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Genome-wide Association Studies-GWAS

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...

Comparing Copy Number Variations and SNPs

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...

Single Nucleotide Polymorphisms-SNPs

Single Nucleotide Polymorphisms-SNPs

A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...

Genetic Variation

Genetic Variation

Genetic variation is the diversity in DNA sequences found among individuals of the same species. This diversity is crucial for a species' survival because it helps organisms adapt to environmental changes. Genetic variation begins with fertilization, where an egg and sperm cell merge. Each of these cells carries 23 chromosomes, up to 46 in the fertilized egg. Chromosomes are long DNA strands that contain genes, the basic units of heredity.
Genes exist in different versions called alleles,...

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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

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Published on: June 21, 2018

Validating Genome-Wide Association Candidates Controlling Quantitative Variation in Nodulation.

Shaun J Curtin^1,2,3, Peter Tiffin^1,2,3, Joseph Guhlin^1,2,3

¹Department of Plant Pathology (S.J.C., R.D., N.D.Y.) and Department of Plant Biology (P.T., J.G., D.T., L.B., N.D.Y.), University of Minnesota, St. Paul, Minnesota 55108.

Plant Physiology

|January 7, 2017

Summary

Genome-wide association studies identified candidate genes for legume symbiosis. Functional validation using gene-disruption technologies confirmed three genes influencing nodule production, revealing novel pathways.

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Published on: January 16, 2019

Area of Science:

Plant genetics
Microbiology
Molecular biology

Background:

Genome-wide association (GWA) studies identify genes linked to trait variation.
Functional validation is crucial for confirming gene roles in quantitative traits.
Legume-rhizobia symbiosis is a complex trait influenced by multiple genes.

Purpose of the Study:

To functionally validate candidate genes for legume-rhizobia symbiosis variation identified by GWA.
To investigate the role of specific genes in nodule production using reverse genetics.
To explore novel biological pathways contributing to symbiosis.

Main Methods:

Utilized gene-disruption platforms: Tnt1 retrotransposons, RNA-interference, and CRISPR/Cas9.
Conducted randomized, well-replicated experiments to assess gene function.
Evaluated ten candidate genes from GWA studies in Medicago truncatula.

Main Results:

Statistically significant effects on nodule production were observed for three candidate genes.
Each validated gene was confirmed in two independent mutants.
Identified roles in phosphorous supply and defense response pathways, previously unconnected to nodulation.

Conclusions:

GWA studies combined with reverse mutagenesis effectively discover and validate genes for quantitative traits.
Functional validation confirmed novel genetic factors influencing legume symbiosis.
Highlights the potential of GWA to complement forward genetics for trait discovery.