Back to Search
Start Over
Comparative study of population genomic approaches for mapping colony-level traits
- Source :
- PLoS Computational Biology, PLoS Computational Biology, Vol 16, Iss 3, p e1007653 (2020)
- Publication Year :
- 2020
- Publisher :
- Public Library of Science, 2020.
-
Abstract
- Social insect colonies exhibit colony-level phenotypes such as social immunity and task coordination, which are produced by the individual phenotypes. Mapping the genetic basis of such phenotypes requires associating the colony-level phenotype with the genotypes in the colony. In this paper, we examine alternative approaches to DNA extraction, library construction, and sequencing for genome wide association studies (GWAS) of colony-level traits using a population sample of Cataglyphis niger ants. We evaluate the accuracy of allele frequency estimation from sequencing a pool of individuals (pool-seq) from each colony using either whole-genome sequencing or reduced representation genomic sequencing. Based on empirical measurement of the experimental noise in sequenced DNA pools, we show that reduced representation pool-seq is drastically less accurate than whole-genome pool-seq. Surprisingly, normalized pooling of samples did not result in greater accuracy than un-normalized pooling. Subsequently, we evaluate the power of the alternative approaches for detecting quantitative trait loci (QTL) of colony-level traits by using simulations that account for an environmental effect on the phenotype. Our results can inform experimental designs and enable optimizing the power of GWAS depending on budget, availability of samples and research goals. We conclude that for a given budget, sequencing un-normalized pools of individuals from each colony provides optimal QTL detection power.<br />Author summary Genomic mapping techniques are used to map phenotypes to genotypes. Mapping is of general interest in any biological system, including fundamental studies of biological traits, clinical studies of genetic predisposition to disease, and agro- and bio-technological studies of domesticated plants and animals. Typically, such studies associate phenotypic measurements of individuals with their genotypes. Here we evaluate methodological approaches for genomic mapping of phenotypes that are expressed at the level of a group rather than that of individuals. We demonstrate that genomic sequencing of a DNA pool from multiple samples provides increased statistical power within a limited budget. Our results facilitate more efficient use of resources in genomic mapping studies that investigate group-level phenotypes.
- Subjects :
- 0301 basic medicine
Heredity
Pooling
Genome-wide association study
0302 clinical medicine
Sequencing techniques
DNA library construction
Gene Frequency
Genotype
DNA sequencing
Biology (General)
DNA extraction
education.field_of_study
Ecology
Behavior, Animal
Chromosome Mapping
Genomics
Genomic Library Construction
Phenotype
Genetic Mapping
Computational Theory and Mathematics
Modeling and Simulation
Research Article
QH301-705.5
Population
Quantitative Trait Loci
Single-nucleotide polymorphism
Variant Genotypes
Computational biology
Biology
Quantitative trait locus
DNA construction
Polymorphism, Single Nucleotide
Molecular Genetics
03 medical and health sciences
Cellular and Molecular Neuroscience
Extraction techniques
Genome-Wide Association Studies
Genetics
Animals
Allele
education
Social Behavior
Allele frequency
Molecular Biology
Ecology, Evolution, Behavior and Systematics
Alleles
Whole Genome Sequencing
Ants
Biology and Life Sciences
Computational Biology
Human Genetics
Genome Analysis
Research and analysis methods
030104 developmental biology
Molecular biology techniques
Genetic Loci
Metagenomics
030217 neurology & neurosurgery
Genome-Wide Association Study
Subjects
Details
- Language :
- English
- ISSN :
- 15537358 and 1553734X
- Volume :
- 16
- Issue :
- 3
- Database :
- OpenAIRE
- Journal :
- PLoS Computational Biology
- Accession number :
- edsair.doi.dedup.....1802ae2bb13c18acc2b8a765433756e4