Related Experiment Video
Updated: May 13, 2026
05:53
Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
Published on: June 21, 2018
Simultaneous mapping of multiple gene loci with pooled segregants
Jürgen Claesen1, Lieven Clement, Ziv Shkedy
1I-BioStat, Hasselt University, Diepenbeek, Belgium. jurgen.claesen@uhasselt.be
Plos One
|February 27, 2013
Summary
Analyzing polygenic traits requires scoring many genetic markers. This study uses next-generation sequencing (NGS) with bulked segregant analysis (BSA) to map multiple genetic loci simultaneously, identifying trait-associated markers.
Area of Science:
- Genetics and Genomics
- Quantitative Trait Analysis
- Bioinformatics
Background:
- Analyzing polygenic traits and inheritable diseases is challenging due to the need for comprehensive genome-wide genetic marker scoring.
- High-throughput sequencing technologies, like next-generation sequencing (NGS), enable the evaluation of numerous single nucleotide polymorphisms (SNPs) as genetic markers.
- Bulked segregant analysis (BSA) combined with sequencing offers a potential method for simultaneous mapping of multiple genomic loci.
Purpose of the Study:
- To develop and apply a method for simultaneous mapping of multiple genetic loci associated with polygenic traits.
- To leverage next-generation sequencing (NGS) data within a bulked segregant analysis (BSA) framework for gene mapping.
- To identify genetic markers and loci underlying complex phenotypic characteristics.
Main Methods:
- Controlled crosses between parents with and without a specific trait.
- Phenotypic screening of offspring followed by mapping short sequences against a parental reference.
- Utilizing next-generation sequencing (NGS) to detect genetic markers (SNPs, insertions, deletions) and analyzing binomial read counts.
- Employing smoothing splines and generalized mixed models to analyze SNP count trends for trait-associated locus discovery.
Main Results:
- Demonstrated a method for simultaneous mapping of multiple genetic loci using NGS and BSA.
- Identified genetic markers in close proximity to trait-associated genomic loci.
- Showcased the utility of analyzing NGS-derived binomial counts to infer genetic associations.
- Successfully applied smoothing splines and generalized mixed models to SNP data for locus discovery.
Conclusions:
- The integration of NGS with BSA provides a powerful approach for mapping multiple genetic loci simultaneously.
- This method facilitates the discovery of genetic markers and mechanisms underlying complex quantitative traits and diseases.
- Statistical modeling, specifically smoothing splines and generalized mixed models, is effective for analyzing NGS count data in gene mapping.
Related Concept Videos
01:49Multiple Allele Traits
The Concept of Multiple Allelism
01:11Genome-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...
GWAS does not require the identification of the target gene involved in...
01:09Epistasis Analysis
Although Mendel chose seven unrelated traits in peas to study gene segregation, most traits involve multiple gene interactions that create a spectrum of phenotypes. When the interaction of various genes or alleles at different locations influences a phenotype, this is called epistasis. Epistasis often involves one gene masking or interfering with the expression of another (antagonistic epistasis). Epistasis often occurs when different genes are part of the same biochemical pathway. The...
01:00Punnett Squares
Overview
01:49Law of Segregation
When crossing pea plants, Mendel noticed that one of the parental traits would sometimes disappear in the first generation of offspring, called the F1 generation, and could reappear in the next generation (F2). He concluded that one of the traits must be dominant over the other, thereby causing masking of one trait in the F1 generation. When he crossed the F1 plants, he found that 75% of the offspring in the F2 generation had the dominant phenotype, while 25% had the recessive phenotype.
01:18Dihybrid Crosses
Overview