N E W G E N E T I C S, F O O D A N D A G R I C U LT U R E 55C. GlossaryB i o i n fo r m ati cs : the as s e m bly of data fro mgenomic an a l ysis into acces s i ble forms. Iti nvol ves the appl i cation of info r m ation te c h-n ol ogy to an a l yze <strong>and</strong> manage large data setsres u l ting from gene sequencing or re l ate dte c h n i q u es .D i a gn o s ti cs :m o re accurate <strong>and</strong> qui c ker identifi cation of path ogens using new diagn o s ti csbased on mol e cu l ar chara c te r i zation of th epath og e n s .Fun c tional genomics is the knowledge th atco nverts the mol e cu l ar info r m ation re p rese n ted by DNA into an un d e rs t<strong>and</strong>ing of genefun c tions <strong>and</strong> effects: how <strong>and</strong> why genesbe h ave in ce r tain spe c i es <strong>and</strong> under spe c i fi cco n d i tions. To address gene fun c tion an de x p ression spe c i fi ca l l y, the re cove ry <strong>and</strong> identification of mutant <strong>and</strong> ove r - e x p ressed ph e n o-types can be empl oyed. Fun c tional genomicsalso entails res e arch on the pro tein fun c ti o n( p ro te o m i cs) or, even more broa dl y, the wh ol em e ta bolism (meta bol o m i cs) of an org an i s m .Gene chips (also called DNA chips) or microarrays.Id e n ti fied expressed gene sequences ofan org anism can, as expressed sequence ta g sor sy n th es i zed ol i g o n u c l e o ti d es, be pl a ced on am atrix. This matrix can be a solid support suchas glass. If a sam ple co n taining DNA or RNA isa d d e d, those mol e cu l es th at are co m pl e m e n-tary in sequence will hyb r i d i ze. By making th eadded mol e cu l es fl u o res ce n t, it is po s s i ble tod e tect wh e ther the sam ple co n tains DNA orR NA of the res pe c tive genetic sequence initiallymoun ted on the matrix.G e n e ti cally mod i fi ed food (GM food ) : <strong>Food</strong>th at co n tains above a ce r tain minimum co n-tent of raw material from geneti cally mod i fi e do rg anisms (GMO).G e n o m i cs : the mol e cu l ar chara c te r i zation ofall the genes in a spe c i es .High th ro u g h p ut (HTP) screening makes us eof te c h n i q u es th at allow for a fast <strong>and</strong> simpl etest on the pres e n ce or absence of a des i ra bl es tr u c ture, such as a spe c i fic DNA sequence<strong>and</strong> the expression patterns of genes inres ponse to diffe rent stimuli. HTP scre e n i n goften us es DNA chips or microar rays <strong>and</strong> automated data processing for larg e - s cale scre e n-i n g, for exam ple to identi fy new targets fo rdrug deve l o p m e n t .I n s e r tion mutan t s are mutants of genes th atare ob tained by inserting DNA, for instan ceth rough mobile DNA sequences, tran s po s o n s .In pl ant res e arch, the ca pa c i ty of the ba c-te r i um A groba c te r i um to introdu ce DNA intothe pl ant genome is empl oyed to indu cem utants. In bo th cas es, mutations lead to lackingor changing gene fun c tions th at arerevealed by abe r rant ph e n o types. Inserti o nm utant isol ation, <strong>and</strong> subsequent identi fi cation<strong>and</strong> an a l ysis are empl oyed in mod e lpl ants such as A rabidopsis <strong>and</strong> in crop pl an t ssuch as mai ze <strong>and</strong> rice .Living mod i fi ed org an i s m(LM O) m e ans any livingorg anism th at po s s es s es a novel co m b i n ati o nof genetic material ob tained th rough the use ofm odern biote c h n ol ogy. (Sy n o nym of GMO).Modern biotec h n ol ogy m e ans the appl i cationof: a) In vitro nucleic acid te c h n i q u es,including re co m b i n ant deox y r i bonucleic acid( DNA) <strong>and</strong> direct injection of nucleic acid intocells or org an e l l es, or b) Fusion of cells beyo n dthe ta xonomic fam i l y, th at ove rcome natura lphys i ol og i cal re p rodu c tive or re co m b i n ati o nbar r i e rs <strong>and</strong> th at are not te c h n i q u es used intra d i tional breeding <strong>and</strong> selecti o n .Mol ecu l ar breed i n g : i d e n ti fi cation <strong>and</strong> eva l u-ation of us e ful traits using mar ke r - as s i s te ds e l e c ti o n .Sh o tg un genome seq u e n c i n g is a sequencings trate gy for which parts of DNA are ran d o m l ys e q u e n ced. The sequences ob tained have aco n s i d e ra ble overlap <strong>and</strong> by using appro p r i-ate co m p uter software it is po s s i ble to co m-pare sequences <strong>and</strong> align them to build larg e runits of genetic info r m ation. This sequencings trate gy can be auto m ated <strong>and</strong> leads to ra p i dsequencing info r m ation, but it is less pre c i s eth an a sys te m atic sequencing approa c h .Single nucleo tide pol ym o r ph i s m s ( SN Ps) arethe most common type of genetic var i ati o n .SN Ps are sta ble mutations co n s i s ting of ac h ange at a single base in a DNA mol e cu l e .SN Ps can be dete c ted by HTP an a l ys es, fo ri n s tan ce with DNA chips, <strong>and</strong> th ey are th e nm a p ped by DNA sequencing.Tran s fo r m ati o n : i n trodu c tion of single genesco n ferring po te n tially us e ful trai t s .Va ccine tec h n ol ogy : using modern immun ologyto develop re co m b i n ant DNA va cc i n es fo ri m p roved co n trol of animal <strong>and</strong> fi sh diseas e .
56N E W G E N E T I C S, F O O D A N D A G R I C U LT U R ED. List of Tables, Boxes <strong>and</strong> FiguresLIST OF TA B LESTa ble 2.1Co m plex traits being addressed th ro u g he m e rging scienceTa ble 3.1I m pl i cations of Geneti cally Mod i fied <strong>Food</strong> s<strong>and</strong> Crops for Hum an He a l thTa ble 4.1I m pl i cations of Gene Te c h n ol ogy forB i od ive rs i ty <strong>and</strong> the Env i ro n m e n tTa ble 5.1Co m parison of food safe ty re g u l ationsfor genetic alte rations of food cro p sTa ble 5.2Typ i cal info r m ation re q ui red for as s es s m e n tof env i ro n m e n tal re l e ase of GM pl an t sLIST OF BOXES AND FI GU R ESFi g ure 2.1Co m m e rcially cu l tivated geneti cally mod i fi e dc rops 2002B ox 3.1I s s u es of modern geneti cs in agr i cu l turefor hum an healthFi g ure 3.1Safe ty issues with re g ard to geneti callym od i fied food sFi g ure 3.2The co n cept of substan tial equiva l e n ceB ox 6.1Key Co n c l usions of the UNDP Hum anD evelopment Re portTa ble 5.3Fre q u e n cy of gene fl ow from out - c rossingin selected crops in Euro peTa ble 6.1D e m <strong>and</strong>s for improving breeding of seve nAfr i can cro p s
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