scholarly journals Detection of genomic regions associated malformations in newborn piglets: a machine-learning approach

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11580
Author(s):  
Siroj Bakoev ◽  
Aleksei Traspov ◽  
Lyubov Getmantseva ◽  
Anna Belous ◽  
Tatiana Karpushkina ◽  
...  
Keyword(s):  
Congenital Anomalies ◽  
Genome Wide Association Study ◽  
Significant Proportion ◽  
Data Availability ◽  
Gradient Boosting ◽  
Large White ◽  
Newborn Piglets ◽  
A Genome ◽  
Gradient Boosting Machine ◽  
Fetal Malformations

Background A significant proportion of perinatal losses in pigs occurs due to congenital malformations. The purpose of this study is the identification of genomic loci associated with fetal malformations in piglets. Methods The malformations were divided into two groups: associated with limb defects (piglet splay leg) and associated with other congenital anomalies found in newborn piglets. 148 Landrace and 170 Large White piglets were selected for the study. A genome-wide association study based on the gradient boosting machine algorithm was performed to identify markers associated with congenital anomalies and piglet splay leg. Results Forty-nine SNPs (23 SNPs in Landrace pigs and 26 SNPs in Large White) were associated with congenital anomalies, 22 of which were localized in genes. A total of 156 SNPs (28 SNPs in Landrace; 128 in Large White) were identified for piglet splay leg, of which 79 SNPs were localized in genes. We have demonstrated that the gradient boosting machine algorithm can identify SNPs and their combinations associated with significant selection indicators of studied malformations and productive characteristics. Data availability Genotyping and phenotyping data are available at http://www.compubioverne.group/data-and-software/.

A genome‐wide association study reveals additive and dominance effects on growth and fatness traits in large white pigs

2021 ◽  
Vol 52 (5) ◽  
pp. 749-753
Author(s):  
W. Yang ◽  
J. Wu ◽  
J. Yu ◽  
X. Zheng ◽  
H. Kang ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Large White ◽  
Genome Wide ◽  
A Genome

scholarly journals A Genome-Wide Association Study in Large White and Landrace Pig Populations for Number Piglets Born Alive

PLoS ONE ◽  
2015 ◽  
Vol 10 (3) ◽  
pp. e0117468 ◽  
Author(s):  
Sarah Bergfelder-Drüing ◽  
Christine Grosse-Brinkhaus ◽  
Bianca Lind ◽  
Malena Erbe ◽  
Karl Schellander ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Large White ◽  
Genome Wide ◽  
A Genome ◽  
Landrace Pig

Abstract P430: Educational Attainment, Adherence to Healthy Lifestyle, and Risk of Cardiovascular Diseases

Circulation ◽  
2020 ◽  
Vol 141 (Suppl_1) ◽  
Author(s):  
Xiang Li ◽  
Tao Zhou ◽  
Hao Ma ◽  
Dianjianyi Sun ◽  
Yoriko Heianza ◽  
...  
Keyword(s):  
Cardiovascular Diseases ◽  
Educational Attainment ◽  
Genome Wide Association Study ◽  
Healthy Lifestyle ◽  
Smoking Status ◽  
Significant Proportion ◽  
Nucleotide Polymorphisms ◽  
Uk Biobank ◽  
Mediation Analyses ◽  
A Genome

Introduction: Lower educational attainment is one of the major socioeconomic factors contributing to cardiovascular diseases (CVD); higher education tends to be associated with healthier behaviors and lower risk of CVD. However, whether education plays a causal role in adherence to a healthy lifestyle, and if there is causality, how much of the education-CVD association is mediated by the lifestyle factors, has not been established. Methods: A healthy lifestyle score was constructed on body mass index, smoking status, physical activity, and diet. The causal relations between educational attainment and adherence to a healthy lifestyle was assessed by two-sample Mendelian Randomization analyses using summary statistics for single nucleotide polymorphisms (SNPs) identified from a genome-wide association study (GWAS) of educational attainment (N=1,131,881) and the UK Biobank cohort (N=425,770). We further performed mediation analyses to quantify the effect of educational attainment on the risk of CVD through healthy lifestyle among 386,442 participants in UK Biobank. Results: We found a significant positive causal relationship between years of education and adherence to a healthy lifestyle, independent of age, sex, alcohol intake, and person’s socioeconomic status. In addition, we found that adherence to favorable lifestyle mediated a 42.1%, 40.3%, and 33.5% reduction in the incidence of coronary heart disease (CHD), CVD events, and CVD mortality, respectively (all p <0.05). Conclusions: Our results indicate that educational attainment is causally associated with adherence to a healthy lifestyle, which in turn, mediates a significant proportion of the effect of educational attainment on cardiovascular events.

scholarly journals Natural variation in insect egg-induced cell death uncovers a role for L-type LECTIN RECEPTOR KINASE-I.1 in Arabidopsis

2020 ◽  
Author(s):  
Raphaël Groux ◽  
Caroline Gouhier-Darimont ◽  
Envel Kerdaffrec ◽  
Philippe Reymond
Keyword(s):  
Signaling Pathway ◽  
Genome Wide Association Study ◽  
Balancing Selection ◽  
Pieris Brassicae ◽  
Receptor Kinase ◽  
Large White ◽  
Lectin Receptor ◽  
Genome Wide ◽  
A Genome ◽  
Close Homolog

