Longevity in South African Afrikaner cows as assessed through survival analysis.

The Afrikaner breed of cattle is indigenous to South Africa and, due to their hardiness, was once the most popular breed amongst South African farmers, although in recent years their numbers have decreased. The goal of this study was to assess factors affecting length of productive life, defined as the interval between production of the first and last calf, in Afrikaner cattle using survival analysis. The data spanned 40 years with an observed measure of length of life for 29,379 cows from 374 herds. Relative to similar analyses, few (n = 2964; 8.4%) cows had records that were right censored. The median length of productive life of an Afrikaner cow was just less than 6 years. Cows that were younger at their first parturition had longer productive lives than those that were older at their first calving. Cows that were born in the period from December to February had shorter productive lives than those born between March and November. The estimated animal genetic variance of 0.266 resulted in a heritability estimate for length of productive life in Afrikaner cattle of 0.225. Thus, there appeared to be sufficient additive genetic variance in Afrikaner cattle to enable genetic improvement in their length of productive life.

Phenotypic and genetic relationships among anogenital distance, anti-Müllerian hormone, and in vitro embryo production in Gyr dairy cattle.

Anti-Müllerian hormone (AMH) concentration and number of recovered oocytes (ROOC) are phenotypic parameters associated with in vitro embryo production (IVEP). More recently, anogenital distance (AGD) has been proposed as a proxy for fertility in dairy cattle that is easy to collect at a low cost. The aim of this study was to characterize the AGD and its phenotypic and genetic associations with AMH and IVEP in Bos indicus Gyr dairy cattle. The hypothesis was that the number of ROOC, in vitro-produced embryos, and AMH concentration would increase as the AGD decreases. From July to December 2021, a single morphometrical measurement of AGD was collected in 552 donors from 6 herds in Brazil. A subset of donors had AMH assayed on the same day. Only ovum pick-up events that occurred up to 12 mo preceding and 7 mo succeeding the AGD measurement were used to assess the association between AGD, AMH, and IVEP. Thus, 472 donors (1,551 ovum pick-up events and 140 donors with AMH) were considered in the analysis. A raw average was calculated for each individual donor's ROOC, viable oocytes, total produced embryos, viability rate, and embryo rate (defined as total produced embryos/viable oocytes). Comparisons were conducted within the age categories of 3 to <6 yr or 6 to <10 yr. Phenotypic associations were performed in SAS software (SAS Institute Inc., Cary, NC). Genetic correlations were estimated using the BLUPF90 family of programs. The AGD (128.7 mm ± 14; mean ± standard deviation) had a normal distribution and was highly variable (83 to 172 mm) among the Gyr population. Our experimental hypothesis was partially supported by a phenotypic association of a greater number of total produced embryos (R2 = 0.023) as AGD decreased. Our results failed to support an increase in AMH concentration along with a decrease in AGD. In addition, positive and low genetic correlations were observed between AGD and viable oocytes (r = 0.08), and embryo rate (r = 0.20). A greater number of viable oocytes and embryos were observed in donors in the high compared with intermediate and low ROOC categories within both age categories. The age interval of 3 to <6 yr showed a greater number of recovered and viable oocytes for the high AMH compared with the low category, but no differences were observed among the AGD categories. In summary, for the Gyr breed, AGD was phenotypically inversely associated with a quantity-related parameter, such as the total number of produced embryos. In contrast, AGD showed a low genetic correlation with qualitative-related outcomes such as viable oocytes and embryo rate. Further studies should be performed to validate these retrospective analyses and to better understand the association between AGD and IVEP.

Strategies for accommodating gene-edited sires and their descendants in genetic evaluations.

Gene editing has the potential to expedite the rate of genetic gain for complex traits. However, changing nucleotides (i.e., QTN) in the genome can affect the additive genetic relationship among individuals and, consequently, impact genetic evaluations. Therefore, the objectives of this study were to estimate the impact of including gene-edited individuals in the genetic evaluation and investigate modeling strategies to mitigate potential errors. For that, a beef cattle population was simulated for nine generations (N = 13,100). Gene-edited sires (1, 25, or 50) were introduced in generation 8. The number of edited QTN was 1, 3, or 13. Genetic evaluations were performed using pedigree, genomic data, or a combination of both. Relationships were weighted based on the effect of the edited QTN. Comparisons were made using the accuracy, average absolute bias, and dispersion of the estimated breeding values (EBV). In general, the EBV of the first generation of progeny of gene-edited sires were associated with greater average absolute bias and overdispersion than the EBV of the progeny of non-gene-edited sires (P ≤ 0.001). Weighting the relationship matrices increased (P ≤ 0.001) the accuracy of EBV when the gene-edited sires were introduced by 3% and decreased (P ≤ 0.001) the average absolute bias and dispersion for the progeny of gene-edited sires. For the second generation of descendants of gene-edited sires, the absolute bias increased as the number of edited alleles increased; however, the rate of increase in absolute bias was 0.007 for each allele edited when the relationship matrices were weighted compared with 0.10 when the relationship matrices were not weighted. Overall, when gene-edited sires are included in genetic evaluations, error is introduced in the EBV, such that the EBV of progeny of gene-edited sires are underestimated. Hence, the progeny of gene-edited sires would be less likely to be selected to be parents of the next generation than what was expected based on their true genetic merit. Therefore, modeling strategies such as weighting the relationship matrices are essential to avoid incorrect selection decisions if animals that have been edited for QTN underlying complex traits are introduced into genetic evaluations.

