 in a coordinated fashion, as a consequence of human-mediated selection.These results highlight the complex alteration of the global gene expression machinery that resulted from human selection for a longer, stronger and finer fibre, as well as other aspects of fibre physiology that were not consciously selected.

Background: Understanding the evolutionary genetics of modern crop phenotypes has a dual relevance to evolutionary biology and crop improvement. Modern upland cotton (Gossypium hirsutum L.) was developed following thousands of years of artificial selection from a wild form, G. hirsutum var. yucatanense, which bears a shorter, sparser, layer of single-celled, ovular trichomes ('fibre'). In order to gain an insight into the nature of the developmental genetic transformations that accompanied domestication and crop improvement, we studied the transcriptomes of cotton fibres from wild and domesticated accessions over a developmental time course.

Results: Fibre cells were harvested between 2 and 25 days post-anthesis and encompassed the primary and secondary wall synthesis stages. Using amplified messenger RNA and a custom microarray platform designed to interrogate expression for 40,430 genes, we determined global patterns of expression during fibre development. The fibre transcriptome of domesticated cotton is far more dynamic than that of wild cotton, with over twice as many genes being differentially expressed during development (12,626 versus 5273). Remarkably, a total of 9465 genes were diagnosed as differentially expressed between wild and domesticated fibres when summed across five key developmental time points. Human selection during the initial domestication and subsequent crop improvement has resulted in a biased upregulation of components of the transcriptional network that are important for agronomically advanced fibre, especially in the early stages of development. About 15% of the differentially expressed genes in wild versus domesticated cotton fibre have no homology to the genes in databases.

Conclusions: We show that artificial selection during crop domestication can radically alter the transcriptional developmental network of even a single-celled structure, affecting nearly a quarter of the genes in the genome. Gene expression during fibre development within accessions and expression alteration arising from evolutionary change appears to be'modular' - complex genic networks have been simultaneously and similarly transformed, in a coordinated fashion, as a consequence of human-mediated selection. These results highlight the complex alteration of the global gene expression machinery that resulted from human selection for a longer, stronger and finer fibre, as well as other aspects of fibre physiology that were not consciously selected. We illustrate how the data can be mined for genes
in a coordinated fashion, as a consequence of human - mediated selection. These result foreground the complex alteration of the global gene formula machinery that leave from human selection for a longer, impregnable and finer fibre, equally well as early aspects of fibre physiology that were not consciously choose. 

 Background: Understanding the evolutionary genetics of modern craw phenotypes has a dual relevance to evolutionary biology and crop improvement. Modern upland cotton (Gossypium hirsutum L.) was develop following thousands of year of artificial selection from a wild form, G. hirsutum var. yucatanense, which bears a short, sparser, layer of single - celled, ovular trichomes (' fibre'). In order to gain an penetration into the nature of the developmental genetic transformations that accompanied domestication and crop improvement, we studied the transcriptomes of cotton character from wild and domesticated accessions over a developmental time course. 

 Results: Fibre cells were harvested between 2 and 25 days military post - anthesis and encompassed the basal and secondary wall synthesis stages. use amplified messenger RNA and a customs microarray platform designed to interrogate expression for 40,430 gene, we determined global patterns of expression during fibre development. The fiber transcriptome of domesticated cotton is far more dynamic than that of wild cotton, with over doubly as many gene being differentially expressed during development (12,626 versus 5273). Remarkably, a total of 9465 genes were diagnosed as differentially express between wild and domesticated fibres when summarize across five key developmental time points. Human selection during the initial tameness and subsequent crop improvement has resulted in a biased upregulation of components of the transcriptional network that are important for agronomically advance fibre, especially in the early stages of development. approximately 15% of the differentially expressed genes in wild versus domesticate cotton fibre have no homology to the gene in databases. 

 Conclusions: We show that artificial selection during crop domestication can radically alter the transcriptional developmental network of even a single - celled structure, affecting nearly a one-fourth of the genes in the genome. Gene expression during fiber development within accessions and construction alteration arising from evolutionary change appear to be'modular' - complex genic networks have been simultaneously and similarly transformed, in a coordinated fashion, as a consequence of human - mediated selection. These results foreground the complex alteration of the global gene expression machinery that resulted from human selection for a longer, stronger and finer fiber, as well as other aspects of fiber physiology that were not consciously selected. We illustrate how the data can be mined for genes
 in a coordinated fashion, ar a consequence of humen-mediafed seleztion.These results highlight tye conplex alteration of thd global hene expeessmon machinery thef resulbzd frkl huken selection fot a longer, sdronger and fitef yibre, as well as other aspects of fifre phyxillogy that werg not sonsdpomsly selected.

Background: Understahding tie evolutionary genetics of modern crop pjenohypes has a dual rflevance to evojytionary biouogy and cgmp improvejent. Modern upland cotton (Gossyoium kirsutum L.) qaw dfeeloped foloowind thousands of years of artoficial selectlon fcom q wild form, G. hirsutuk var. yucatanense, rhich beass a shorter, sparsee, oayer of vinguw-ceules, pvhlar tgiciomes ('fibre'). In order ti gain an insight imtj the nature or the qedelopmental genetic transformations thau acckmpanied domestication qnd crop improvement, ae studieq the transcriptomes of cotton fibres from wild atd dojdstngwgwd accessions over a developmental time course.

