq) were 0.40 ± 0.02 and 0.83 ± 0.02, respectively, for across farm, 0.13 ± 0.07 and 0.20 ± 0.10, respectively, for Farm1, 0.07 ± 0.07 and 0.09 ± 0.09, respectively, for Farm2, and 0.20 ± 0.03 and 0.34 ± 0.05, respectively, for Farm3. For across farms, favorable genetic correlations estimates were found for TNB (0.28 ± 0.19) and NBA (0.26 ± 0.17). Within farms, moderate genetic correlations between VSC with reproductive traits were found for TNB (0.61 ± 0.47) and MUM (0.69 ± 0.47) for farm 1, for number of services until first farrow (NS; 0.69 ± 0.38) and unique service with successful first farrow (SFS; − 0.71 ± 0.38) for farm 3. Multiple genomic regions associated with VSC_c were identified. Of these, a QTL located on chromosome 3 at 33–34 Mb accounted for about 7.1% of the genetic variance for VSC_c and VSC_q. This region harbors the gene PRM1 that has been associated with early embryonic development in pigs.

Conclusions

The results support potential of VSC for improved reproductive efficiency on first-parity performance, but the results might depend on the interaction between environmental factors and VSC, as well as potentially additive genetics.

Characterisation of sperm piRNAs and their correlation with semen quality traits in swine

Piwi-interacting RNAs (piRNAs) are a class of non-coding RNAs that are essential in the transcriptional silencing of transposable elements and warrant genome stability in the mammalian germline. In this study, we have identified piRNAs in porcine sperm using male germline and zygote datasets from human, mice, cow and pig, and evaluated the relation between their abundances and sperm quality traits. In our analysis, we identified 283 382 piRNAs, 1355 of which correlated with P ≤ 0.01 to at least one semen quality trait. Fifty-seven percent of the correlated piRNAs mapped less than 50 kb apart from any other piRNA in the pig genome. Furthermore, piRNA location was significantly enriched near long interspersed nuclear elements. Moreover, some of the significant piRNAs mapped within or close to genes relevant for fertility or spermatogenesis such as CSNK1G2 and PSMF1.

Identification of Functional Single Nucleotide Polymorphisms in Porcine HSD17B14 Gene Associated with Estrus Behavior Difference between Large White and Mi Gilts

Steroid hormone levels are associated with estrous behavior, which affects timely mating and reproductive efficiency in pigs. 17β-hydroxysteroid dehydrogenase type 14 (HSD17B14) modulates steroid synthesis and metabolism. To identify the functional single nucleotide polymorphisms (SNPs) in the porcine HSD17B14 gene, ear tissues from Large White and Mi gilts were collected to extract genomic DNA. Variable lengths of truncated promoter of HSD17B14 gene were used to determine the promoter activity by a dual luciferase reporter system. The vector HSD17B14^Phe or HSD17B14^Val was transfected into porcine granulosa cells (GCs). The core promoter region was identified between -72bp and -218bp. Six of seven SNPs had significant differences of allele frequency between Large White and Mi gilts. The plasmids with the wild genotype AA of rs329427898 maintained a smaller fraction of promoter activity compared with the plasmids with the mutant genotype GG, while the plasmids with wild the genotype TT of rs319864566 had a greater promoter activity than the plasmids with the mutant genotype CC. A missense mutation (Phe73Val) caused changes in the structural dynamics and function of the HSD17B14 protein. The highly expressed HSD17B14^Val degraded less estradiol into estrone, while the relatively lowly expressed HSD17B14^Phe degraded more estradiol into estrone, suggesting the protein activity of HSD17B14^Phe was greater than that of HSD17B14^Val. Moreover, the HSD17B14^Phe group has a greater apoptosis rate of porcine GCs. The HSD17B14 gene could been used as a candidate molecular marker for estrus behavior in pigs.

