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Glossary Amplified fragment length A highly sensitive polymerase chain polymorphism reaction for detecting polymorphisms in DNA. Annotation The process of adding an explanatory note or a body of notes to a biological subject. For example, sequencing annotation involves identifying the locations and coding regions of genes on a sequence. In functional genomics, annotation is the determination of what various gene products do. In mutational studies, annotation is the recording of observed phenotypes. Artificial micro-RNA A transgene engineered to produce a micro RNA targeted against a particular DNA sequence. Bacterial artificial chromosome Vectors used to clone large (100-300 kb) DNA fragments. Bioinformatics The study of genetic and other biological information using computer, mathematical, and statistical techniques. 109

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110 Achievements of the N at i o na l P l a n t G e n o m e I n i t i at i v e cDNA Complementary DNA; made from messenger RNA (mRNA). Commensals Two organisms of different species in a relationship that benefits one but does not affect the other species. Common query language A formal language for representing queries to information retrieval systems. Comparative genomics The comparison of gene and genome structure, function, and evolution across taxa. DNA fingerprinting An analysis used to identify an individual’s unique sequence of DNA base pairs by exposing the individual’s DNA sample to molecular probes. DNA marker A DNA sequence in a known location of a chromosome that has a particular trait. Epigenetics The study of heritable changes in gene function that occur without a change in the DNA sequence. Epigenomics The study of alterations to the genome DNA sequence that alters gene function without a change in DNA sequence. Expressed gene content The sum of all mRNAs expressed in a given sample. Expressed sequence tag (ESTs) The result of large-scale partial sequencing of randomly selected cDNA clones. ESTs are a useful tool for gene identification, localization, and mapping. Extensible markup language A general purpose language used to describe data in a platform-neutral way so that data can be shared across multiple platforms. Functional genomics The study of genomes to determine the biological function of all the genes and their products. Gene expression The transcription, translation, and phenotypic manifestation of a gene.

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Glossary 111 Gene Ontology The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism. Read more about the Gene Ontology at Genetic polymorphism Different forms of a genetic sequence that arise from mutation. Genetic redundancy The overlapping of function of two or more genes that results in no change in the biological phenotype if one of those genes is inactivated. Genome The entire chromosomal genetic material of an organism. Genome sequencing Determination of the order of nucleotides (base sequences) of an entire genome. Genomics The comprehensive study of whole sets of genes and their interactions rather than single genes or proteins. Germplasm The genetic material that carries the inherited characteristics of an organism. High throughput Rapid (and simultaneous) processing of large sample sets. Informatics The study of the application of computer and statistical techniques to the management of information (also see bioinformatics). Kinase An enzyme that adds phosphate groups to proteins. Marker-assisted breeding The use of DNA polymorphisms as a means to rapidly test progeny from a cross for the introgression of a desired chromosomal segment. Metabolomics The global analysis of metabolites and metabolic networks in cells, tissues, and organ systems. Metadata Data that describe other data.

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112 Achievements of the N at i o na l P l a n t G e n o m e I n i t i at i v e Metagenome The collective genome of a community of microorganisms, obtained without first isolating individual community members. Metagenomics The study of genetic material recovered directly from environmental samples. Microarray A microscope slide or other solid support on which many distinct cDNAs or DNA oligonucleotides are patterned at high density in an addressable array. Microarrays are interrogated by hybridization to fluorescently labeled cDNAs or RNAs to detect the genes that are actively transcribed. Microsatellite A polymorphic sequence of DNA consisting of tandemly repeated units of DNA where the repeat unit is usually 1-4 nucleotides long. mRNA Messenger RNA. Mutagenesis The development of a mutation. Mutualists Organisms that are associated with each other in a mutually beneficial relationship. Open reading frame A reading frame in a sequence of nucleotides in DNA that contains no termination codons and so can potentially translate as a polypeptide chain. Organogenesis The development of organs in living organisms. Phenomics The study of the full complement of phenotypic traits expressed as a result of genetic and environmental influences. Phylogeny Evolutionary relationships among organisms; the developmental history among organisms. Ploidy A multiple of the basic number of chromosomes in a cell.

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Glossary 113 Positional cloning The isolation of a gene based solely on its position along a chromosome and its mutant of epigenetic phenotypic alteration. Protease An enzyme that hydrolyzes proteins. Protein interactome The full complement of protein-protein interaction in a cell. Proteomics The study of a full set of proteins encoded by a genome. Putative unique transcript An assembled complementary DNA (cDNA) sequence generated by sampling many overlapping expressed sequence tags. Quantitative trait loci Genetic loci that affect a quantitatively inherited trait. Reference sequence An accurately assembled genomic sequence that can serve as a reference for comparative genomic studies. Rhizosphere The zone around plant roots. Shared descriptive language A computer language used in annotation to express a quality of the biological subject of interest, for example the “transcribed region” of this sequence. The annotators in the genomics community jointly use the terms or words in this common language to facilitate comparisons of data. Single-nucleotide polymorphism DNA sequence variation that occurs when a single nucleotide (A, T, G, or C) is altered. SNPs can be useful in detecting genetic variation among individuals in a given population. Splicing The process that removes intron sequences and covalently joins exon sequences. Structured query language A standard interactive and programming language for getting information from and updating a database. Symbionts Organisms that are associated with each other in a mutually beneficial relationship.

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114 Achievements of the N at i o na l P l a n t G e n o m e I n i t i at i v e T-DNA Transferred DNA from Agrobacterium. Targeting Induced Local Lesions in A method for identifying mutations in a Genomes (TILLING) specific target gene. Transcriptomics The study of the full complement of activated genes, transcripts, and mRNA in a given tissue at any particular time. Translational genomics Translation of genomic findings from experimental model species to crop species Transposon A segment of DNA that moves, jumps, and can be integrated into many different sites along a chromosome.