Coupling gene editing, a technology with the potential to make specific changes to DNA sequence (e.g., quantitative trait nucleotide, QTN), with genomic selection can generate faster genetic gain in economically important traits. However, gene editing would impact the genetic relationship among individuals and, consequently, genetic evaluations. The objectives of this study were to understand how gene editing impacts genetic prediction and develop strategies to mitigate potential errors in estimated breeding values (EBV). A beef cattle population was simulated (N = 13,100; nine generations) with the introduction of gene-edited sires in generation 8. Genetic evaluations were performed using pedigree and genomic data. Relationships were weighted based on the effect of the edited QTN. In general, the EBV of the first generation of progeny of gene-edited sires were associated with greater average absolute bias and overdispersion than the EBV of the progeny of non-gene-edited sires. Weighting the relationship matrices decreased the average absolute bias and dispersion for the progeny of gene-edited sires. For the second generation of descendants of gene-edited sires, the absolute bias increased by 0.10 for each allele edited. By weighting the relationship matrices, the rate of increase in absolute bias per allele decreased to 0.007. Therefore, when gene-edited sires are included in genetic evaluations, strategies such as weighting the relationship matrices should be considered to avoid incorrect selection decisions.

Temporality of ovarian steroids and LH/FSH pulse profiles encompassing selection of the dominant follicle in heifers†.

The tested hypotheses were (1) LH/FSH pulses and F2 diameter are diminished by P4 and, (2) E2 increases during the transition to deviation and alters LH/FSH pulses. On Day 5 (Day 0 = ovulation), heifers were randomized into an untreated group (HiP4, n = 11), and a prostaglandin analog treated group (NoP4, n = 10). On Day 6, a follicular wave was induced by follicle ablation. Ultrasound and blood collections were performed every 12 h from Days 7 to 11. Blood was collected every 15 min for 10 h on Day 9 (largest follicle expected to be ~7.5 mm). Estradiol was ~75% greater (0.36 ± 0.14 vs 0.63 ± 0.19 pg/mL) in heifers with F1 ≥ 7.2 mm than in heifers with F1 < 7.2 mm. The HiP4 had smaller second largest follicle (F2) diameter, lower estradiol (P = 0.06), LH pulse baseline and peak concentrations (P < 0.007), in addition to half the frequency of LH/FSH pulses (4.1 ± 0.3 vs 9.6 ± 0.7 in 10 h) than the NoP4. Within HiP4, heifers with F1 ≥ 7.2 mm had ~25% fewer (P = 0.03) LH pulses compared to heifers with F1 < 7.2 mm. In contrast, within the NoP4, heifers with F1 ≥ 7.2 mm had ~75% greater LH (P = 0.05) and FSH (P = 0.08) pulse amplitude. We propose that greater F2 diameter at deviation in low P4 is related to greater LH baseline and peak concentrations, and greater frequency of LH/FSH pulses. A greater increase in E2 after F1 reaches ~7.2 mm results in further stimulation of LH/FSH pulse amplitude. Elevated P4 not only diminished frequency of LH/FSH pulses but also converted an E2 increase into a negative feedback effect on LH/FSH pulse frequency leading to smaller F2 at deviation.

Genetic and phenotypic associations of mitochondrial DNA copy number, SNP, and haplogroups with growth and carcass traits in beef cattle.

Mitochondrial DNA copy number (mtDNA CN) is heritable and easily obtained from low-pass sequencing (LPS). This study investigated the genetic correlation of mtDNA CN with growth and carcass traits in a multi-breed and crossbred beef cattle population. Blood, leucocyte, and semen samples were obtained from 2,371 animals and subjected to LPS that resulted in nuclear DNA (nuDNA) and mtDNA sequence reads. Mitochondrial DNA CN was estimated as the ratio of mtDNA to nuDNA coverages. Variant calling was performed from mtDNA, and 11 single nucleotide polymorphisms (SNP) were identified in the population. Samples were classified in taurine haplogroups. Haplogroup and mtDNA type were further classified based on the 11 segregating SNP. Growth and carcass traits were available for between 7,249 and 60,989 individuals. Associations of mtDNA CN, mtDNA haplogroups, mtDNA types, and mtDNA SNP with growth and carcass traits were estimated with univariate animal models, and genetic correlations were estimated with a bivariate animal model based on pedigree. Mitochondrial DNA CN tended (P-value ≤0.08) to be associated with birth weight and weaning weight. There was no association (P-value >0.10) between mtDNA SNP, haplogroups, or types with growth and carcass traits. Genetic correlation estimates of mtDNA CN were -0.30 ± 0.16 with birth weight, -0.31 ± 0.16 with weaning weight, -0.15 ± 0.14 with post-weaning gain, -0.11 ± 0.19 with average daily dry-matter intake, -0.04 ± 0.22 with average daily gain, -0.29 ± 0.13 with mature cow weight, -0.11 ± 0.13 with slaughter weight, -0.14 ± 0.13 with carcass weight, -0.07 ± 0.14 with carcass backfat, 0.14 ± 0.14 with carcass marbling, and -0.06 ± 0.14 with ribeye area. In conclusion, mtDNA CN was negatively correlated with most traits investigated, and the genetic correlation was stronger with growth traits than with carcass traits.