Goat sperm associated antigen 17 protein gene (SPAG17): Small and large fragment genetic variation detection, association analysis, and mRNA expression in gonads

Transcriptome sequencing analyses have suggested that sperm associated antigen 17 protein gene (SPAG17) may play important regulating roles in litter size. In this study, the expression profiles and genetic variations of the SPAG17 were studied in Shaanbei White Cashmere (SBWC) goats (n=1567). SPAG17 was highly expressed in testis and ovary of SBWC goats. At different developmental stages, it also continued to be highly expressed in testis. In addition, two variations of SPAG17, one indel locus and one copy number variation locus, were significantly associated with first-born litter size. Joint analysis results suggested that two polymorphic loci of the SPAG17 gene may regulate host gene expression in goat ovary and testis. Overall, the results indicated the important role of SPAG17 in the reproductive process of goats.

Genomics of Heat Tolerance in Reproductive Performance Investigated in Four Independent Maternal Lines of Pigs

Improving swine climatic resilience through genomic selection has the potential to minimize welfare issues and increase the industry profitability. The main objective of this study was to investigate the genetic and genomic determinism of tolerance to heat stress in four independent purebred populations of swine. Three female reproductive traits were investigated: total number of piglets born (TNB), number of piglets born alive (NBA) and average birth weight (ABW). More than 80,000 phenotypic and 12,000 genotyped individuals were included in this study. Genomic random-regression models were fitted regressing the phenotypes of interest on a set of 95 environmental covariates extracted from public weather station records. The models yielded estimates of (genomic) reactions norms for individual pigs, as indicator of heat tolerance. Heat tolerance is a heritable trait, although the heritabilities are larger under comfortable than heat-stress conditions (larger than 0.05 vs. 0.02 for TNB; 0.10 vs. 0.05 for NBA; larger than 0.20 vs. 0.10 for ABW). TNB showed the lowest genetic correlation (-38%) between divergent climatic conditions, being the trait with the strongest impact of genotype by environment interaction, while NBA and ABW showed values slightly negative or equal to zero reporting a milder impact of the genotype by environment interaction. After estimating genetic parameters, a genome-wide association study was performed based on the single-step GBLUP method. Heat tolerance was observed to be a highly polygenic trait. Multiple and non-overlapping genomic regions were identified for each trait based on the genomic breeding values for reproductive performance under comfortable or heat stress conditions. Relevant regions were found on chromosomes (SSC) 1, 3, 5, 6, 9, 11, and 12, although there were important regions across all autosomal chromosomes. The genomic region located on SSC9 appears to be of particular interest since it was identified for two traits (TNB and NBA) and in two independent populations. Heat tolerance based on reproductive performance indicators is a heritable trait and genetic progress for heat tolerance can be achieved through genetic or genomic selection. Various genomic regions and candidate genes with important biological functions were identified, which will be of great value for future functional genomic studies.

Identification of new protein biomarkers associated with the boar fertility using iTRAQ-based quantitative proteomic analysis

In this study, we performed the isobaric tags for relative and absolute quantitation (iTRAQ) proteomic analysis in the spermatozoa of Landrace boars with different fertility potentials and investigated the ability of sperm acrosome associated 4 (SPACA4) and IZUMO family member 2 (IZUMO2) to predict the reproductive perform of boars. The iTRAQ results revealed that 202 proteins were up-regulated and 43 proteins were down-regulated in the spermatozoa from high fertility boars. SPACA4 and IZUMO2 protein levels were significantly up-regulated in the spermatozoa from high fertility boars. SPACA4 and IZUMO2 expression were specifically detected in the adult boar testis. SPACA4 levels were positively correlated with Sow's farrowing rate and reproductive efficiency, but not litter size. IZUMO2 were positively correlated with litter size, Sow's farrowing rate and reproductive efficiency. Treating the boar semen with SPACA4 or IZUMO2 antibodies for 30 min and 60 min failed to affect the sperm motility; while treating the semen with SPACA4 antibody significantly reduced the fertilization and cleavage rates. Similar results for fertilization and cleavage rates were found in IZUMO2 antibody-treated semen. Collectively, our results indicated that protein levels of SPACA4 and IZUMO2 in the spermatozoa were positively related to the reproductive performance of Landrace boars.

