scholarly journals Genetic Dissection of Temperament Personality Traits in Italian Isolates

Genes ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 4
Author(s):  
Maria Pina Concas ◽  
Alessandra Minelli ◽  
Susanna Aere ◽  
Anna Morgan ◽  
Paola Tesolin ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Complex Trait ◽  
Domestic Dog ◽  
P Value ◽  
Genetic Dissection ◽  
Novelty Seeking ◽  
Obsessive Compulsive ◽  
Compulsive Disorder ◽  
New Genes ◽  
A Genome

Human personality (i.e., temperament and character) is a complex trait related to mental health, influenced by genetic and environmental factors. Despite the efforts performed during the past decades, its genetic background is only just beginning to be identified. With the aim of dissecting the genetic basis of temperament, we performed a Genome-Wide Association Study (GWAS) on Cloninger’s Temperament and Character Inventory in 587 individuals belonging to different Italian genetic isolates. Data analysis led to the identification of four new genes associated with different temperament scales, such as Novelty Seeking (NS), Harm Avoidance (HA), and Reward Dependence (RD). In detail, we identified suggestive and significant associations between: MAGI2 (highest p-value = 9.14 × 10−8), a gene already associated with schizophrenia and depressive disorder, and the NS–Extravagance scale; CALCB (highest p-value = 4.34 × 10−6), a gene likely involved in the behavioral evolution from wild wolf to domestic dog, and the NS–Disorderliness scale; BTBD3 (highest p-value = 2.152 × 10−8), a gene already linked to obsessive–compulsive disorder, and the HA–Fatigability scale; PRKN (highest p-value = 8.27 × 10−9), a gene described for early onset Parkinson’s disease, and the RD scale. Our work provides new relevant insights into the genetics of temperament, helping to elucidate the molecular basis of psychiatric disorders.

scholarly journals Genetic dissection of climacteric fruit ripening in a melon population segregating for ripening behavior

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Lara Pereira ◽  
Miguel Santo Domingo ◽  
Valentino Ruggieri ◽  
Jason Argyris ◽  
Michael A. Phillips ◽  
...  
Keyword(s):  
Fruit Ripening ◽  
Ethylene Production ◽  
Genome Wide Association Study ◽  
Recombinant Inbred Lines ◽  
Introgression Line ◽  
Complex Trait ◽  
Chromosome 8 ◽  
Genetic Dissection ◽  
Climacteric Fruit ◽  
A Genome

Abstract Melon is as an alternative model to understand fruit ripening due to the coexistence of climacteric and non-climacteric varieties within the same species, allowing the study of the processes that regulate this complex trait with genetic approaches. We phenotyped a population of recombinant inbred lines (RILs), obtained by crossing a climacteric (Védrantais, cantalupensis type) and a non-climcteric variety (Piel de Sapo T111, inodorus type), for traits related to climacteric maturation and ethylene production. Individuals in the RIL population exhibited various combinations of phenotypes that differed in the amount of ethylene produced, the early onset of ethylene production, and other phenotypes associated with ripening. We characterized a major QTL on chromosome 8, ETHQV8.1, which is sufficient to activate climacteric ripening, and other minor QTLs that may modulate the climacteric response. The ETHQV8.1 allele was validated by using two reciprocal introgression line populations generated by crossing Védrantais and Piel de Sapo and analyzing the ETHQV8.1 region in each of the genetic backgrounds. A Genome-wide association study (GWAS) using 211 accessions of the ssp. melo further identified two regions on chromosome 8 associated with the production of aromas, one of these regions overlapping with the 154.1 kb interval containing ETHQV8.1. The ETHQV8.1 region contains several candidate genes that may be related to fruit ripening. This work sheds light into the regulation mechanisms of a complex trait such as fruit ripening.

scholarly journals Natural variation in Arabidopsis thaliana rosette area unveils new genes involved in plant development

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Rubén González ◽  
Anamarija Butković ◽  
Mark Paul Selda Rivarez ◽  
Santiago F. Elena
Keyword(s):  
Arabidopsis Thaliana ◽  
Plant Growth ◽  
Natural Variation ◽  
Mixed Model ◽  
Genome Wide Association Study ◽  
Complex Trait ◽  
Knock Out ◽  
New Genes ◽  
Genome Wide ◽  
A Genome

