TY - JOUR

T1 - A Principal Components Analysis and Functional Annotation of Differentially Expressed Genes in Brain Regions of Gray Rats Selected for Tame or Aggressive Behavior

AU - Chadaeva, Irina

AU - Kozhemyakina, Rimma

AU - Shikhevich, Svetlana

AU - Bogomolov, Anton

AU - Kondratyuk, Ekaterina

AU - Ощепков, Дмитрий Юрьевич

AU - Orlov, Yuriy L.

AU - Markel, Arcady L.

N1 - The experimental work was supported by Russian government projects FWNR-2022-0015. Bioinformatics study on gene network reconstruction was supported by Russian Science Foundation (project 24-24-00563).

PY - 2024/5

Y1 - 2024/5

N2 - The process of domestication, despite its short duration as it compared with the time scale of the natural evolutionary process, has caused rapid and substantial changes in the phenotype of domestic animal species. Nonetheless, the genetic mechanisms underlying these changes remain poorly understood. The present study deals with an analysis of the transcriptomes from four brain regions of gray rats (Rattus norvegicus), serving as an experimental model object of domestication. We compared gene expression profiles in the hypothalamus, hippocampus, periaqueductal gray matter, and the midbrain tegmental region between tame domesticated and aggressive gray rats and revealed subdivisions of differentially expressed genes by principal components analysis that explain the main part of differentially gene expression variance. Functional analysis (in the DAVID (Database for Annotation, Visualization and Integrated Discovery) Bioinformatics Resources database) of the differentially expressed genes allowed us to identify and describe the key biological processes that can participate in the formation of the different behavioral patterns seen in the two groups of gray rats. Using the STRING- DB (search tool for recurring instances of neighboring genes) web service, we built a gene association network. The genes engaged in broad network interactions have been identified. Our study offers data on the genes whose expression levels change in response to artificial selection for behavior during animal domestication.

AB - The process of domestication, despite its short duration as it compared with the time scale of the natural evolutionary process, has caused rapid and substantial changes in the phenotype of domestic animal species. Nonetheless, the genetic mechanisms underlying these changes remain poorly understood. The present study deals with an analysis of the transcriptomes from four brain regions of gray rats (Rattus norvegicus), serving as an experimental model object of domestication. We compared gene expression profiles in the hypothalamus, hippocampus, periaqueductal gray matter, and the midbrain tegmental region between tame domesticated and aggressive gray rats and revealed subdivisions of differentially expressed genes by principal components analysis that explain the main part of differentially gene expression variance. Functional analysis (in the DAVID (Database for Annotation, Visualization and Integrated Discovery) Bioinformatics Resources database) of the differentially expressed genes allowed us to identify and describe the key biological processes that can participate in the formation of the different behavioral patterns seen in the two groups of gray rats. Using the STRING- DB (search tool for recurring instances of neighboring genes) web service, we built a gene association network. The genes engaged in broad network interactions have been identified. Our study offers data on the genes whose expression levels change in response to artificial selection for behavior during animal domestication.

KW - RNA-seq

KW - aggressive and tame rats

KW - animal domestication

KW - artificial selection

KW - behavioral genetics

KW - brain

KW - differentially expressed gene

KW - functional annotation of genes

KW - gene network

KW - principal component analysis

KW - Animals

KW - Rats

KW - Brain/metabolism

KW - Aggression/physiology

KW - Transcriptome/genetics

KW - Principal Component Analysis

KW - Gene Expression Profiling/methods

KW - Behavior, Animal

KW - Domestication

KW - Molecular Sequence Annotation

KW - Male

KW - Gene Regulatory Networks

KW - Gene Expression Regulation

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-85192719070&origin=inward&txGid=4c39662053aa4622ade0d8ead46324fa

UR - https://www.mendeley.com/catalogue/1380463a-78b8-3992-a852-a7a7f3933013/

U2 - 10.3390/ijms25094613

DO - 10.3390/ijms25094613

M3 - Article

C2 - 38731836

VL - 25

JO - International Journal of Molecular Sciences

JF - International Journal of Molecular Sciences

SN - 1661-6596

IS - 9

M1 - 4613

ER -