AbstractIn Arabidopsis thaliana, a hypersensitive-like response (HR-like) is triggered underneath the eggs of the large white butterfly Pieris brassicae, and this response is dependent on salicylic acid (SA) accumulation and signaling. Previous reports indicate that the clade I L-type lectin receptor kinase LecRK-I.8 is involved in early steps of egg recognition. A genome-wide association study (GWAS) was used to better characterize the genetic structure of HR-like and discover loci that contribute to this response. We report here the identification of LecRK-I.1, a close homolog of LecRK-I.8, and show that two main haplotypes that explain part of the variation in HR-like segregate amongst natural Arabidopsis accessions. In addition, signatures of balancing selection at this locus suggest that it may be ecologically important. Disruption of LecRK-I.1 resulted in decreased HR-like and SA signaling, indicating that this protein is important for the observed responses. Furthermore, we provide evidence that LecRK-I.1 functions in the same signaling pathway as LecRK-I.8. Altogether, our results show that the response to eggs of P. brassicae is controlled by LecRKs that operate at various steps of the signaling pathway.

scholarly journals Genome-Wide Association Analysis Identified BMPR1A as a Novel Candidate Gene Affecting the Number of Thoracic Vertebrae in a Large White × Minzhu Intercross Pig Population

Animals ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 2186
Author(s):  
Qian Liu ◽  
Jingwei Yue ◽  
Naiqi Niu ◽  
Xin Liu ◽  
Hua Yan ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Genome Wide Association Study ◽  
Splice Variants ◽  
Genome Wide Association ◽  
Thoracic Vertebrae ◽  
Phenotypic Variance ◽  
Nucleotide Polymorphisms ◽  
Large White ◽  
Genome Wide ◽  
A Genome

The number of vertebrae (NV), especially the number of thoracic vertebrae (NTV), varies among pig breeds. The NTV is controlled by vertebral segmentation and the number of somites during embryonic development. Although there is a high correlation between the NTV and NV, studies on a fixed NV have mainly considered the absolute numbers of thoracic vertebrae instead of vertebral segmentation. Therefore, this study aimed to discover variants associated with the NTV by considering the effect of the NV in pigs. The NTV and NV of 542 F2 individuals from a Large White × Minzhu pig crossbreed were recorded. All animals were genotyped for VRTN g.19034 A > C, LTBP2 c.4481A > C, and 37 missense or splice variants previously reported in a 951-kb interval on SSC7 and 147 single nucleotide polymorphisms (SNPs) on SSC14. To identify NTV-associated SNPs, we firstly performed a genome-wide association study (GWAS) using the Q + K (population structure + kinship matrix) model in TASSEL. With the NV as a covariate, the obtained data were used to identify the SNPs with the most significant genome-wide association with the NTV by performing a GWAS on a PorcineSNP60K Genotyping BeadChip. Finally, a conditional GWAS was performed by fixing this SNP. The GWAS showed that 31 SNPs on SSC7 have significant genome-wide associations with the NTV. No missense or splice variants were found to be associated with the NTV significantly. A linkage disequilibrium analysis suggested the existence of quantitative trait loci (QTL) in a 479-Kb region on SSC7, which contained a critical candidate gene FOS for the NTV in pigs. Subsequently, a conditional GWAS was performed by fixing M1GA0010658, the most significant of these SNPs. Two SNPs in BMPR1A were found to have significant genome-wide associations and a significant dominant effect. The leading SNP, S14_87859370, accounted for 3.86% of the phenotypic variance. Our study uncovered that regulation variants in FOS on SSC7 and in BMPR1A on SSC14 might play important roles in controlling the NTV, and thus these genetic factors may be harnessed for increasing the NTV in pigs.

scholarly journals Estimating the heritability of reporting stressful life events captured by common genetic variants

2012 ◽  
Vol 43 (9) ◽  
pp. 1965-1971 ◽  
Author(s):  
R. A. Power ◽  
T. Wingenbach ◽  
S. Cohen-Woods ◽  
R. Uher ◽  
M. Y. Ng ◽  
...  
Keyword(s):  
Life Events ◽  
Genetic Variants ◽  
Stressful Life Events ◽  
Genome Wide Association Study ◽  
Significant Proportion ◽  
Stressful Life ◽  
Phenotypic Variance ◽  
Genome Wide ◽  
Common Genetic Variants ◽  
A Genome

BackgroundAlthough usually thought of as external environmental stressors, a significant heritable component has been reported for measures of stressful life events (SLEs) in twin studies.MethodWe examined the variance in SLEs captured by common genetic variants from a genome-wide association study (GWAS) of 2578 individuals. Genome-wide complex trait analysis (GCTA) was used to estimate the phenotypic variance tagged by single nucleotide polymorphisms (SNPs). We also performed a GWAS on the number of SLEs, and looked at correlations between siblings.ResultsA significant proportion of variance in SLEs was captured by SNPs (30%, p = 0.04). When events were divided into those considered to be dependent or independent, an equal amount of variance was explained for both. This ‘heritability’ was in part confounded by personality measures of neuroticism and psychoticism. A GWAS for the total number of SLEs revealed one SNP that reached genome-wide significance (p = 4 × 10−8), although this association was not replicated in separate samples. Using available sibling data for 744 individuals, we also found a significant positive correlation of R2 = 0.08 in SLEs (p = 0.03).ConclusionsThese results provide independent validation from molecular data for the heritability of reporting environmental measures, and show that this heritability is in part due to both common variants and the confounding effect of personality.

scholarly journals A Genome-Wide Association Study to Detect QTL for Commercially Important Traits in Swiss Large White Boars

PLoS ONE ◽  
2013 ◽  
Vol 8 (2) ◽  
pp. e55951 ◽  
Author(s):  
Doreen Becker ◽  
Klaus Wimmers ◽  
Henning Luther ◽  
Andreas Hofer ◽  
Tosso Leeb
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Large White ◽  
Genome Wide ◽  
A Genome ◽  
Commercially Important
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