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Suggested Citation: "Appendix G: Glossary." National Academies of Sciences, Engineering, and Medicine. 2016. Genetically Engineered Crops: Experiences and Prospects. Washington, DC: The National Academies Press. doi: 10.17226/23395.

Appendix G

Glossary

Actor	A social scientific concept used to refer to individuals or collective entities (for example, government agencies, firms, retail groups, nonprofit organizations, and citizens) when their behavior is intentional and interactive
Adventitious presence	The unintended and accidental presence of low levels of GE traits in seeds, grains, or foods
Allele	One of the variant forms of a gene at a particular location (that is, locus) on a chromosome. Different alleles produce variation in inherited characteristics, such as blood type
Antinutrient	A compound (in food) that inhibits the normal uptake or utilization of nutrients or that is toxic in itself
Antisense	A complementary RNA sequence that binds to (and thus blocks the transcription of) a naturally-occurring (sense) messenger RNA molecule
Biotechnology	A number of methods other than selective breeding and sexually crossing plants to endow new characteristics in organisms

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Cassette	A sequence of DNA with one or more genes of interest and with their respective promoters for expression, typically flanked by a set of sequences that facilitate insertion and selection into the genome of a recipient organism
Cisgenic plant	A plant that is genetically engineered with an endogenous gene from a sexually compatible species, that is, a transfer that could be accomplished through conventional plant breeding
Coexistence	To exist together or at the same time. In the context of the report, farms with GE and non-GE crops existing together
Conventional plant breeding	Modification of the genetic constitution of a plant through sexually crossing different genomes or mutagenizing a plant’s genome with chemical methods or irradiation, and selecting desirable plants to serve as parent lines
CRISPR (clustered regularly interspaced palindromic repeats)	A naturally occurring mechanism of immunity to viruses found in bacteria that involves identification and degradation of foreign DNA. This natural mechanism has been manipulated by researchers to develop gene editing techniques
Crop	Vascular plants that are grown for subsistence, environmental enhancement, or economic profit
De novo genome sequencing	Determination of the DNA sequence of the genome (full genetic complement) of an organism
Deskilling	The appropriation of labor whereby industry effectively eliminates skilled workers by introducing new technologies that defray labor costs and increase profits
Doubled-stranded RNA (dsRNA)	Two RNA molecules that are bound to each other by complementary base pairing
Endogenous	A naturally occurring substance or feature

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Epigenome	The physical factors affecting the expression of genes without affecting the actual DNA sequence of the genome
Epigenomics	Study of the epigenome using high throughput technologies
Eukaryote	An organism with membrane-bound organelles including the DNA-containing nucleus, mitochondrion, and in plants, the plastid
Event	A unique genetically engineered plant line that is characterized by the location of the transgene in the plant genome
Expression	The result of a gene being transcribed into RNA and ultimately conferring a trait
Gene drive	A system of biased inheritance in which the ability of a genetic element to pass from a parent to its offspring through sexual reproduction is enhanced. Thus, the result of a gene drive is the preferential increase of a specific genotype, the genetic makeup of an organism that determines a specific phenotype (trait), from one generation to the next, and potentially throughout the population
Genetic engineering	The introduction or change of DNA, RNA, or proteins by human manipulation to effect a change in an organism’s genome or epigenome
Genetic modification	The process used to modify the genome of an organism
Genetically modified	Refers to an organism whose genotype has been altered and includes alteration by genetic engineering and nongenetic engineering methods
Genome	The complete sequence of the DNA in an organism
Genome editing	Specific modification of the DNA of an organism to create mutations or introduce new alleles or new genes

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Genomics	The study of the genome which typically involves sequencing the genome and identifying genes and their functions
Genotype	The genetic identity of an individual. Genotype often is evident by outward characteristics
Germplasm	The available set of accessions that represent genetic diversity for a species and are used for breeding including cultivars, landraces, and wild species relatives
Glyphosate	A herbicide widely used and marketed as RoundUp®
Gross income	The total income, both cash and non-cash, received by a farm or business before any expenses are paid
Gross margin	The difference between gross income and variable costs
Homology-directed repair	A naturally occurring mechanism for repair of a DNA sequence in a cell that has a double strand break. This repair mechanism uses the DNA from a homologous chromosome or artificially added DNA with homologous sequence to the DNA that has the break as a template for the repair
Household income	A measure of the combined incomes of all people sharing a particular household or place of residence. It includes every form of income, for example, salaries and wages, retirement income, near-cash government transfers (for example, food stamps), and investment gains
Integrated pest management	A pest control strategy based on the determination of an economic threshold that indicates when a pest population is approaching the level at which control measures are necessary to prevent a decline in net returns. In principle, IPM is an ecologically based strategy that relies on natural mortality factors, such as natural enemies, weather, and crop management, and seeks control tactics that disrupt these factors as little as possible