This study investigated mitochondrial DNA copy number (mtDNA CN) as a potential genetic indicator of growth and carcass traits in a composite beef cattle population. Mitochondrial DNA CN was previously shown to be under genetic control. The current study estimated the genetic relationship of mtDNA CN with growth and carcass traits. Blood, leucocyte, and semen samples were obtained from 2,371 animals and subjected to whole-genome sequencing at a low depth that resulted in nuclear DNA and mtDNA sequence reads. Mitochondrial DNA CN was estimated as the ratio of mtDNA to nuclear DNA coverages. Growth and carcass traits were available for between 7,249 and 60,989 individuals. Genetic parameters were estimated from an animal model based on pedigree. Genetic correlation estimates of mtDNA CN with growth and carcass traits were low to moderate and mostly negative. These indicate that selection for lower mtDNA would be associated with an increase in birth weight, weaning weight, post-weaning gain, average daily dry-matter intake, mature cow weight, slaughter weight, and carcass weight. Therefore, the by-product of whole-genome sequencing at a low depth could be used as an indicator trait for growth and carcass traits in genetic evaluations, but the genetic relationships are not likely strong enough to prioritize mtDNA ahead of routinely used indicator traits.

DNA methylation profile in beef cattle is influenced by additive genetics and age.

DNA methylation (DNAm) has been considered a promising indicator of biological age in mammals and could be useful to increase the accuracy of phenotypic prediction in livestock. The objectives of this study were to estimate the heritability and age effects of site-specific DNAm (DNAm level) and cumulative DNAm across all sites (DNAm load) in beef cattle. Blood samples were collected from cows ranging from 217 to 3,192 days (0.6 to 8.7 years) of age (n = 136). All animals were genotyped, and DNAm was obtained using the Infinium array HorvathMammalMethylChip40. Genetic parameters for DNAm were obtained from an animal model based on the genomic relationship matrix, including the fixed effects of age and breed composition. Heritability estimates of DNAm levels ranged from 0.18 to 0.72, with a similar average across all regions and chromosomes. Heritability estimate of DNAm load was 0.45. The average age effect on DNAm level varied among genomic regions. The DNAm level across the genome increased with age in the promoter and 5' UTR and decreased in the exonic, intronic, 3' UTR, and intergenic regions. In addition, DNAm level increased with age in regions enriched in CpG and decreased in regions deficient in CpG. Results suggest DNAm profiles are influenced by both genetics and the environmental effect of age in beef cattle.

Influence of environmental factors and genetic variation on mitochondrial DNA copy number.

Mitochondrial DNA copy number (mtDNA CN) has been shown to be highly heritable and associated with traits of interest in humans. However, studies are lacking in the literature for livestock species such as beef cattle. In this study, 2,371 individuals from a crossbred beef population comprising the Germplasm Evaluation program from the U.S. Meat Animal Research Center had samples of blood, leucocyte, or semen collected for low-pass sequencing (LPS) that resulted in both nuclear DNA (nuDNA) and mitochondrial DNA (mtDNA) sequence reads. Mitochondrial DNA CN was estimated based on the ratio of mtDNA to nuDNA coverages. Genetic parameters for mtDNA CN were estimated from an animal model based on a genomic relationship matrix (~87K SNP from the nuDNA). Different models were used to test the effects of tissue, sex, age at sample collection, heterosis, and breed composition. Maternal effects, assessed by fitting a maternal additive component and by fitting eleven SNP on the mtDNA, were also obtained. As previously reported, mtDNA haplotypes were used to classify individuals into Taurine haplogroups (T1, T2, T3/T4, and T5). Estimates of heritability when fitting fixed effects in addition to the intercept were moderate, ranging from 0.11 to 0.31 depending on the model. From a model ignoring contemporary group, semen samples had the lowest mtDNA CN, as expected, followed by blood and leucocyte samples (P ≤ 0.001). The effect of sex and the linear and quadratic effects of age were significant (P ≤ 0.02) depending on the model. When significant, females had greater mtDNA CN than males. The effects of heterosis and maternal heterosis were not significant (P ≥ 0.47). The estimates of maternal and mtDNA heritability were near zero (≤0.03). Most of the samples (98%) were classified as haplogroup T3. Variation was observed in the mtDNA within Taurine haplogroups, which enabled the identification of 24 haplotypes. These results suggest that mtDNA CN is under nuclear genetic control and would respond favorably to selection.

Mitochondrial DNA copy number (mtDNA CN) is related to mitochondrial function and thus may be indicative of energy efficiency. This study investigated the genetic and non-genetic factors associated with mtDNA CN in a beef cattle population of 2,371 animals using whole-genome sequencing at low depth. Blood, leucocyte, and semen samples were subjected to whole-genome sequencing, resulting in mtDNA and nuclear DNA to estimate mtDNA CN. Findings revealed that 11% to 31% of the variation in mtDNA CN is under genetic control. Non-genetic effects of tissue type, age, and sex were significantly associated with mtDNA CN. Semen samples had the lowest mtDNA CN, followed by blood and leucocyte samples. Younger and older ages were associated with a greater mtDNA CN than intermediate ages. Females had greater mtDNA CN than males. Heterosis and breed composition were not significantly associated with mtDNA CN. These results suggest that mtDNA CN is heritable and would respond favorably to genetic selection.

Genetic parameters, heterosis, and breed effects for body condition score and mature cow weight in beef cattle.