Are Larger Litters a Concern for Piglet Survival or an Effectively Manageable Trait?

As sows continue to be selected for greater prolificacy, it is important to review problems that arise in larger litters, and whether these issues can be appropriately managed. Although a proportion of piglets in larger litters can be born underweight, proper supervision around farrowing and adequate colostrum intake has the potential to improve the survival of low-birth-weight piglets and their ongoing growth to weaning. As larger litters can impart greater stress and discomfort on sows, implementing a low-stress environment leading up to parturition may improve sow performance and subsequent survival of piglets. Additionally, treating sows with anti-inflammatory compounds, either dietary or pharmacologically, shows some promise for alleviating sow discomfort and improving piglet survival in larger litters. Understanding that selecting sows for larger litters not only affects piglet survival but the well-being of the sow, the decision to continue selecting for larger litters, regardless of management strategies, remains a topic of ethical concern.

Estimation of the Genetic Parameters for Semen Traits in Spanish Dairy Sheep

Simple Summary

The limited studies addressing the estimation of genetic parameters for ram semen traits in different breeds show a wide variation, highlighting the importance of studying these traits for individual breeds. Therefore, this work aimed to estimate genetic parameters for traits related to semen production and quality in five dairy sheep breeds. For that, ejaculates of rams from Assaf, Churra, Latxa Cara Negra, Latxa Cara Rubia, and Manchega breeds were analyzed. Estimates of the genetic covariance structure were obtained with multiple-trait animal models using the average information REML (restricted maximum likelihood) method in the BLUPF90 family of programs. Repeatability estimates for all the traits were also calculated. Heritability estimates were of low to moderate magnitude, although the estimates differed among the breeds. The estimated genetic correlations among the three semen traits showed adequate precision only in the Manchega (MAN) breed. The heritability estimates reported here suggest that improvement of these traits may be achieved by genetic selection.

Abstract

This work aimed to estimate genetic parameters for traits related to semen production and quality in Spanish dairy sheep breeds. For that, ejaculates of rams from Assaf, Churra, Latxa Cara Negra, Latxa Cara Rubia, and Manchega breeds were analyzed to measure volume, semen concentration, and motility. Estimates of variance components were obtained with multiple-trait animal models using the average information REML method in the BLUPF90 family of programs. Repeatability estimates for all the traits were also calculated, with values ranging from 0.077 to 0.304 for the motility and the semen concentration traits, respectively. Heritability estimates were of low to moderate magnitude, ranging from 0.014 (motility in Latxa Cara Rubia) to 0.198 (volume in Churra), although the estimates differed among the breeds. The estimated genetic correlations among the three semen traits showed adequate precision only in the MAN breed. The heritability estimates for the semen traits reported in the present paper suggest an adequate response to selection. The practical extension of these results to the other breeds studied here will be secondary to the estimation of more reliable genetic correlations in these breeds.

Genome-Wide Differential Expression Profiling of Ovarian circRNAs Associated With Litter Size in Pigs

Circular RNAs (circRNAs) have been emerging as an important regulator in mammalian reproduction via acting as miRNA sponges. However, the circRNAs in porcine ovaries related with litter size remains largely unknown. In this study, porcine ovaries with smaller or larger litter size (LLS) were subjected to high-throughput RNA sequencing. In total, 38,722 circRNAs were identified, of which 1,291 circRNAs were commonly expressed in all samples. There were 56 circRNAs significantly down-regulated and 54 circRNAs up-regulated in LLS pig (|log2 (fold change) | > 1, FDR < 0.05). Bioinformatics predicted that most of circRNAs harbored miRNA binding sites, and the expression patterns of circRNAs and their putative binding miRNAs were validated by qPCR. Moreover, the expression of circ-TCP11/miR-183 was significantly reversely correlated and their direct interaction was confirmed by dual-luciferase assay. Our study indicates that circRNAs may play potential effects on modulating porcine litter size.

