Dataset Information

Genome-Wide Association Study of Piglet Uniformity and Farrowing Interval.

ABSTRACT: Piglet uniformity (PU) and farrowing interval (FI) are important reproductive traits related to production and economic profits in the pig industry. However, the genetic architecture of the longitudinal trends of reproductive traits still remains elusive. Herein, we performed a genome-wide association study (GWAS) to detect potential genetic variation and candidate genes underlying the phenotypic records at different parities for PU and FI in a population of 884 Large White pigs. In total, 12 significant SNPs were detected on SSC1, 3, 4, 9, and 14, which collectively explained 1-1.79% of the phenotypic variance for PU from parity 1 to 4, and 2.58-4.11% for FI at different stages. Of these, seven SNPs were located within 16 QTL regions related to swine reproductive traits. One QTL region was associated with birth body weight (related to PU) and contained the peak SNP MARC0040730, and another was associated with plasma FSH concentration (related to FI) and contained the SNP MARC0031325. Finally, some positional candidate genes for PU and FI were identified because of their roles in prenatal skeletal muscle development, fetal energy substrate, pre-implantation, and the expression of mammary gland epithelium. Identification of novel variants and candidate genes will greatly advance our understanding of the genetic mechanisms of PU and FI, and suggest a specific opportunity for improving marker assisted selection or genomic selection in pigs.

SUBMITTER: Wang Y

PROVIDER: S-EPMC5712316 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Genome-Wide Association Study of Piglet Uniformity and Farrowing Interval.

Wang Yuan Y Ding Xiangdong X Tan Zhen Z Ning Chao C Xing Kai K Yang Ting T Pan Yongjie Y Sun Dongxiao D Wang Chuduan C

Frontiers in genetics 20171128

Piglet uniformity (PU) and farrowing interval (FI) are important reproductive traits related to production and economic profits in the pig industry. However, the genetic architecture of the longitudinal trends of reproductive traits still remains elusive. Herein, we performed a genome-wide association study (GWAS) to detect potential genetic variation and candidate genes underlying the phenotypic records at different parities for PU and FI in a population of 884 Large White pigs. In total, 12 si ...[more]

PMID: 29234349

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Project description:BackgroundSince 01.01.2021, suckling piglets may no longer be castrated without anaesthesia in Germany. Previous studies showed castration using isoflurane anaesthesia in combination with a suitable analgesic, meet the requirements of the German Animal Welfare Act. It can be carried out independently by farmers and other qualified persons with an automated and certified isoflurane device. Therefore, the aim of the present field study was to implement the use of three different anaesthetic devices for surgical castration of male piglets under automated isoflurane anaesthesia on 15 conventional pig farms in southern Germany. In addition, the depth of anaesthesia based on defensive movements, the labour time required in contrast to anaesthetic-free castration, castration-related anaesthetic incidents and the piglet mortality rate as well as occupational safety were investigated. For this purpose, farrowing batches of 11,574 piglets castrated under isoflurane anaesthesia (IA) were compared with the results of the 1568 piglets of anaesthetic-free farrowing batches (AF).ResultsIn total, 80.1% of the castrated piglets showed sufficient depth of anaesthesia, although this varied significantly between devices. 1.7% of the piglets suffered an anaesthetic incident, of which 0.1% died during or within 24 h after anaesthesia. The required time for the complete working process differed significantly between AF (1.7 ± 0.8 min/piglet) and IA batches (2.2 ± 0.8 min/piglet) but not for castration itself. The mean isoflurane consumption was 0.57 ± 0.27 ml/piglet and differed significantly between the devices (p < 0.001). The isoflurane concentration in the ambient air of the person-related workplace safety measurements was below the internationally lowest value of 15 mg/m3 from Ontario and Israel.ConclusionIn conclusion, 2 of the 3 types of devices used, a sufficient depth of anaesthesia during castration under isoflurane was achieved in 85% of castrated piglets. Anaesthetic incidents occurred in 1.7% of the animals, of which 0.1% died. Castration under isoflurane is more time-consuming than anaesthetic-free castration, but the castration time itself did not differ significantly. The occupational exposure limits were below the internationally lowest limit value of 15 mg/m3 for the persons involved. Even though castration under isoflurane is more time consuming than anaesthetic-free castration, it is a well-establishable method for practice and a dear improvement for animal welfare.