Understanding the genetic relationship between mature cow weight (MWT) and body condition score (BCS) is useful to implement selection programs focused on cow efficiency. The objectives of this study were to estimate genetic parameters, heterosis, and breed effects for MWT and BCS. In total, 25,035 and 24,522 overlapping records were available for MWT and BCS on 6,138 and 6,131 cows, respectively, from the Germplasm Evaluation program, a crossbred beef population at the U.S. Meat Animal Research Center. Pedigree was available for 48,013 individuals. Univariate animal models were used to estimate heritabilities for each trait by parity. Bivariate animal models were used to estimate genetic correlations between parities within a trait and between traits within parities. Bivariate repeatability animal models were used to estimate genetic correlations between traits across parities. Estimates of heritability for different parities ranged from 0.43 ±â€…0.05 to 0.55 ±â€…0.07 for MWT and from 0.12 ±â€…0.03 to 0.25 ±â€…0.04 for BCS and were lower with the repeatability model at 0.40 ±â€…0.02 and 0.11 ±â€…0.01 for MWT and BCS, respectively. Estimates of repeatability were high for MWT (0.67 ±â€…0.005) and low for BCS (0.22 ±â€…0.006). Estimates of genetic correlation for MWT and BCS between parities were, in general, high, especially between consecutive parities. Estimates of genetic correlation between MWT and BCS were positive and moderate, ranging from 0.32 ±â€…0.09 to 0.68 ±â€…0.14. The direct heterosis estimates were 21.56 ±â€…3.53 kg (P ≤ 0.001) for MWT and 0.095 ±â€…0.034 (P ≤ 0.001) for BCS. Ordered by decreasing MWT, the breeds ranked Brahman, Charolais, Angus, Simmental, Salers, Hereford, Santa Gertrudis, Chiangus, Brangus, Red Angus, Shorthorn, Maine-Anjou, Gelbvieh, Beefmaster, Limousin, and Braunvieh. Ordered by decreasing BCS, the breeds ranked Brahman, Red Angus, Charolais, Angus, Hereford, Brangus, Beefmaster, Chiangus, Salers, Simmental, Maine-Anjou, Limousin, Santa Gertrudis, Shorthorn, Gelbvieh, and Braunvieh. Estimates of breed differences for MWT were also adjusted for BCS (AMWT), and in general, AMWT depicted smaller differences between breeds with some degree of re-ranking (r = 0.59). These results suggest that MWT and BCS are at least moderately genetically correlated and that they would respond favorably to selection. Estimates of breed differences and heterotic effects could be used to parameterize multibreed genetic evaluations for indicators of cow maintenance energy requirements.

The current study estimated the genetic relationship between mature cow weight (MWT) and body condition score (BCS), heterosis, and breed effects for these traits in a crossbred beef population. In total, 25,035 and 24,522 overlapping records were available for MWT and BCS, respectively. Pedigree was available for 48,013 individuals. Heritability and genetic correlations were estimated within a trait between parities, between traits within parities, and between traits across parities. Estimates of heritability ranged from 0.40 ±â€…0.02 to 0.55 ±â€…0.07 for MWT and from 0.11 ±â€…0.01 to 0.25 ±â€…0.04 for BCS. Genetic correlations within a trait and between parities were, in general, high. Estimates of genetic correlation between MWT and BCS were positive and moderate, ranging from 0.32 ±â€…0.09 to 0.68 ±â€…0.14. Heterosis effects were 21.56 ±â€…3.53 kg for MWT and 0.095 ±â€…0.034 for BCS. For both traits, Brahman and Braunvieh were associated with the highest and lowest breed effects, respectively. These results suggest that MWT and BCS would respond favorably to selection and are moderately genetically correlated. Breed differences and heterotic effects could be used to parameterize multibreed genetic evaluations for indicators of cow maintenance energy requirements.

Further host-genomic characterization of total antibody response to PRRSV vaccination and its relationship with reproductive performance in commercial sows: genome-wide haplotype and zygosity analyses.

BACKGROUND: The possibility of using antibody response (S/P ratio) to PRRSV vaccination measured in crossbred commercial gilts as a genetic indicator for reproductive performance in vaccinated crossbred sows has motivated further studies of the genomic basis of this trait. In this study, we investigated the association of haplotypes and runs of homozygosity (ROH) and heterozygosity (ROHet) with S/P ratio and their impact on reproductive performance. RESULTS: There was no association (P-value ≥ 0.18) of S/P ratio with the percentage of ROH or ROHet, or with the percentage of heterozygosity across the whole genome or in the major histocompatibility complex (MHC) region. However, specific ROH and ROHet regions were significantly associated (P-value ≤ 0.01) with S/P ratio on chromosomes 1, 4, 5, 7, 10, 11, 13, and 17 but not (P-value ≥ 0.10) with reproductive performance. With the haplotype-based genome-wide association study (GWAS), additional genomic regions associated with S/P ratio were identified on chromosomes 4, 7, and 9. These regions harbor immune-related genes, such as SLA-DOB, TAP2, TAPBP, TMIGD3, and ADORA. Four haplotypes at the identified region on chromosome 7 were also associated with multiple reproductive traits. A haplotype significantly associated with S/P ratio that is located in the MHC region may be in stronger linkage disequilibrium (LD) with the quantitative trait loci (QTL) than the previously identified single nucleotide polymorphism (SNP) (H3GA0020505) given the larger estimate of genetic variance explained by the haplotype than by the SNP. CONCLUSIONS: Specific ROH and ROHet regions were significantly associated with S/P ratio. The haplotype-based GWAS identified novel QTL for S/P ratio on chromosomes 4, 7, and 9 and confirmed the presence of at least one QTL in the MHC region. The chromosome 7 region was also associated with reproductive performance. These results narrow the search for causal genes in this region and suggest SLA-DOB and TAP2 as potential candidate genes associated with S/P ratio on chromosome 7. These results provide additional opportunities for marker-assisted selection and genomic selection for S/P ratio as genetic indicator for litter size in commercial pig populations.

