Glossary
The words of genomics, explained simply.
eDNA, metabarcoding, dPCR, SNP, GWAS: the terms we use on this site, defined in a few lines.
- ASVamplicon sequence variant
- A unique sequence found in metabarcoding data after sequencing errors are corrected. Each ASV is then compared with reference databases to assign it to a species or group.
- Bioinformatics
- The discipline that processes and analyses biological data, especially DNA sequences, using software, statistics and reproducible analysis pipelines.Bioinformatics
- Digital PCRdPCR
- A technique that splits a sample into thousands of partitions before amplification: those containing the target DNA give a signal, so the DNA can be detected and quantified as a number of copies, without a standard curve.Targeted DNA tests
- Environmental DNAeDNA
- Traces of DNA that organisms leave in their surroundings (cells, mucus, faeces, gametes). Analysed from a water, soil, sediment or biofilm sample, they reveal species without capturing them.Environmental DNA
- EpigeneticsDNA methylation
- Chemical marks, such as DNA methylation, that modulate gene activity without changing the sequence. They can vary with the environment or with age.
- Genetic marker12S, COI, 16S, 18S, ITS
- A region of DNA whose variation identifies species or individuals. Metabarcoding uses marker genes: 12S for fish, COI for many animals, 16S for bacteria, ITS for fungi.
- Genomic selection
- Choosing breeders from genetic values predicted by markers covering the genome, calibrated on a reference population whose traits are measured.Genomic selection
- Genotyping by sequencingGBS, 3D-GBS
- A method that sequences a reduced fraction of the genome, cut by restriction enzymes, to genotype thousands of SNP markers in many individuals at low cost. 3D-GBS combines three enzymes.
- GWASgenome-wide association study
- An analysis that tests associations between genetic markers and a trait (growth, disease resistance, sex…) across the genome. Associated regions guide the search for candidate genes, without establishing a causal relationship on their own.
- Heritability
- The share of variation in a trait attributable to genetic differences in a particular population and environment. Heritability does not measure the genetic share of an individual’s trait; the response to selection also depends on available genetic variation and the breeding programme.
- InbreedingFis
- Mating between related individuals, which increases the probability of carrying two copies of an allele inherited from a common ancestor. Fis measures a deficit or excess of heterozygotes relative to expectations under random mating within a population; a value near 0 does not, on its own, demonstrate the absence of genetic structure.
- Introgressionhybridisation
- The lasting transfer of genes from one population or species to another through hybridisation and backcrossing. It can be traced along the genome with genetic markers.
- Long-read sequencingNanopore
- Sequencing long DNA fragments in one piece, often several thousand bases long. Depending on the protocol and available references, it can improve genome assembly or taxonomic resolution.
- Metabarcoding
- Surveying many species from a single sample: a genetic marker is amplified and sequenced, and each sequence is assigned to a species or group.Environmental DNA
- Metagenomics
- Sequencing all the DNA in a sample, without targeting a marker, to describe the composition and potential functions of the communities it contains.Microbial communities
- Mitigation hierarchyavoid, reduce, offset (ERC in France)
- The approach that organises how development projects take the environment into account: avoid impacts, reduce those that cannot be avoided, offset residual impacts.Environmental studies
- Population genomics
- The study of genetic variation within and between populations at genome scale: diversity, structure, connectivity, inbreeding and adaptation.Population genomics
- Primers and probe
- Short DNA fragments designed for one species: the two primers frame a region of its genome that PCR copies, and the fluorescent probe recognises that region. Their specificity avoids confusing the target with related species.Targeted DNA tests
- qPCRquantitative PCR
- Amplification of a DNA region monitored in real time by fluorescence. qPCR detects a target and supports absolute quantification using a standard curve, or relative quantification against a reference.
- QTLquantitative trait locus
- A region of the genome associated with variation in a measurable trait, such as disease resistance. A QTL guides the search for candidate genes and can be used in selection.
- RADseq
- Sequencing the DNA fragments around restriction sites spread across the genome. It provides thousands of SNPs for population genomics without sequencing whole genomes.
- Research tax creditCIR, crédit d’impôt recherche
- A tax credit on eligible research and development expenditure. In mainland France, the rate is 30% up to €100 million of expenditure, then 5% above that threshold. Work outsourced to an approved organisation such as LDgenX may qualify, subject to the conditions applying to the project, expenditure and company.Public & private research
- SNPsingle nucleotide polymorphism
- A position in the genome where a single base (A, C, G or T) varies between individuals. Being very numerous, SNPs serve as markers to measure the diversity, structure or ancestry of populations.
- SNP panel
- A set of a few dozen to a few thousand SNPs chosen to answer a question: assigning individuals, checking parentage, monitoring a population or a breeding programme.
- Taxonomic assignment
- The bioinformatics step that assigns a species, genus or family to a DNA sequence by comparing it with reference sequence databases.
- WGSwhole-genome sequencing
- Sequencing that aims to cover an individual’s whole genome to investigate variants, adaptation, history or the genetic architecture of traits. Coverage and detectable variants depend on the technology, sequencing depth and analysis.
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