Gene-set association and epistatic analyses reveal complex gene interaction networks affecting flowering time in a worldwide barley collection.

08:00 EDT 27th August 2019 | BioPortfolio

Summary of "Gene-set association and epistatic analyses reveal complex gene interaction networks affecting flowering time in a worldwide barley collection."

Single-marker genome-wide association studies (GWAS) have successfully detected associations between single nucleotide polymorphisms (SNPs) and agronomic traits such as flowering time and grain yield in barley. However, the analysis of individual SNPs can only account for a small proportion of genetic variation, and can only provide limited knowledge on gene network interactions. Gene-based GWAS approaches provide enormous opportunity both to combine genetic information and to examine interactions among genetic variants. Here, we revisited a previously published phenotypic and genotypic data set of 895 barley varieties grown in two years at four different field locations in Australia. We employed statistical models to examine gene-phenotype associations, as well as two-way epistasis analyses to increase the capability to find novel genes that have significant roles in controlling flowering time in barley. Genetic associations were tested between flowering time and corresponding genotypes of 174 putative flowering time-related genes. Gene-phenotype association analysis detected 113 genes associated with flowering time in barley, demonstrating the unprecedented power of gene-based analysis. Subsequent two-way epistasis analysis revealed 19 pairs of gene×gene interactions involved in controlling flowering time. Our study demonstrates that gene-based association approaches can provide higher capacity for future crop improvement to increase crop performance and adaptation to different environments.


Journal Details

This article was published in the following journal.

Name: Journal of experimental botany
ISSN: 1460-2431


DeepDyve research library

PubMed Articles [31853 Associated PubMed Articles listed on BioPortfolio]

Interaction among GRIK2 gene on epilepsy susceptibility in Chinese children.

The association of single-nucleotide polymorphisms (SNPs) of glutamate receptor 2 (GRIK2) gene, as well as gene- gene interaction with the risk of Early-onset epilepsy susceptibility was studied in Ch...

Association between Interleukin-10 Gene Polymorphisms and Severe Chronic Periodontitis.

Periodontitis is an inflammatory disease that is a result of the interaction between pathogenic bacteria and host immune response. Genetic alterations in interleukin-10 (IL-10) gene may be associated ...

Modular epistasis and the compensatory evolution of gene deletion mutants.

Screens for epistatic interactions have long been used to characterize functional relationships corresponding to protein complexes, metabolic pathways, and other functional modules. Although epistasis...

Interactions between environmental pollutants and genetic susceptibility in asthma risk.

Exposure to air pollution is associated with enhanced risk of developing asthma, notably in the presence of genetic risk factors. Interaction analyses have shown that both outdoor and indoor air pollu...

Prediction of key gene function in spinal muscular atrophy using guilt by association method based on network and gene ontology.

Guilt by association (GBA) algorithm has been widely used to predict gene functions statistically, and a network-based approach may increase the confidence and veracity of identifying molecular signat...

Clinical Trials [7406 Associated Clinical Trials listed on BioPortfolio]

Epigenomic and Metabolomic Signatures of APOA2 Gene by Saturated Fat Interaction

Obesity is driven by genetic and environmental factors. Among the latter, diet is a most important one. The investigators refer to these combinations of genetic and dietary factors as 'gen...

C-Reactive Protein (CRP) Gene Variants and Coronary Artery Disease in a Chinese Han Population

The recognition of the association between circulating C-reactive protein (CRP) levels and risk of coronary heart disease (CHD) has led to an increased emphasis on CRP genetic effects on C...

Association of BsmI Polymorphisms in Vitamin D Receptor Gene With Diabetic Kidney Disease

Background: Diabetic kidney disease (DKD), as one of chronic complication of type 2 diabetes mellitus, is common cause of end stage renal disease (ESRD). Vitamin D deficiency is known as o...

The TCF7L2 Gene: Dietary Prevention of T2DM

Nutrients and chemicals in food are able to regulate expression of genetic elements. Gene-nutrient interaction in response specific diets can increase an individual's risk, shifting the in...

Gene Polymorphism in ARDS

Few patients who have major risk factors develop Acute Respiratory Distress Syndrome (ARDS). The heritable determinants might be the reason. The multicenter study is to investigate the ass...

Medical and Biotech [MESH] Definitions

A form of gene interaction whereby the expression of one gene interferes with or masks the expression of a different gene or genes. Genes whose expression interferes with or masks the effects of other genes are said to be epistatic to the effected genes. Genes whose expression is affected (blocked or masked) are hypostatic to the interfering genes.

The number of copies of a given gene present in the cell of an organism. An increase in gene dosage (by GENE DUPLICATION for example) can result in higher levels of gene product formation. GENE DOSAGE COMPENSATION mechanisms result in adjustments to the level GENE EXPRESSION when there are changes or differences in gene dosage.

The use of techniques that produce a functional MUTATION or an effect on GENE EXPRESSION of a specific gene of interest in order to identify the role or activity of the gene product of that gene.

Techniques to alter a gene sequence that result in an inactivated gene, or one in which the expression can be inactivated at a chosen time during development to study the loss of function of a gene.

The GENETIC RECOMBINATION of the parts of two or more GENES resulting in a gene with different or additional regulatory regions, or a new chimeric gene product. ONCOGENE FUSION includes an ONCOGENE as at least one of the fusion partners and such gene fusions are often detected in neoplastic cells and are transcribed into ONCOGENE FUSION PROTEINS. ARTIFICIAL GENE FUSION is carried out in vitro by RECOMBINANT DNA technology.

Quick Search

DeepDyve research library

Relevant Topic

Bioinformatics is the application of computer software and hardware to the management of biological data to create useful information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied...

Searches Linking to this Article