Project description:BackgroundLow cardiorespiratory fitness (V̇O2peak) is highly associated with chronic disease and mortality from all causes. Whilst exercise training is recommended in health guidelines to improve V̇O2peak, there is considerable inter-individual variability in the V̇O2peak response to the same dose of exercise. Understanding how genetic factors contribute to V̇O2peak training response may improve personalisation of exercise programs. The aim of this study was to identify genetic variants that are associated with the magnitude of V̇O2peak response following exercise training.MethodsParticipant change in objectively measured V̇O2peak from 18 different interventions was obtained from a multi-centre study (Predict-HIIT). A genome-wide association study was completed (n = 507), and a polygenic predictor score (PPS) was developed using alleles from single nucleotide polymorphisms (SNPs) significantly associated (P < 1 × 10-5) with the magnitude of V̇O2peak response. Findings were tested in an independent validation study (n = 39) and compared to previous research.ResultsNo variants at the genome-wide significance level were found after adjusting for key covariates (baseline V̇O2peak, individual study, principal components which were significantly associated with the trait). A Quantile-Quantile plot indicates there was minor inflation in the study. Twelve novel loci showed a trend of association with V̇O2peak response that reached suggestive significance (P < 1 × 10-5). The strongest association was found near the membrane associated guanylate kinase, WW and PDZ domain containing 2 (MAGI2) gene (rs6959961, P = 2.61 × 10-7). A PPS created from the 12 lead SNPs was unable to predict V̇O2peak response in a tenfold cross validation, or in an independent (n = 39) validation study (P > 0.1). Significant correlations were found for beta coefficients of variants in the Predict-HIIT (P < 1 × 10-4) and the validation study (P < × 10-6), indicating that general effects of the loci exist, and that with a higher statistical power, more significant genetic associations may become apparent.ConclusionsOngoing research and validation of current and previous findings is needed to determine if genetics does play a large role in V̇O2peak response variance, and whether genomic predictors for V̇O2peak response trainability can inform evidence-based clinical practice. Trial registration Australian New Zealand Clinical Trials Registry (ANZCTR), Trial Id: ACTRN12618000501246, Date Registered: 06/04/2018, http://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=374601&isReview=true .

Project description:The PR interval on the electrocardiogram reflects atrial and atrioventricular nodal conduction time. The PR interval is heritable, provides important information about arrhythmia risk, and has been suggested to differ among human races. Genome-wide association (GWA) studies have identified common genetic determinants of the PR interval in individuals of European and Asian ancestry, but there is a general paucity of GWA studies in individuals of African ancestry. We performed GWA studies in African American individuals from four cohorts (n?=?6,247) to identify genetic variants associated with PR interval duration. Genotyping was performed using the Affymetrix 6.0 microarray. Imputation was performed for 2.8 million single nucleotide polymorphisms (SNPs) using combined YRI and CEU HapMap phase II panels. We observed a strong signal (rs3922844) within the gene encoding the cardiac sodium channel (SCN5A) with genome-wide significant association (p<2.5 x 10??) in two of the four cohorts and in the meta-analysis. The signal explained 2% of PR interval variability in African Americans (beta ?=?5.1 msec per minor allele, 95% CI ?=?4.1-6.1, p?=?3 x 10?²³). This SNP was also associated with PR interval (beta?=?2.4 msec per minor allele, 95% CI?=?1.8-3.0, p?=?3 x 10?¹?) in individuals of European ancestry (n?=?14,042), but with a smaller effect size (p for heterogeneity <0.001) and variability explained (0.5%). Further meta-analysis of the four cohorts identified genome-wide significant associations with SNPs in SCN10A (rs6798015), MEIS1 (rs10865355), and TBX5 (rs7312625) that were highly correlated with SNPs identified in European and Asian GWA studies. African ancestry was associated with increased PR duration (13.3 msec, p?=?0.009) in one but not the other three cohorts. Our findings demonstrate the relevance of common variants to African Americans at four loci previously associated with PR interval in European and Asian samples and identify an association signal at one of these loci that is more strongly associated with PR interval in African Americans than in Europeans.

Dataset Information

Genome-Wide Association Study of Piglet Uniformity and Farrowing Interval.

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Genome-Wide Association Study of Piglet Uniformity and Farrowing Interval.

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