Host Genetics of Response to Porcine Reproductive and Respiratory Syndrome in Sows: Reproductive Performance.

Porcine Reproductive and Respiratory Syndrome (PRRS) is historically the most economically important swine disease worldwide that severely affects the reproductive performance of sows. However, little is still known about the genetic basis of reproductive performance in purebred herds during a PRRS outbreak through the comparison of maternal and terminal breeds. Thus, the objective of this work was to explore the host genetics of response to PRRS in purebred sows from two breeds. Reproductive data included 2546 Duroc and 2522 Landrace litters from 894 and 813 purebred sows, respectively, which had high-density genotype data available (29,799 single nucleotide polymorphisms; SNPs). The data were split into pre-PRRS, PRRS, and post-PRRS phases based on standardized farrow-year-week estimates. Heritability estimates for reproductive traits were low to moderate (≤0.20) for Duroc and Landrace across PRRS phases. On the other hand, genetic correlations of reproductive traits between PRRS phases were overall moderate to high for both breeds. Several associations between MARC0034894, a candidate SNP for response to PRRS, with reproductive performance were identified (P-value < 0.05). Genomic analyses detected few QTL for reproductive performance across all phases, most explaining a small percentage of the additive genetic variance (≤8.2%, averaging 2.1%), indicating that these traits are highly polygenic. None of the identified QTL within a breed and trait overlapped between PRRS phases. Overall, our results indicate that Duroc sows are phenotypically more resilient to PRRS than Landrace sows, with a similar return to PRRS-free performance between breeds for most reproductive traits. Genomic prediction results indicate that genomic selection for improved reproductive performance under a PRRS outbreak is possible, especially in Landrace sows, by training markers using data from PRRS-challenged sows. On the other hand, the high genetic correlations with reproductive traits between PRRS phases suggest that selection for improved reproductive performance in a clean environment could improve performance during PRRS, but with limited efficiency due to their low heritability estimates. Thus, we hypothesize that an indicator trait that could be indirectly selected to increase the response to selection for these traits would be desirable and would also improve the reproductive performance of sows during a PRRS outbreak.

Host Genetics of Response to Porcine Reproductive and Respiratory Syndrome in Sows: Antibody Response as an Indicator Trait for Improved Reproductive Performance.

Antibody response to porcine reproductive and respiratory syndrome (PRRS) virus (PRRSV) infection, measured as sample-to-positive (S/P) ratio, has been proposed as an indicator trait for improved reproductive performance during a PRRS outbreak in Landrace sows. However, this result has not yet been validated in Landrace sows or evaluated in terminal sire lines. The main objectives of this work were to validate the use of S/P ratio as an indicator trait to select pigs during a PRRS outbreak and to explore the genetic basis of antibody response to PRRSV. Farrowing data included 2,546 and 2,522 litters from 894 Duroc and 813 Landrace sows, respectively, split into pre-PRRS, PRRS, and post-PRRS phases. Blood samples were taken from 1,231 purebred sows (541 Landrace and 690 Duroc) following a PRRS outbreak for subsequent PRRSV ELISA analysis for S/P ratio measurement. All animals had high-density genotype data available (29,799 single nucleotide polymorphisms; SNPs). Genetic parameters and genome-wide association studies (GWAS) for S/P ratio were performed for each breed separately. Heritability estimates (± standard error) of S/P ratio during the PRRS outbreak were moderate, with 0.35 ± 0.08 for Duroc and 0.34 ± 0.09 for Landrace. During the PRRS outbreak, favorable genetic correlations of S/P ratio with the number of piglets born alive (0.61 ± 0.34), number of piglets born dead (-0.33 ± 0.32), and number of stillborn piglets (-0.27 ± 0.31) were observed for Landrace sows. For Duroc, the GWAS identified a major quantitative trait locus (QTL) on chromosome (Chr) 7 (24-15 megabases; Mb) explaining 15% of the total genetic variance accounted for by markers (TGVM), and another one on Chr 8 (25 Mb) explaining 2.4% of TGVM. For Landrace, QTL on Chr 7 (24-25 Mb) and Chr 7 (108-109 Mb), explaining 31% and 2.2% of TGVM, respectively, were identified. Some of the SNPs identified in these regions for S/P ratio were associated with reproductive performance but not during the PRRS outbreak. Genomic prediction accuracies for S/P ratio were moderate to high for the within-breed analysis. For the between-breed analysis, these were overall low. These results further support the use of S/P ratio as an indicator trait for improved reproductive performance during a PRRS outbreak in Landrace sows.

Genomics of response to porcine reproductive and respiratory syndrome virus in purebred and crossbred sows: antibody response and performance following natural infection vs. vaccination.