Identification of measures predictive of age of puberty onset in gilts

A potential indicator of female lifetime productivity in swine is age of puberty, when a gilt achieves her first behavioral estrus. Follicular activity, as determined by tertiary follicle development, in prepubertal gilts begins during postnatal day (PND) 75 to 115. The central hypothesis of this study is that gilts demonstrating tertiary follicle development earlier in life, assessed using vulva size as a proxy, achieve puberty earlier in life compared with counterparts of a similar age and weight that lack tertiary follicle development. The objectives of this project were to identify a developmental time point when variation in ovarian development exists and to determine whether a relationship between the age prepubertal ovarian development and the age at onset of puberty exists. To accomplish this, 155 gilts of similar age (± 2 d) were weighed and vulva size measured on PND 75, 85, 95, 105, and 115. Vulva measures, including vulva width (VW), vulva length (VL), and vulva area (VA), were utilized as developmental proxies for follicular activity. At each time point, gilts (n = 10) were sacrificed and ovarian follicular activity recorded. In a subset of gilts (n = 105), estrus detection was conducted daily on PND days 126 to 200. Mean VA on PND 75, 85, 95, 105, and 115 was 596 ± 206, 683 ± 190, 864 ± 212, 1014 ± 228, and 1265 ± 252 mm², respectively. Of the gilts demonstrating behavioral estrus, 28 were within PND 140 to 160, 36 between PND 161 to 180, 15 between PND 181 to 200, and 26 did not demonstrate estrus behavior within 200 d of age. All gilts euthanized at PND 75 lacked follicular activity as defined by having a minimum of 2 antral follicles per ovary, whereas 60%, 80%, 90%, and 100% demonstrated follicular activity on PND 85, 95, 105, and 115, respectively. Body weight at PND 75 and VW at PND 115 were correlated to age at first estrus (P < 0.05). Of the gilts whose VA was less than 1 SD from the mean on PND 95 (i.e., <652 mm²), 31% and 50% demonstrated their first behavioral estrus by PND 180 and 200, respectively. However, of gilts whose VA was within or greater than 1 SD of the mean (i.e., ≥652 mm²), 66% and 79% exhibited estrus prior to PND 180 and 200, respectively. These data support utilization of VA changes between 95 and 115 d of age as a useful tool to identify replacement gilts prior to puberty for inclusion into the sow herd.

Variants in BMP7 and BMP15 3'-UTRs Associated with Reproductive Traits in a Large White Pig Population

Bone morphogenetic protein 7 (BMP7) and BMP15, which encode members of the BMP family, have been identified by whole-genome resequencing as breeding-related genes that overlap with a known quantitative trait locus for reproductive traits. In this study, we investigated the effects of variants at the BMP7 and BMP15 gene loci on sow reproductive traits. We isolated 669 and 1213 bp sequences of the 3’-untranslated region (3’-UTR) of the porcine BMP7 and BMP15 genes, respectively, and detected several RNA regulatory elements, such as miRNA response elements and AU-rich elements. Pooled DNA sequencing identified two novel point mutations (viz., BMP7 c.1569A>G and BMP15 c.2366G>A) in the 3’-UTR. Association analysis showed that the c.1569A>G polymorphism was associated with the litter weight trait in a Large White pig population. Furthermore, analysis of the combined genetic effects revealed that AA/GA and AG/GG were the favorable combined genotypes for the total number of piglets born (TNB) and the total number of piglets born alive (NBA), whereas. Together, our findings confirm that BMP7 and BMP15 are candidate genes for porcine reproductive performance.

Genetic Parameter Estimation and Genomic Prediction of Duroc Boars' Sperm Morphology Abnormalities

Artificial insemination (AI) has been used globally as a routine technology in the swine production industry. However, genetic parameters and genomic prediction accuracy of semen traits have seldom been reported. In this study, we estimated genetic parameters and conducted genomic prediction for five types of sperm morphology abnormalities in a large Duroc boar population. The estimated heritability of the studied traits ranged from 0.029 to 0.295. In the random cross-validation scenario, the predictive ability ranged from 0.212 to 0.417 for genomic best linear unbiased prediction (GBLUP) and from 0.249 to 0.565 for single-step GBLUP (ssGBLUP). In the forward prediction scenario, the predictive ability ranged from 0.069 to 0.389 for GBLUP and from 0.085 to 0.483 for ssGBLUP. In conclusion, the studied sperm morphology abnormalities showed moderate to low heritability. Both GBLUP and ssGBLUP showed comparative predictive abilities of breeding values, and ssGBLUP outperformed GBLUP under many circumstances in respect to predictive ability. To our knowledge, this is the first time that the genetic parameters and genomic predictive ability of these traits were reported in such a large Duroc boar population.

