Determination of genetic variation within the &lt;i&gt;DYRK2&lt;/i&gt; gene and its associations with milk traits in cattle

Abstract. To speed up the progress of marker-assisted selection (MAS) in cattle breeding, the dual-specificity tyrosine phosphorylation-regulated kinase 2 (DYRK2), cadherin 2 (CDH2), and kinesin family member 1A (KIF1A) genes were chosen based on our pervious genome-wide association study (GWAS) analysis results. DYRK2 is a kinase that may participate in cell growth and/or development; it shows phosphorylation activity toward serine, threonine, and tyrosine fragments of proteins, and it is different from other protein kinases. The CDH2 gene encodes a classic cadherin, which is a member of the cadherin superfamily. The protein encoded by KIF1A is a member of the kinesin family and plays a role in the transportation of membrane organelles along axon microtubules. We detected insertion/deletion (InDel) variation in these three candidate genes in 438 individual cattle (Xinjiang Brown cattle and Wagyu × Luxi crossbreed cattle). Only DYRK2-P3-11 bp was polymorphic and genotyped. The polymorphism information content of DYRK2-P3-11 bp was 0.336. Correlation analyses showed that InDel polymorphism was significantly associated with six different milk traits. These findings may aid future analyses of InDel genotypes in cattle breeds, and speed up the progress of MAS in cattle breeding.

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Determination of shared genetic etiology and possible causal relations between tobacco smoking and depression

Psychological Medicine ◽

10.1017/s003329172000063x ◽

2020 ◽

pp. 1-10

Author(s):

Yinghao Yao ◽

Yi Xu ◽

Zhen Cai ◽

Qiang Liu ◽

Yunlong Ma ◽

...

Keyword(s):

Genome Wide Association Study ◽

Strong Positive Correlation ◽

Gamma Aminobutyric Acid ◽

Self Medication ◽

Genetic Etiology ◽

Causal Relations ◽

Psychiatric Genetic ◽

Genome Wide ◽

Summary Data

Abstract Backgrounds Cigarette smoking is strongly associated with major depressive disorder (MDD). However, any genetic etiology of such comorbidity and causal relations is poorly understood, especially at the genome-wide level. Methods In the present in silico research, we analyzed summary data from the genome-wide association study of the Psychiatric Genetic Consortium for MDD (n = 191 005) and UK Biobank for smoking (n = 337 030) by using various biostatistical methods including Bayesian colocalization analysis, LD score regression, variant effect size correlation analysis, and Mendelian randomization (MR). Results By adopting a gene prioritization approach, we identified 43 genes shared by MDD and smoking, which were significantly enriched in membrane potential, gamma-aminobutyric acid receptor activity, and retrograde endocannabinoid signaling pathways, indicating that the comorbid mechanisms are involved in the neurotransmitter system. According to linkage disequilibrium score regression, we found a strong positive correlation between MDD and current smoking (rg = 0.365; p = 7.23 × 10−25) and a negative correlation between MDD and former smoking (rg = −0.298; p = 1.59 × 10−24). MR analysis suggested that genetic liability for depression increased smoking. Conclusions These findings inform the concomitant conditions of MDD and smoking and support the use of self-medication with smoking to counteract depression.

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A genome-wide association study, supported by a new chromosome-level genome assembly, suggests sox2 as a main driver of the undifferentiatiated ZZ/ZW sex determination of turbot (Scophthalmus maximus)

Genomics ◽

10.1016/j.ygeno.2021.04.007 ◽

2021 ◽

Author(s):

Paulino Martínez ◽

Diego Robledo ◽

Xoana Taboada ◽

Andrés Blanco ◽

Michel Moser ◽

...

Keyword(s):

Genome Assembly ◽

Genome Wide Association Study ◽

Scophthalmus Maximus ◽

Genome Wide Association ◽

Genome Wide ◽

A Genome ◽

Main Driver ◽

Turbot Scophthalmus Maximus ◽

Chromosome Level

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Testing implications of the polygenic model for the genetic analysis of loci identified through genome-wide association

10.1101/639955 ◽

2019 ◽

Cited By ~ 1

Author(s):

Wenyu Zhang ◽

R. Guy Reeves ◽

Diethard Tautz

Keyword(s):

Quantitative Traits ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Genome Wide ◽

A Genome ◽

Length Determination ◽

Gwa Studies ◽

Pupation Site ◽

Core Genes

AbstractIt has been proposed that many loci with no significant association in GWA studies can nonetheless contribute to the phenotype through modifier interactions with the core genes, implying a polygenic determination of quantitative traits. We have tested this hypothesis by using Drosophila pupal phenotypes. We identified candidate genes for pupal length determination in a GWA and show for disrupted versions of the genes that most are indeed involved in the phenotype, presumably forming a core pathway. We then randomly chose genes below the GWA threshold and found that three quarters of them had also an effect on the trait. We further tested the effects of these knockout lines on an independent behavioral pupal trait (pupation site choice) and found that a similar, but non-correlated fraction of them had a significant effect as well. Our data thus confirm the prediction that a large number of genes can influence independent quantitative traits.Impact statementQuantitative traits are similarly likely influenced by randomly picked loci as by loci identified in a genome-wide association study.

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