Antibody response, measured as sample-to-positive (S/P) ratio, to porcine reproductive and respiratory syndrome virus (PRRSV) following a PRRSV-outbreak (S/POutbreak) in a purebred nucleus and following a PRRSV-vaccination (S/PVx) in commercial crossbred herds have been proposed as genetic indicator traits for improved reproductive performance in PRRSV-infected purebred and PRRSV-vaccinated crossbred sows, respectively. In this study, we investigated the genetic relationships of S/POutbreak and S/PVx with performance at the commercial (vaccinated crossbred sows) and nucleus level (non-infected and PRRSV-infected purebred sows), respectively, and tested the effect of previously identified SNP for these indicator traits. Antibody response was measured on 541 Landrace sows ~54 d after the start of a PRRSV outbreak, and on 906 F1 (Landrace × Large White) gilts ~50 d after vaccination with a commercial PRRSV vaccine. Reproductive performance was recorded for 711 and 428 Landrace sows before and during the PRRSV outbreak, respectively, and for 811 vaccinated F1 animals. The estimate of the genetic correlation (rg) of S/POutbreak with S/PVx was 0.72 ± 0.18. The estimates of rg of S/POutbreak with reproductive performance in vaccinated crossbred sows were low to moderate, ranging from 0.05 ± 0.23 to 0.30 ± 0.20. The estimate of rg of S/PVx with reproductive performance in non-infected purebred sows was moderate and favorable with number born alive (0.50 ± 0.23) but low (0 ± 0.23 to -0.11 ± 0.23) with piglet mortality traits. The estimates of rg of S/PVx were moderate and negative (-0.38 ± 0.21) with number of mummies in PRRSV-infected purebred sows and low with other traits (-0.30 ± 0.18 to 0.05 ± 0.18). Several significant associations (P0 > 0.90) of previously reported SNP for S/P ratio (ASGA0032063 and H3GA0020505) were identified for S/P ratio and performance in non-infected purebred and PRRSV-exposed purebred and crossbred sows. Genomic regions harboring the major histocompatibility complex class II region significantly contributed to the genetic correlation of antibody response to PRRSV with most of the traits analyzed. These results indicate that selection for antibody response in purebred sows following a PRRSV outbreak in the nucleus and for antibody response to PRRSV vaccination measured in commercial crossbred sows are expected to increase litter size in purebred and commercial sows.

Assessing the statistical training in animal science graduate programs in the United States: survey on statistical training.

Statistical analysis of data and understanding of experimental design are critical skills needed by animal science graduate students (ASGS). These skills are even more valuable with the increased development of high-throughput technologies. The objective of this study was to evaluate the perceived statistical training of U.S. ASGS. A survey with 38 questions was shared across U.S. universities, and 416 eligible ASGS from 43 universities participated in this study. The survey included questions on the demographics and overall training, graduate education on statistics, and self-assessment on statistics and career path of ASGS. Several analyses were performed: relationship between perceived received education (PRE; i.e., how ASGS evaluated their graduate education in statistics) and perceived knowledge (PK; i.e., how ASGS evaluated their knowledge in statistics from their education); ranking of statistical topics based on PRE, PK, and confidence in performing statistical analyses (CPSA); cluster analysis of statistical topics for PRE, PK, and CPSA; and factors (demographic, overall training, interest in statistics, and field of study) associated with the overall scores (OS) for PRE, PK, and CPSA. Students had greater (P < 0.05) PRE than PK for most of the statistical topics included in this study. The moderate to high repeatability of answers within statistical topics indicates substantial correlations in ASGS answers between PRE and PK. The cluster analysis resulted in distinct groups of "Traditional" and "Nontraditional" statistical topics. ASGS showed lower (P < 0.05) scores of PRE, PK, and CPSA in "Nontraditional" compared with "Traditional" statistical methods. Several factors were associated (P < 0.05) with the OS of PRE, PK, and CSPA. In general, factors related to greater training and interest in statistics of ASGS were associated with greater OS, such as taking more credits in statistics courses, having additional training in statistics outside the classroom, knowing more than one statistics software, and more. This study provided comprehensive information on the perceived level of education, knowledge, and confidence in statistics in ASGS in the United States. Although objective measurements of their training in statistics are needed, the current study suggests that ASGS have limited statistical training on topics of major importance for the current and future trends of data-driven research in animal sciences.

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 VSCc were identified. Of these, a QTL located on chromosome 3 at 33-34 Mb accounted for about 7.1% of the genetic variance for VSCc and VSCq. 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.

Genomic Analysis of IgG Antibody Response to Common Pathogens in Commercial Sows in Health-Challenged Herds.

