scholarly journals 27 Genomic relationship between antibody response to porcine reproductive and respiratory syndrome virus vaccination and reproductive performance in commercial sows

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 20-21
Author(s):  
Leticia P Sanglard ◽  
Rohan Fernando ◽  
Kent A Gray ◽  
Daniel C Linhares ◽  
Jack C Dekkers ◽  
...  

Abstract Antibody response, measured as sample-to-positive ratio (S/P), to porcine reproductive and respiratory syndrome (PRRS) after PRRS outbreaks has been proposed as an indicator trait to improve reproductive performance in PRRS-infected sows. However, waiting for a PRRS outbreak to occur and having different relationships in healthy pigs may limit the use of this trait. Thus, we proposed to investigate if this relationship also occurs between S/P to PRRS vaccination and reproductive performance in sows without exposure to PRRS. Nine hundred six F1 replacement gilts (139□17 days old) from two commercial farms were vaccinated with a commercial modified live PRRS virus vaccine. Blood samples were collected at 52 days after vaccination to measure S/P to PRRS and SNP genotyping. Reproductive performance included: number born alive (NBA), number of piglets weaned, number born mummified (MUM), number stillborn (NSB), and pre-weaning mortality (PWM) at parities (P) 1 to 3. Average performance was calculated for each trait per sow per year (PSY). Farrowing rate and age at first service were also analyzed. BayesC0 was used to estimate genetic correlations between S/P and reproductive performance. Bivariate genome-wide association studies of antibody response and reproductive traits were performed using BayesB. High genetic correlations between S/P and farrowing performance were identified for NBA_P1 (0.61±0.16), PWM_P2 (-0.64±0.15), PWM_P2 (-0.63±0.20), NSB_P3 (-0.84±0.05), MUM_P3 (-0.83±0.11), and NSB_PSY (-0.90±0.05). A QTL was identified on chromosome 7 (MHC region) for these reproductive traits and for S/P, explaining from 1.2% (PWM_P2) to 22.4% (S/P) of the genetic variance. SNP H3GA0020505 explained most of the variance in this region for these traits. Heterozygote animals for this SNP had overall better performance: greater S/P (P = 0.001), greater (P = 0.06) NBA_P1, and lesser (P = 0.06) MUM_P3 than other genotypes. These results suggest that antibody response to PRRS vaccination may be used as a genetic indicator to improve reproductive performance in commercial pigs.

2021 ◽  
Vol 12 ◽  
Author(s):  
Felipe M. W. Hickmann ◽  
José Braccini Neto ◽  
Luke M. Kramer ◽  
Yijian Huang ◽  
Kent A. Gray ◽  
...  

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.


2021 ◽  
Vol 99 (Supplement_1) ◽  
pp. 19-20
Author(s):  
Felipe Hickmann ◽  
José Braccini Neto ◽  
Luke M Kramer ◽  
Kent A Gray ◽  
Yijian Huang ◽  
...  

Abstract Previous studies proposed the use of antibody response to Porcine Reproductive and Respiratory Syndrome virus (PRRSV), measured as sample-to-positive (S/P) ratio, as a potential indicator trait to improve the reproductive performance of PRRSV-infected Landrace sows. However, this indicator trait has not yet been validated in Landrace sows or evaluated in a terminal sire line, such as Duroc. The main objective of this work was to perform host-genetic analyses of S/P ratio and reproductive traits during a PRRSV outbreak in maternal and terminal breeds. The data consisted of 690 Duroc and 541 Landrace multiparous sows (1.9±1.2 and 2.3±1.5, respectively) with S/P ratio collected at approximately 54 days after the predicted beginning of the outbreak. Of these, 644 Duroc and 528 Landrace sows also had reproductive data recorded during the PRRSV outbreak comprising number of piglets born alive (NBA), stillborn piglets (NSB), mummified piglets (NBM), number born dead (NBD; sum of NSB and NBM), total number born (TNB; sum of NBA and NBD), and number weaned (NW). All animals had genotype data on ~30K SNPs common across both breeds. Heritability estimates (± standard error) of S/P ratio during the PRRSV outbreak were moderate, with 0.33±0.06 for Duroc and 0.28±0.07 for Landrace. Reproductive traits during the PRRSV outbreak had overall low heritability estimates (≤0.18). Favorable genetic correlations of S/P ratio with NBA (0.65±0.33), in accordance with previous studies, and NBD (-0.33±0.28) were observed for Landrace sows only. Estimates of genetic correlation with other traits were -0.21±0.30 (NBM), -0.12±0.29 (NSB), 0.10±0.38 (NW), and 0.54±1.29 (TNB) for Landrace. For Duroc, these estimates were weaker: -0.33±0.40 (NBA), 0.26±0.27 (NBA), and 0.28±0.30 (NW), with convergence issues for mortality traits. These results further support the use of S/P ratio as an indicator trait for improved reproductive performance during a PRRSV outbreak in Landrace sows.


