Genotyping Techniques in Population Genomics

Population genomics employs molecular markers across genomes to characterise variation within and between populations. Genotyping—determining the genetic constitution of individuals at specific loci—has moved from low-throughput assays to high-density platforms. Microarray-based SNP chips provided early large-scale genotyping by targeting known polymorphisms, offering high accuracy and ease of analysis but limited discovery of novel or rare variants. Next-generation sequencing has enabled genotyping-by-sequencing (GBS) approaches, combining complexity reduction and multiplexing to survey thousands to millions of loci without prior genomic resources. Reduced representation methods such as restriction-site associated DNA sequencing (RAD-seq) and its refinements—double-digest RAD-seq (ddRAD-seq) and exon capture—allow tailored marker density and cost control. Whole-genome resequencing delivers comprehensive variant calls but remains costly for large sample sets. Advances in library preparation, barcoding and combinatorial indexing have improved throughput, while bioinformatic pipelines facilitate de novo locus assembly, SNP calling and genotype imputation. Careful attention to biases—restriction enzyme selection, fragment size distribution, PCR amplification and missing data—ensures reliable allele-frequency estimation, population-structure inference and selection scans. This suite of techniques underpins studies of demographic history, adaptive variation, conservation management, crop improvement and disease surveillance, with method choice guided by trade-offs among marker density, cost, sample size and prior genomic knowledge.

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Genotyping Techniques in Population Genomics publication trend

The graph below shows the total number of articles in genotyping techniques in population genomics across all publications each year (not limited to Nature Index journals).

Technical terms

Single nucleotide polymorphism (SNP): A single-base variation at a specific genomic position among individuals.

Restriction-site associated DNA sequencing (RAD-seq): A reduced representation method using restriction enzymes to target and sequence genomic fragments adjacent to cut sites.

Double-digest RAD-seq (ddRAD-seq): A variant of RAD-seq using two enzymes to improve fragment size consistency and locus recovery.

Genotyping-by-sequencing (GBS): A family of methods combining genome reduction and high-throughput sequencing to simultaneously discover and genotype markers.

Microarray-based genotyping: A platform that assays predefined SNPs on a chip, offering high throughput but limited to known variants.

References

1. Limited genetic diversity found among genotypes of the Entada landrace (Ensete ventricosum, (Welw.) Chessman) from Ethiopia. Frontiers in Plant Science (2024).
2. Conservation Genetics of the Endangered Lompoc Yerba Santa (Eriodictyon capitatum Eastw., Namaceae), including Phylogenomic Insights into the Evolution of Eriodictyon. Plants (2023).
3. Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species. PLOS ONE (2012).
4. Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers. PLOS ONE (2008).
5. Special features of RAD Sequencing data: implications for genotyping. Molecular Ecology (2012).
6. Amplification Biases and Consistent Recovery of Loci in a Double-Digest RAD-seq Protocol. PLOS ONE (2014).
7. Defining Loci in Restriction‐Based Reduced Representation Genomic Data from Nonmodel Species: Sources of Bias and Diagnostics for Optimal Clustering. BioMed Research International (2014).
8. Stacks: Building and Genotyping Loci De Novo From Short-Read Sequences. G3: Genes, Genomes, Genetics (2011).
9. Genome-Wide SNP Calling from Genotyping by Sequencing (GBS) Data: A Comparison of Seven Pipelines and Two Sequencing Technologies. PLOS ONE (2016).
10. Adapterama III: Quadruple-indexed, double/triple-enzyme RADseq libraries (2RAD/3RAD). PeerJ (2019).