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Intragenic plant	A plant that is genetically engineered with various plant DNAs, all of which come from varieties of the plant or sexually compatible relatives that are combined into a gene and then inserted into the genome
Isoline	An individual that differs genetically from another by only a small number of genetic loci
Landraces	A collection of accessions of a crop species that were developed and maintained by traditional farmers. They are typically not as genetically uniform as modern commercial cultivars and often have traits of interest to local farming communities
Marker-assisted selection	The use of DNA sequences to determine which plants or organisms have particular version (allele) of existing genes. Markers do not become part of the plant’s genome
Messenger RNA (mRNA)	A nucleic acid molecule that is transcribed from DNA and provides instructions to the cell’s translational machinery to produce specific proteins
Metabolomics	Systematic global analysis of nonpeptide small molecules, such as vitamins, sugars, hormones, fatty acids, and other metabolites. It is distinct from traditional analyses that target only individual metabolites or pathways
Net farm income	The difference between total revenue and total expenses, including gain or loss on the sale of capital assets
Net return	Gross income minus a set of expenses. It is usually estimated for a specific resource
Nonhomologous end joining	A naturally occurring mechanism in which DNA molecules with double strand breaks are repaired. Typically results in insertions and deletions

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Nucleotide	One of the four repeating subunits of DNA and RNA that consists of a five-carbon sugar, phosphoric acid, and an organic base that contains nitrogen. The nucleotides are adenine, guanine, cytosine, and thymine for DNA; uracil substitutes for thymine in RNA
Phenotype/Phenotypic	The visible and/or measurable characteristics of an organism (i.e., how it appears outwardly and physiologically) as opposed to its genotype, or genetic characteristics
Plasmid vector	A circular DNA molecule endogenous to bacteria that is used to replicate and transfer DNA to new cells
Plastome	The genome of plastids such as the chloroplasts
Post-transcriptional modification	Modification of a mRNA after it is synthesized
Profit	Gross income less expenses
Prokaryote	An organism that lacks membrane bound organelles
Proteomics	The analysis of the complete complements of proteins. Proteomics includes not only the identification and quantification of proteins, but also the determination of their localization, modifications, interactions, and activities
Quantitative trait locus (QTL)	A region of the genome that contributes to a phenotype in a quantitative manner
Reagent	Generally a chemical used in a science experiment; in the context of genome editing, a chemical that is used to modify DNA
Recombinant DNA	Any novel DNA sequence created using genetic engineering

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Reference genome	The DNA sequence from a single individual of a species that is used as a reference in subsequent sequencing of other individuals
Refuge (plural = refugia)	A place protected from danger. In the context of the report, a part of a farm or field where the crop does not produce insecticidal toxins, where a pest with a toxin-susceptible genotype can survive
Resequencing	Generation of whole genome shotgun sequences of individuals that are overlaid on a reference genome
Revenue	See Gross income
RNA interference (RNAi)	A natural mechanism found in nearly all organisms in which the levels of transcripts are reduced or suppressed
Single nucleotide polymorphism (SNP)	Variation in a single DNA base pair that occurs at a specific position in the genome
Small interfering RNA (siRNA)	RNA molecules that function in RNA interference
Somaclonal variation	Epigenetic or genetic changes, sometimes expressed as a new trait, resulting from in vitro culture of higher plants
Synthetic biology	The ability to generate novel traits or organisms using synthetic genes or by bringing together genes from multiple organisms. Also defined as the ability to generate novel traits or organisms using computationally designed DNA or reagents that are not directly found in nature
TILLING (targeting induced local lesions in genomes)	A method to efficiently screen for a specific mutation within a population of mutagenized plants
Trait	A genetically determined characteristic or condition that is the target of plant breeders and important in crop production

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Transcriptomics	The study of transcripts including the number, type, and modification; many of which can impact phenotype
Transgene	Any gene transferred into an organism by genetic engineering
Transgenic organism	An organism that has had genes that contain sequences from another species or synthetic sequences introduced into its genome by genetic engineering
Variety	A specific accession of a crop species that has been bred for improved agronomic traits variety that has been intentionally selected for specific phenotypic features such as yield. Crops that are typically sold and planted are cultivars
Yield drag	Yield drag is a reduction in yield potential owing to the insertion or positional effect of a transgene. Yield drag can be overcome by increased effort in conventional breeding to increase yield of the cultivar to balance out effects of yield drag
Yield lag	A cultivar with a transgene has a tendency to initially yield lower than elite cultivars without the novel traits because of yield-reducing genes that have accompanied the transgene due to genetic linkage. Over time, the yield lag usually disappears as the transgene is genetically separated from the yield reducing genes