AbstractGrowth is a complex trait influenced by multiple genes that act at different moments during the development of an organism. This makes it difficult to spot its underlying genetic mechanisms. Since plant growth is intimately related to the effective leaf surface area (ELSA), identifying genes controlling this trait will shed light on our understanding of plant growth. To find new genes with a significant contribution to plant growth, here we used the natural variation in Arabidopsis thaliana to perform a genome-wide association study of ELSA. To do this, the projected rosette area of 710 worldwide distributed natural accessions was measured and analyzed using the genome-wide efficient mixed model association algorithm. From this analysis, ten genes were identified having SNPs with a significant association with ELSA. To validate the implication of these genes into A. thaliana growth, six of them were further studied by phenotyping knock-out mutant plants. It was observed that rem1.2, orc1a, ppd1, and mcm4 mutants showed different degrees of reduction in rosette size, thus confirming the role of these genes in plant growth. Our study identified genes already known to be involved in plant growth but also assigned this role, for the first time, to other genes.

scholarly journals Uncovering genomic regions controlling plant architectural traits in hexaploid wheat using different GWAS models

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ali Muhammad ◽  
Jianguo Li ◽  
Weichen Hu ◽  
Jinsheng Yu ◽  
Shahid Ullah Khan ◽  
...  
Keyword(s):  
Plant Height ◽  
Genome Wide Association Study ◽  
Flag Leaf ◽  
Significant Snps ◽  
Complex Trait ◽  
Leaf Length ◽  
Candidate Snps ◽  
A Genome ◽  
Multiple Environments ◽  
Architectural Traits

AbstractWheat is a major food crop worldwide. The plant architecture is a complex trait mostly influenced by plant height, tiller number, and leaf morphology. Plant height plays a crucial role in lodging and thus affects yield and grain quality. In this study, a wheat population was genotyped by using Illumina iSelect 90K single nucleotide polymorphism (SNP) assay and finally 22,905 high-quality SNPs were used to perform a genome-wide association study (GWAS) for plant architectural traits employing four multi-locus GWAS (ML-GWAS) and three single-locus GWAS (SL-GWAS) models. As a result, 174 and 97 significant SNPs controlling plant architectural traits were detected by ML-GWAS and SL-GWAS methods, respectively. Among these SNP makers, 43 SNPs were consistently detected, including seven across multiple environments and 36 across multiple methods. Interestingly, five SNPs (Kukri_c34553_89, RAC875_c8121_1490, wsnp_Ex_rep_c66315_64480362, Ku_c5191_340, and tplb0049a09_1302) consistently detected across multiple environments and methods, played a role in modulating both plant height and flag leaf length. Furthermore, candidate SNPs (BS00068592_51, Kukri_c4750_452 and BS00022127_51) constantly repeated in different years and methods associated with flag leaf width and number of tillers. We also detected several SNPs (Jagger_c6772_80, RAC875_c8121_1490, BS00089954_51, Excalibur_01167_1207, and Ku_c5191_340) having common associations with more than one trait across multiple environments. By further appraising these GWAS methods, the pLARmEB and FarmCPU models outperformed in SNP detection compared to the other ML-GWAS and SL-GWAS methods, respectively. Totally, 152 candidate genes were found to be likely involved in plant growth and development. These finding will be helpful for better understanding of the genetic mechanism of architectural traits in wheat.

A genome‐wide association study identifies new genes associated with developmental dysplasia of the hip

2019 ◽  
Vol 95 (3) ◽  
pp. 345-355 ◽  
Author(s):  
Wenjin Yan ◽  
Zheng Hao ◽  
Shuyan Tang ◽  
Jin Dai ◽  
Liming Zheng ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Developmental Dysplasia ◽  
Genome Wide Association ◽  
New Genes ◽  
Genome Wide ◽  
A Genome ◽  
Dysplasia Of The Hip

Integrative Analysis of shared Genetic Pathogenesis by Autism Spectrum Disorder and Obsessive-Compulsive Disorder

2019 ◽  
Author(s):  
Dongbai Liu ◽  
Hongbao Cao ◽  
Kamil Can Kural ◽  
Qi Fang ◽  
Fuquan Zhang
Keyword(s):  
Obsessive Compulsive Disorder ◽  
Large Scale ◽  
Genetic Network ◽  
Autism Spectrum ◽  
P Value ◽  
Genetic Associations ◽  
Obsessive Compulsive ◽  
Systematic Analysis ◽  
Gene Markers ◽  
Compulsive Disorder