Losses due to infectious diseases are one of the main factors affecting productivity in the swine industry, motivating the investigation of disease resilience-related traits for genetic selection. However, these traits are not expected to be expressed in the nucleus herds, where selection is performed. One alternative is to use information from the commercial level to identify and select nucleus animals genetically superior for coping with pathogen challenges. In this study, we analyzed the genetic basis of antibody (Ab) response to common infectious pathogens in health-challenged commercial swine herds as potential indicator traits for disease resilience, including Ab response to influenza A virus of swine (IAV), Mycoplasma hyopneumoniae (MH), porcine circovirus (PCV2), and Actinobacillus pleuropneumoniae (APP; different serotypes). Ab response was measured in blood at entry into gilt rearing, post-acclimation (∼40 days after entering the commercial herd), and parities 1 and 2. Heritability estimates for Ab response to IAV, MH, and PCV2 ranged from 0 to 0.76. Ab response to APP ranged from 0 to 0.40. The genetic correlation (r G ) of Ab response to IAV with MH, PCV2, PRRSV, and APPmean (average Ab responses for all serotypes of APP) were positive (>0.29) at entry. APPmean was negatively correlated with PCV2 and MH at entry and parity 2 but positively correlated with MH at post-acclimation and parity 1. Genomic regions associated with Ab response to different APP serotypes were identified on 13 chromosomes. The region on chromosome 14 (2 Mb) was associated with several serotypes of APP, explaining up to 4.3% of the genetic variance of Ab to APP7 at entry. In general, genomic prediction accuracies for Ab response were low to moderate, except average Ab response to all infectious pathogens evaluated. These results suggest that genetic selection of Ab response in commercial sows is possible, but with variable success depending on the trait and the time-point of collection. Future work is needed to determine genetic correlations of Ab response with disease resilience, reproductive performance, and other production traits.

Genetic Analysis of Antibody Response to Porcine Reproductive and Respiratory Syndrome Vaccination as an Indicator Trait for Reproductive Performance in Commercial Sows.

We proposed to investigate the genomic basis of antibody response to porcine reproductive and respiratory syndrome (PRRS) virus (PRRSV) vaccination and its relationship to reproductive performance in non-PRRSV-infected commercial sows. Nine hundred and six F1 replacement gilts (139 ± 17 days old) from two commercial farms were vaccinated with a commercial modified live PRRSV vaccine. Blood samples were collected about 52 days after vaccination to measure antibody response to PRRSV as sample-to-positive (S/P) ratio and for single-nucleotide polymorphism (SNP) genotyping. Reproductive performance was recorded for up to 807 sows for number born alive (NBA), number of piglets weaned, number born mummified (MUM), number of stillborn (NSB), and number of pre-weaning mortality (PWM) at parities (P) 1-3 and per sow per year (PSY). Fertility traits such as farrowing rate and age at first service were also analyzed. BayesC0 was used to estimate heritability and genetic correlations of S/P ratio with reproductive performance. Genome-wide association study (GWAS) and genomic prediction were performed using BayesB. The heritability estimate of S/P ratio was 0.34 ± 0.05. High genetic correlations (r g) of S/P ratio with farrowing performance were identified for NBA P1 (0.61), PWM P2 (-0.70), NSB P3 (-0.83), MUM P3 (-0.84), and NSB PSY (-0.90), indicating that genetic selection for increased S/P ratio would result in improved performance of these traits. A quantitative trait locus was identified on chromosome 7 (∼25 Mb), at the major histocompatibility complex (MHC) region, explaining ∼30% of the genetic variance for S/P ratio, mainly by SNPs ASGA0032113, H3GA0020505, and M1GA0009777. This same region was identified in the bivariate GWAS of S/P ratio and reproductive traits, with SNP H3GA0020505 explaining up to 10% (for NBA P1) of the genetic variance of reproductive performance. The heterozygote genotype at H3GA0020505 was associated with greater S/P ratio and NBA P1 (P = 0.06), and lower MUM P3 and NSB P3 (P = 0.07). Genomic prediction accuracy for S/P ratio was high when using all SNPs (0.67) and when using only those in the MHC region (0.59) and moderate to low when using all SNPs excluding those in the MHC region (0.39). These results suggest that there is great potential to use antibody response to PRRSV vaccination as an indicator trait to improve reproductive performance in commercial pigs.

Genetic and genomic characterization of vulva size traits in Yorkshire and Landrace gilts.

BACKGROUND: Reproductive performance is critical for efficient swine production. Recent results indicated that vulva size (VS) may be predictive of reproductive performance in sows. Study objectives were to estimate genetic parameters, identify genomic regions associated, and estimate genomic prediction accuracies (GPA) for VS traits. RESULTS: Heritability estimates of VS traits, vulva area (VA), height (VH), and width (VW) measurements, were moderately to highly heritable in Yorkshire, with 0.46 ± 0.10, 0.55 ± 0.10, 0.31 ± 0.09, respectively, whereas these estimates were low to moderate in Landrace, with 0.16 ± 0.09, 0.24 ± 0.11, and 0.08 ± 0.06, respectively. Genetic correlations within VS traits were very high for both breeds, with the lowest of 0.67 ± 0.29 for VH and VW for Landrace. Genome-wide association studies (GWAS) for Landrace, reveled genomic region associated with VS traits on Sus scrofa chromosome (SSC) 2 (154-157 Mb), 7 (107-110 Mb), 8 (4-6 Mb), and 10 (8-19 Mb). For Yorkshire, genomic regions on SSC 1 (87-91 and 282-287 Mb) and 5 (67 Mb) were identified. All regions explained at least 3.4% of the genetic variance. Accuracies of genomic prediction were moderate in Landrace, ranging from 0.30 (VH) to 0.61 (VA), and lower for Yorkshire, with 0.07 (VW) to 0.11 (VH). Between-breed and multi-breed genomic prediction accuracies were low. CONCLUSIONS: Our findings suggest that VS traits are heritable in Landrace and Yorkshire gilts. Genomic analyses show that major QTL control these traits, and they differ between breed. Genomic information can be used to increase genetic gains for these traits in gilts. Additional research must be done to validate the GWAS and genomic prediction results reported in our study.

Investigating the relationship between vaginal microbiota and host genetics and their impact on immune response and farrowing traits in commercial gilts.