Application of preserved boar semen for artificial insemination: Past, present and future challenges

Artificial insemination (AI) is now used for breeding more than 90% of the sows in most of the world's primary pork producing countries. Despite the advancement of methods to cryopreserve boar semen, frozen semen has not been routinely used on farms because of limited efficiency. Liquid semen on the other hand, with 1.5-3 billion sperm per dose preserved up to seven days in long-term extenders, is in common use and is largely responsible for the widespread use of AI. Breeding organizations have defined individual thresholds for useable semen at 60-80% for motility and bacterial load of 0-1000 CFU/mL. Improvement in preservation techniques for liquid semen and better education of producers has been responsible for the higher efficiency of pig breeding, as measured by conception rate and increased litter size, with a minimum number of sperm. The introduction of deep intrauterine AI and advances in breeding management have also been contributing factors. The present article reviews the worldwide application of preserved boar semen from past to present and delineates future challenges. Pathways to increase breeding efficiency are outlined. The reconciliation of AI with sustainable breeding strategies is increasingly important. In this sense, guidelines for the prudent use of antibiotics in semen extenders are proposed. More efficient and sustainable pig AI awaits the introduction of sex-sorted sperm into AI practice. Another critical milestone that needs to be achieved is the replacement of conventional antibiotics in extenders.

Estimation of genetic parameters and season effects for semen traits in three pig breeds of South China

The economic profitability of a boar station largely depends on semen quantity and quality traits. However, genetic analysis of semen traits has not yet been done in the boar population in China. In this study, we aimed to estimate genetic parameters for semen traits and the influence of seasons on these traits by using data of Duroc, Landrace and Yorkshire boars in South China. The following four semen traits were analysed: semen volume (ml; VOL), sperm concentration (10⁶ /ml; DEN), sperm motility (MOT) and percentage of abnormal sperm (ABN). Genetic parameters and season effects were estimated simultaneously for each breed by using a multiple-trait (4 × 4) repeatability animal model. The four traits had a moderate heritability with average estimates of 0.23, 0.28, 0.26 and 0.17 across the three breeds, respectively. The estimates of genetic correlations among four traits differed in the three breeds. In particular, in Yorkshire, the four traits were nearly genetically independent. The season of collecting semen had a significant impact on these four semen traits except ABN in Duroc (Bonferroni adjusted p < 0.05/6). The moderate heritabilities indicate the possibility of effective selection of boars for semen traits. Different genetic correlations for the three breeds suggest that the selection strategy for the four traits should be investigated separately for each breed. Some necessary actions should be taken to reduce the influence of seasons on semen traits.

Loss of function mutations in essential genes cause embryonic lethality in pigs

Lethal recessive alleles cause pre- or postnatal death in homozygous affected individuals, reducing fertility. Especially in small size domestic and wild populations, those alleles might be exposed by inbreeding, caused by matings between related parents that inherited the same recessive lethal allele from a common ancestor. In this study we report five relatively common (up to 13.4% carrier frequency) recessive lethal haplotypes in two commercial pig populations. The lethal haplotypes have a large effect on carrier-by-carrier matings, decreasing litter sizes by 15.1 to 21.6%. The causal mutations are of different type including two splice-site variants (affecting POLR1B and TADA2A genes), one frameshift (URB1), and one missense (PNKP) variant, resulting in a complete loss-of-function of these essential genes. The recessive lethal alleles affect up to 2.9% of the litters within a single population and are responsible for the death of 0.52% of the total population of embryos. Moreover, we provide compelling evidence that the identified embryonic lethal alleles contribute to the observed heterosis effect for fertility (i.e. larger litters in crossbred offspring). Together, this work marks specific recessive lethal variation describing its functional consequences at the molecular, phenotypic, and population level, providing a unique model to better understand fertility and heterosis in livestock.