Abstract Background Many common pathological features have been observed for both autism spectrum disorders (ASD) and obsessive-compulsive disorder (OCD). However, no systematic analysis of the common gene markers associated both ASD and OCD has been conducted so far. Results Here, two batches of large-scale literature based disease-gene relation data (updated in 2017 and 2019, respectively) and gene expression data were integrated to study the possible association between OCD and ASD at the genetic level. Genes linked to OCD and ASD present significant overlap (p-value<2.64e-39). A genetic network of over 20 genes was constructed, through which OCD and ASD may exert influence on each other. The 2017-based analysis suggested six potential common risk genes for OCD and ASD (CDH2, ADCY8, APOE, TSPO, TOR1A, and OLIG2), and the 2019-based study identified two more genes (DISP1 and SETD1A). Notably, the gene APOE identified by the 2017-based analysis has been implicated to have an association with ASD in a recently study (2018) with DNA methylation analysis. Conclusions Our results support the possible complex genetic associations between OCD and ASD. Genes linked to one disease is worthy of further investigation as potential risk factors for the other.

scholarly journals GWAS with principal component analysis identifies a gene comprehensively controlling rice architecture

2019 ◽  
Vol 116 (42) ◽  
pp. 21262-21267 ◽  
Author(s):  
Kenji Yano ◽  
Yoichi Morinaka ◽  
Fanmiao Wang ◽  
Peng Huang ◽  
Sayaka Takehara ◽  
...  
Keyword(s):  
Principal Component Analysis ◽  
Genome Wide Association Study ◽  
Crop Yields ◽  
Principal Component ◽  
Complex Trait ◽  
Component Analysis ◽  
Gene Encoding ◽  
Signal Suppression ◽  
Genome Wide ◽  
A Genome

Elucidation of the genetic control of rice architecture is crucial due to the global demand for high crop yields. Rice architecture is a complex trait affected by plant height, tillering, and panicle morphology. In this study, principal component analysis (PCA) on 8 typical traits related to plant architecture revealed that the first principal component (PC), PC1, provided the most information on traits that determine rice architecture. A genome-wide association study (GWAS) using PC1 as a dependent variable was used to isolate a gene encoding rice, SPINDLY (OsSPY), that activates the gibberellin (GA) signal suppression protein SLR1. The effect of GA signaling on the regulation of rice architecture was confirmed in 9 types of isogenic plant having different levels of GA responsiveness. Further population genetics analysis demonstrated that the functional allele of OsSPY associated with semidwarfism and small panicles was selected in the process of rice breeding. In summary, the use of PCA in GWAS will aid in uncovering genes involved in traits with complex characteristics.

A genome-wide association study to identify candidate genes for erectile dysfunction

2020 ◽  
Author(s):  
Elham Kazemi ◽  
Javaad Zargooshi ◽  
Marzieh Kaboudi ◽  
Parviz Heidari ◽  
Danial Kahrizi ◽  
...  
Keyword(s):  
Erectile Dysfunction ◽  
Protein Interactions ◽  
Genome Wide Association Study ◽  
Expression Profiles ◽  
Regulatory Elements ◽  
Local Alignment ◽  
Conserved Motifs ◽  
New Genes ◽  
A Genome ◽  
Ucsc Database

Abstract Erectile dysfunction (ED) can be caused by different diseases and controlled by several genetic networks. In this study, to identify the genes related to ED, the expression profiles of normal and ED samples were investigated by the Gene Expression Omnibus (GEO) database. Seventeen genes were identified as associated genes with ED. The protein and nucleic acid sequences of selected genes were retrieved from the UCSC database. Selected genes were diverse according to their physicochemical properties and functions. Category function revealed that selected genes are involved in pathways related to humans some diseases. Furthermore, based on protein interactions, genes associated with the insulin pathway had the greatest interaction with the studied genes. To identify the common cis-regulatory elements, the promoter site of the selected genes was retrieved from the UCSC database. The Gapped Local Alignment of Motifs tool was used for finding common conserved motifs into the promoter site of selected genes. Besides, INSR protein as an insulin receptor precursor showed a high potential site for posttranslation modifications, including phosphorylation and N-glycosylation. Also, in this study, two Guanine-Cytosine (GC)-rich regions were identified as conserved motifs in the upstream of studied genes which can be involved in regulating the expression of genes associated with ED. Also, the conserved binding site of miR-29-3p that is involved in various cancers was observed in the 3′ untranslated region of genes associated with ED. Our study introduced new genes associated with ED, which can be good candidates for further analyzing related to human ED.

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