2021 ◽  
Vol 99 (Supplement_1) ◽  
pp. 18-18
Author(s):  
Leticia P Sanglard ◽  
Felipe Hickmann ◽  
Yijian Huang ◽  
Kent A Gray ◽  
Daniel Linhares ◽  
...  

Abstract Immunoglobulin G antibody response, measured as sample-to-positive (S/P) ratio, to Porcine Reproductive and Respiratory Syndrome virus (PRRSV) has been proposed as an indicator trait for improved reproductive performance in PRRSV-infected purebred sows and PRRSV-vaccinated crossbred gilts. In this study, we investigated the genetic correlations (rg) of S/P ratio following a PRRSV outbreak and PRRSV-vaccination with performance in non-exposed and PRRSV-exposed sows. PRRSV outbreak phase was defined based on previously described methodologies after the detection of typical clinical signs of PRRSV infection. 541 Landrace sows had S/P ratio measured at ~54 days after the beginning of the PRRSV outbreak (S/Poutbreak), and 906 Landrace x Large White naïve F1 gilts had S/P ratio measured at ~50 days after vaccination with a commercial modified live PRRSV vaccine (S/PVx). 711 and 428 Landrace sows had reproductive performance recorded before and during the PRRSV outbreak, respectively. 811 vaccinated F1 animals had farrowing performance for up to 3 parities. All animals were genotyped for ~28K SNPs. The estimate of rg of S/Poutbreakwith S/PVx was high (rg±SE = 0.72±0.18). Estimates of rg of S/Poutbreak with reproductive performance in F1 sows were low to moderate, ranging from 0.05±0.23 (number stillborn) to 0.30±0.20 (total number born). Estimates of rg of S/PVxwith reproductive performance in non-infected purebred sows were moderate and favorable with number born alive (0.50±0.23), but low (0 to -0.11±0.23) with litter mortality traits. Estimates of rg of S/PVx were moderate and negative (-0.47±0.18) with the number of mummies in PRRSV-infected purebred sows and low with other traits (-0.29±0.18 for total number born to 0.05±0.18 for number stillborn). These results indicate that selection for antibody response following a PRRSV outbreak collected in purebred sows and to PRRSV vaccination collected in commercial crossbred gilts may increase litter size of non-infected and PRRSV-exposed purebred and commercial crossbred sows.


Animals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 393
Author(s):  
Nora Laseca ◽  
Gabriel Anaya ◽  
Zahira Peña ◽  
Yamila Pirosanto ◽  
Antonio Molina ◽  
...  

Fertility is one of the key factors in the economic and productive success of the equine industry. Despite this, studies on the genetic causes affecting reproductive performance are scarce, especially in mares, where the genetic architecture of the reproductive traits is extremely complex. Today, with the increasing availability of new genomic methodologies for this species, we are presented with an interesting opportunity to understand the genetic basis of equine reproductive disorders. These include, among others, novel techniques for detecting chromosomal abnormalities, whose association with infertility in horses was established over 50 years ago; new sequencing technologies permitting an accurate detection of point mutations influencing fertility, as well as the study of inbreeding and molecular homozygosity, which has been widely suggested as one of the main causes of low reproductive performance in horses. Finally, over the last few years, reproductive performance has also been associated with copy number variants and candidate genes detected by genome-wide association studies on fertility traits. However, such studies are still scarce, probably because they depend on the existence of large and accurate phenotypic datasets of reproductive and/or fertility traits, which are still difficult to obtain in equines.


2020 ◽  
Vol 98 (Supplement_3) ◽  
pp. 162-163
Author(s):  
Felipe Hickmann ◽  
José Braccini Neto ◽  
Luke Kramer ◽  
Kent Gray ◽  
Yijian Huang ◽  
...  