Our objectives were to evaluate the interaction between host genetics and vaginal microbiota and their relationships with antibody (Ab) response to porcine reproductive and respiratory syndrome virus (PRRSV) vaccination and farrowing performance in commercial gilts. The farrowing performance traits were number born alive, number weaning (NW), total number born, number born dead, stillborn, mummies and preweaning mortality (PWM). The vaginal microbiota was collected on days 4 (D4) and 52 (D52) after vaccination for PRRSV. Blood samples were collected on D52 for Ab measurement. Actinobacteria, Bacterioidetes, Firmicutes, Proteobacteria and Tenericutes were the most abundant Phyla identified in the vaginal microbiota. Heritability ranged from ~0 to 0.60 (Fusobacterium) on D4 and from ~0 to 0.63 (Terrisporobacter) on D52, with 43 operational taxonomic units (OTUs) presenting moderate to high heritability. One major QTL on chromosome 12 was identified for 5 OTUs (Clostridiales, Acinetobacter, Ruminococcaceae, Campylobacter and Anaerococcus), among other 19 QTL. The microbiability for Ab response to PRRSV vaccination was low for both days (<0.07). For farrowing performance, microbiability varied from <0.001 to 0.15 (NW on D4). For NW and PWM, the microbiability was greater than the heritability estimates. Actinobacillus, Streptococcus, Campylobacter, Anaerococcus, Mollicutes, Peptostreptococcus, Treponema and Fusobacterium showed different abundance between low and high Ab responders. Finally, canonical discriminant analyses revealed that vaginal microbiota was able to classify gilts in high and low Ab responders to PRRSV vaccination with a misclassification rate of <0.02. Although the microbiota explained limited variation in Ab response and farrowing performance traits, there is still potential to explore the use of vaginal microbiota to explain variation in traits such as NW and PWM. In addition, these results revealed that there is a partial control of host genetic over vaginal microbiota, suggesting a possibility for genetic selection on the vaginal microbiota.

Effect of maternal feed restriction in dairy goats at different stages of gestation on skeletal muscle development and energy metabolism of kids at the time of births.

The aim was to determine effects of maternal feed restriction in dairy goats at gestational different stages on skeletal muscle development and energy metabolism in kids at birth. Six pregnant goats were fed 50% of total digestible nutrients (TDN) and crude protein (CP) (NRC, 2007) recommendations in the first half of gestation and then fed to 100% of the recommendations in the second half of gestation (treatment R-M). In the other group, eight pregnant goats were fed 100% of TDN and CP in the first half of gestation and 50% of a restricted diet the second half of gestation (treatment M-R). Birth weight, blood glucose concentration, muscle fiber number, and size of kids at birth were not affected by maternal feed restriction. The mRNA and protein abundance of myogenic, adipogenic and fibrogenic markers were not affected (P > 0.05) by maternal diet. With regard to values for variables in kid energy metabolism, mRNA abundance of the glycolic enzyme HKII was less (P = 0.03) in the M-R group. In conclusion, maternal feed restriction in the first or second half of gestation had no affect mRNA abundance on myogenic, adipogenic, and fibrogenic markers nor were there changes in skeletal muscle mesenchymal stem cell population of kids at the time of birth. There, however, may be detrimental effects on energy metabolism by reducing HKII gene expression in skeletal muscle of dairy goat kids at the time of birth.

Impact of energy restriction during late gestation on the muscle and blood transcriptome of beef calves after preconditioning.

BACKGROUND: Maternal nutrition has been highlighted as one of the main factors affecting intra-uterine environment. The increase in nutritional requirements by beef cows during late gestation can cause nutritional deficiency in the fetus and impact the fetal regulation of genes associated with myogenesis and immune response. METHODS: Forty days before the expected calving date, cows were assigned to one of two diets: 100% (control) or 70% (restricted group) of the daily energy requirement. Muscle samples were collected from 12 heifers and 12 steers, and blood samples were collected from 12 steers. The objective of this work was to identify and to assess the biological relevance of differentially expressed genes (DEG) in the skeletal muscle and blood of beef calves born from cows that experienced [or not] a 30% energy restriction during the last 40 days of gestation. RESULTS: A total of 160, 164, and 346 DEG (q-value< 0.05) were identified in the skeletal muscle for the effects of diet, sex, and diet-by-sex interaction, respectively. For blood, 452, 1392, and 155 DEG were identified for the effects of diet, time, and diet-by-time interaction, respectively. For skeletal muscle, results based on diet identified genes involved in muscle metabolism. In muscle, from the 10 most DEG down-regulated in the energy-restricted group (REST), we identified 5 genes associated with muscle metabolism and development: SLCO3A1, ATP6V0D1, SLC2A1, GPC4, and RASD2. In blood, among the 10 most DEG, we found genes related to response to stress up-regulated in the REST after weaning, such as SOD3 and INO80D, and to immune response down-regulated in the REST after vaccination, such as OASL, KLRF1, and LOC104968634. CONCLUSION: In conclusion, maternal energy restriction during late gestation may limit the expression of genes in the muscle and increase expression in the blood of calves. In addition, enrichment analysis showed that a short-term maternal energy restriction during pregnancy affects the expression of genes related to energy metabolism and muscle contraction, and immunity and stress response in the blood. Therefore, alterations in the intra-uterine environment can modify prenatal development with lasting consequences to adult life.