Lethal recessives are mutations that cause early lethality in homozygous state that usually occur at very low frequency in wild and domestic populations. In livestock, however, those mutations might become more prevalent as a result of inbreeding. In this study, we report five such recessive lethal haplotypes that cause embryonic lethality in homozygous state in pigs. The causal mutations are of different type but all destroy the structure of essential genes involved in cellular housekeeping processes, essential for embryonic development. The lethal recessives have substantial impact on the population fitness affecting up to 3% of the population litters, causing the death of 0.52% of the total population of embryos. Moreover, these 'natural knockouts' can increase understanding of gene function within the mammalian clade. Together, our study will allow monitoring, and facilitate the purging and partial elimination of recessive lethal mutations in frequently used pig breeds.

Recent advances in pig reproduction: Focus on impact of genetic selection for female fertility

In the past 30 years, sows have been successfully selected for a shorter weaning-to-oestrus interval and increased litter size. This review discusses the consequences of this selection for the reproductive physiology of sows, including the consequences for litter characteristics at birth. It also discusses breeding and management opportunities to deal with this changed genetics.

Balancing selection on a recessive lethal deletion with pleiotropic effects on two neighboring genes in the porcine genome

Livestock populations can be used to study recessive defects caused by deleterious alleles. The frequency of deleterious alleles including recessive lethal alleles can stay at high or moderate frequency within a population, especially if recessive lethal alleles exhibit an advantage for favourable traits in heterozygotes. In this study, we report such a recessive lethal deletion of 212kb (del) within the BBS9 gene in a breeding population of pigs. The deletion produces a truncated BBS9 protein expected to cause a complete loss-of-function, and we find a reduction of approximately 20% on the total number of piglets born from carrier by carrier matings. Homozygous del/del animals die mid- to late-gestation, as observed from high increase in numbers of mummified piglets resulting from carrier-by-carrier crosses. The moderate 10.8% carrier frequency (5.4% allele frequency) in this pig population suggests an advantage on a favourable trait in heterozygotes. Indeed, heterozygous carriers exhibit increased growth rate, an important selection trait in pig breeding. Increased growth and appetite together with a lower birth weight for carriers of the BBS9 null allele in pigs is analogous to the phenotype described in human and mouse for (naturally occurring) BBS9 null-mutants. We show that fetal death, however, is induced by reduced expression of the downstream BMPER gene, an essential gene for normal foetal development. In conclusion, this study describes a lethal 212kb deletion with pleiotropic effects on two different genes, one resulting in fetal death in homozygous state (BMPER), and the other increasing growth (BBS9) in heterozygous state. We provide strong evidence for balancing selection resulting in an unexpected high frequency of a lethal allele in the population. This study shows that the large amounts of genomic and phenotypic data routinely generated in modern commercial breeding programs deliver a powerful tool to monitor and control lethal alleles much more efficiently.

We report a large deletion within the BBS9 gene that induces late fetal mortality in homozygous affected animals in a commercial pig population. This late fetal mortality causes the fetus to become encapsulated and desiccated during the remaining time of the pregnancy, a process called mummification. The unusually high carrier frequency for this lethal deletion (10.8%) likely results from its strong positive association with growth rate in heterozygous individuals, an important selection trait in the pig breeding industry. Interestingly, we show that the positive effect on growth is induced by a heterozygous loss-of-function of the BBS9 gene, associated with obesity in human and mouse. However, late fetal mortality is induced by insufficient expression of the BMPER gene located directly downstream of the deletion which affects its regulatory elements required for gene expression. Together, our study shows an unique example of allelic pleiotropy in which one allele (deletion) is responsible for both increased growth and late fetal mortality by affecting two different genes.