Abstract Previous studies have shown that reproductive traits in sows during porcine reproductive and respiratory syndrome (PRRS) outbreaks are lowly heritable. However, little is known about the genomic basis of reproductive performance in PRRS virus (PRRSV)-infected sows. Thus, the objective of this work was to evaluate the genomic basis of reproductive performance in PRRSV-infected sows. Farrowing data from 475 Duroc and 405 Landrace sows that experienced a PRRS outbreak were used. Heritability and genome-wide association studies (GWAS) based on ~30K SNP genotypes were performed for each breed separately, for number of piglets born alive (NBA), stillborn piglets (NSB), mummified piglets (NM), piglets born dead (NBD; NSB+NM), total number of piglets born (TNB; NBA+NBD), and piglets weaned (NW). Heritabilities were estimated with ASReml using a model with the fixed-effect of parity and an animal random-effect, using a genomic-relationship matrix. GWAS was performed using Bayes-B in GenSel with a model fitting parity as fixed-effect and SNP effects as random. Heritability estimates (± standard error) for NBA, NSB, NM, NBD, TNB, and NW were 0.07±0.07, 0.02±0.11, 0.04±0.10, 0.08±0.08, 0.08±0.07, 0.06±0.04, respectively, for Duroc, and 0.09±0.07, 0.10±0.07, 0.10±0.08, 0.11±0.07, 0.07±0.08, 0.07±0.08, respectively, for Landrace. For Duroc, GWAS identified a quantitative trait locus (QTL) on chromosome (chr) 3 [114-120 megabases (Mb)] explaining 3.9% of the genetic variance (GV) for NBA, on chr 13 (189-193 Mb) explaining 2.7% GV for NBD, and on chr 5 (36-41 Mb) explaining 4.3% GV for TNB. For Landrace, GWAS identified a QTL on chr 13 (154-162 Mb) explaining 12.8% GV for NBA, on chr 14 (59-69 Mb) explaining 2.5% GV for NBD, and on chr 10 (7-9 Mb) explaining 4.1% GV for NW. These results indicate that reproductive traits are lowly heritable during a PRRS outbreak with few QTL identified in Duroc and Landrace sows.


2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 26-27
Author(s):  
Shafagh Valipour ◽  
Karim Karimi ◽  
Younes Miar

Abstract Improving reproductive efficiency is one of the main breeding goals in mink farming. Understanding the genetics of reproductive performance is essential for the development of effective breeding programs in mink. The objectives of this study are to 1) estimate the phenotypic and genetic parameters for litter sizes (LS), mortality rate at birth. (MB) and gestation-length (GL) traits; 2) perform genome-wide association studies (GWAS) for these reproductive traits; 3) implement GWAS results in the selection of mink for reproductive performance; 4) explore the potential for genomic selection in mink. The detailed reproductive performance on 3,500 female mink has been collected at the Canadian Center for Fur Animal Research at Dalhousie University (Truro, NS, Canada), in which, 1,000 of them will be genotyped with Affymetrix 50k SNP panel. A series of univariate and bivariate analyses were implemented in ASREML software to estimate the genetic and phenotypic parameters. Heritability estimates (±SE) were low-to-moderate, ranged from 0.06±0.02 for total number born to 0.23±0.03 for GL. High positive genetic correlations (±SE) were observed between LS traits, ranged from 0.59±0.18 to 0.85±0.11. There was a moderate genetic correlation (±SE) between MB and total number of kits born (0.46±0.15). However, MB had a favorable strong negative genetic correlation (±SE) with the number of weaned kits (–0.75±0.16). These estimated genetic parameters can be incorporated into Canadian mink breeding programs. Considering the low-to-moderate heritability of reproduction traits, the availability of the mink reference genome and genotyping panel will provide opportunities to accelerate mink breeding through genomics. The results of this project will contribute significantly to the current genetic knowledge of reproductive traits and identify the opportunities for genetic improvement through the application of genomics. The overall project aim is to develop a cost-effective, low-density panel of markers for the implementation of genomic selection for reproductive performance in mink.


2017 ◽  
Author(s):  
Jorien L. Treur ◽  
Mark Gibson ◽  
Amy E Taylor ◽  
Peter J Rogers ◽  
Marcus R Munafò

AbstractStudy Objectives:Higher caffeine consumption has been linked to poorer sleep and insomnia complaints. We investigated whether these observational associations are the result of genetic risk factors influencing both caffeine consumption and poorer sleep, and/or whether they reflect (possibly bidirectional) causal effects.Methods:Summary-level data were available from genome-wide association studies (GWAS) on caffeine consumption (n=91,462), sleep duration, and chronotype (i.e., being a ‘morning’ versus an ‘evening’ person) (both n=128,266), and insomnia complaints (n=113,006). Linkage disequilibrium (LD) score regression was used to calculate genetic correlations, reflecting the extent to which genetic variants influencing caffeine consumption and sleep behaviours overlap. Causal effects were tested with bidirectional, two-sample Mendelian randomization (MR), an instrumental variable approach that utilizes genetic variants robustly associated with an exposure variable as an instrument to test causal effects. Estimates from individual genetic variants were combined using inverse-variance weighted meta-analysis, weighted median regression and MR Egger regression methods.Results:There was no clear evidence for genetic correlation between caffeine consumption and sleep duration (rg=0.000,p=0.998), chronotype (rg=0.086,p=0.192) or insomnia (rg=-0.034,p=0.700). Two-sample Mendelian randomization analyses did not support causal effects from caffeine consumption to sleep behaviours, or the other way around.Conclusions:We found no evidence in support of genetic correlation or causal effects between caffeine consumption and sleep. While caffeine may have acute effects on sleep when taken shortly before habitual bedtime, our findings suggest that a more sustained pattern of high caffeine consumption is likely associated with poorer sleep through shared environmental factors.


2021 ◽  
Author(s):  
Zachary F Gerring ◽  
Jackson G Thorp ◽  
Eric R Gamazon ◽  
Eske M Derks

ABSTRACTGenome-wide association studies (GWASs) have identified thousands of risk loci for many psychiatric and substance use phenotypes, however the biological consequences of these loci remain largely unknown. We performed a transcriptome-wide association study of 10 psychiatric disorders and 6 substance use phenotypes (collectively termed “mental health phenotypes”) using expression quantitative trait loci data from 532 prefrontal cortex samples. We estimated the correlation due to predicted genetically regulated expression between pairs of mental health phenotypes, and compared the results with the genetic correlations. We identified 1,645 genes with at least one significant trait association, comprising 2,176 significant associations across the 16 mental health phenotypes of which 572 (26%) are novel. Overall, the transcriptomic correlations for phenotype pairs were significantly higher than the respective genetic correlations. For example, attention deficit hyperactivity disorder and autism spectrum disorder, both childhood developmental disorders, showed a much higher transcriptomic correlation (r=0.84) than genetic correlation (r=0.35). Finally, we tested the enrichment of phenotype-associated genes in gene co-expression networks built from prefrontal cortex. Phenotype-associated genes were enriched in multiple gene co-expression modules and the implicated modules contained genes involved in mRNA splicing and glutamatergic receptors, among others. Together, our results highlight the utility of gene expression data in the understanding of functional gene mechanisms underlying psychiatric disorders and substance use phenotypes.


2019 ◽  
Vol 29 (4) ◽  
pp. 689-702 ◽  
Author(s):  
Thibaud S Boutin ◽  
David G Charteris ◽  
Aman Chandra ◽  
Susan Campbell ◽  
Caroline Hayward ◽  
...  

Abstract Retinal detachment (RD) is a serious and common condition, but genetic studies to date have been hampered by the small size of the assembled cohorts. In the UK Biobank data set, where RD was ascertained by self-report or hospital records, genetic correlations between RD and high myopia or cataract operation were, respectively, 0.46 (SE = 0.08) and 0.44 (SE = 0.07). These correlations are consistent with known epidemiological associations. Through meta-analysis of genome-wide association studies using UK Biobank RD cases (N = 3 977) and two cohorts, each comprising ~1 000 clinically ascertained rhegmatogenous RD patients, we uncovered 11 genome-wide significant association signals. These are near or within ZC3H11B, BMP3, COL22A1, DLG5, PLCE1, EFEMP2, TYR, FAT3, TRIM29, COL2A1 and LOXL1. Replication in the 23andMe data set, where RD is self-reported by participants, firmly establishes six RD risk loci: FAT3, COL22A1, TYR, BMP3, ZC3H11B and PLCE1. Based on the genetic associations with eye traits described to date, the first two specifically impact risk of a RD, whereas the last four point to shared aetiologies with macular condition, myopia and glaucoma. Fine-mapping prioritized the lead common missense variant (TYR S192Y) as causal variant at the TYR locus and a small set of credible causal variants at the FAT3 locus. The larger study size presented here, enabled by resources linked to health records or self-report, provides novel insights into RD aetiology and underlying pathological pathways.


1981 ◽  
Vol 96 (1) ◽  
pp. 107-113 ◽  
Author(s):  
T. G. Martin ◽  
D. Nicholson ◽  
C. Smith ◽  
D. I. Sales

SUMMARYData on 902 ewes (1755 records) bom over 7 years in the synthetic ABRO Dam Line were analysed by least squares. Reproductive traits of the ewe were not affected by whether she was a single or a twin or by the age of her dam. Ewe age had major effects on all reproductive traits. Litter weight traits were affected by the sex distribution and the age of the litter when weighed.Heritability estimates, both by half sib and regression methods, were low for litter size, low to moderate for litter weights, and higher for ewe and fleece weights. Genetic correlations among the litter-weight traits were high. Together with the heritability estimates, they indicated that selection on litter weight at birth (and perhaps other traits) might give a greater change in total litter weight at weaning, the main measure of ewe productivity and the objective in improvement, than would direct selection.


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