Rqauktx: Fibre cells cere harvested brtaerg 2 and 25 days kost-antkssjs and encompassed the prymary and secogdaru wall synthesis stages. Usibg amplified nessenger RNA and c custom micxoarrai platgorm designed to interrugats expressioj for 40,430 gehds, we determined glpbdl patterns of expression quring fiure dzvelopmevt. Tne fibwe transcrlptomc of domesticated cltton iv far more dynamic than that of wild cotton, with over teiwe ds many yenes neing differentyally expresseb during deveuopment (12,626 vvrsus 5273). Rekarkably, a eotal of 9465 genad were diagnmsed as qiffwrenrially dbpressed betwern wild aub domestixated fibres when xumosd across five jey developmental yimd pjijtx. Rgman selectimn djrivb the initial dondstivation and subsequend crkp improvement has rcsulted ib a biasqd upregulatipn of components ov the trenscriltijnal network that are importanf for agrlnoiically advagced fibre, especnally in the early stages of development. About 15% of the difderentially expressgd nenes in wilv versts domesthcated cotton fibre yave no homology uo the genes in databasss.

Concnusiojs: We show that artificial selection during crop domestication can radicaoly alvew the transdripyionan bevzlopmeneal ievwork of even a spngle-celled structure, affecting iearly a qgaxter of the genes in the genoke. Gene expresskon during fibre developjent witnin accessions and expression akteration arising from eyolutionaey chznge aikeacs to be'modular' - comllex gznic nwtworks havc been simultaveoispy and sililacly transformed, in a coordinated fawhion, qs a consequence oh human-mediabea selgction. Trese results higgliggh the complex altetation of the blobal gene expressimn machinery thau resulted from human velection foc a longer, sdronger and finer fibre, as well as other aspects of fibre phgsiology vhat were not vlnsciously selected. We ijlustratd how the dada can be mined for genes
in a coordinated fashion, as a consequence selection.These highlight the alteration of the resulted human selection for longer, stronger and fibre, as well as other aspects fibre physiology that were not consciously selected. Background: Understanding the evolutionary genetics of crop phenotypes has a dual relevance to evolutionary biology and crop improvement. Modern cotton hirsutum was following thousands of years of artificial selection from a wild form, G. hirsutum var. yucatanense, which a shorter, sparser, layer of single-celled, ovular trichomes In order to gain insight into the nature of developmental transformations that domestication crop we studied the of cotton fibres from wild and domesticated accessions over a developmental time course. Results: Fibre cells were between 2 days post-anthesis encompassed primary secondary wall synthesis amplified messenger RNA and a custom to interrogate expression for 40,430 genes, we determined patterns of during fibre development. The fibre transcriptome domesticated cotton is far more dynamic than that wild cotton, with over twice as many genes being differentially expressed during development (12,626 versus a total of 9465 were diagnosed as expressed wild domesticated when summed five key developmental time points. Human selection during the initial domestication subsequent crop improvement has resulted in a biased upregulation of the network that are for agronomically advanced fibre, in early stages of development. of differentially wild domesticated fibre have no homology the genes in databases. Conclusions: show that artificial selection alter the transcriptional developmental network of even a structure, affecting nearly a quarter of the in the genome. Gene expression during fibre development within accessions and expression arising from appears to be'modular' - complex genic networks have simultaneously and similarly transformed, a coordinated fashion, as a consequence of human-mediated selection. results the complex of the global expression machinery that from human selection longer, stronger finer as aspects of fibre physiology that were consciously We illustrate how the data be genes
 in a coordinated fashion, as a cOnsequence Of humAn-mEdiAtEd seLectIon.These resultS HighLight the complex alteratIon of ThE GlobAL gEne exPressioN MaCHIneRy ThAt rEsULtEd froM huMan seleCtion for a lOngEr, Stronger and fINeR fibre, as weLl aS other aspectS of Fibre pHySioLOgy thAt wEre noT conscIOusly sElected.

BaCkGRound: UNDerstanDINg The eVolutionary genetiCS oF Modern crop phenOtypes HaS A dUAL reLevAnce to evolUtIonarY Biology ANd CROP imPRovement. ModerN upland cottON (GoSsypiuM hIrsUTum L.) waS deveLoPEd fOllowing thoUsanDs of years Of artiFIcial seLEction fRom a wiLd fOrm, g. hirSUtUm Var. YuCAtaNEnSe, wHIch Bears a shOrTeR, sparSer, lAYER Of siNglE-celLed, ovUlar trichomes ('FibRe'). In ORdeR to gaIn an iNsigHt Into tHe natuRe of tHe Developmental geNetiC transforMatIoNs tHaT accoMPanied DomEstIcation And crop IMprOvEMENt, We studied the transcRiPTOmEs of cottOn fibrES fRoM Wild and dOmEstIcatED AccesSionS OvEr a develOpmentAL tImE course.

reSults: FIbRe cEllS were HArveSted beTween 2 and 25 Days pOSt-anthesis and eNCompassed the pRImARY aND secOndAry wall syntHesiS StagEs. UsINg AmpLIfied MesseNgER Rna and a custom microarrAy PlatfoRm desIgned to interrOgate expreSSIOn for 40,430 genEs, we DEtERmined global paTternS of expressIOn during Fibre DevelopmEnt. The fibRE TranscriPtoMe oF doMesTICaTed cotton is faR MOre dYnAmic thaN thAt of wilD coTtoN, wiTh oVeR twice as mAny genes BeInG dIfFerEntiaLLy expresSeD duRiNg dEveloPMent (12,626 veRsus 5273). REmarKaBlY, A toTal of 9465 geNEs WERe diAgNoSed aS diFfErentIallY ExpRessed bEtween wilD anD DomeStIcAted fibRes when summed AcRoss five keY dEveLopmenTAL time poiNts. Human selection during THe initiAl dOmestIcatIon and subSeqUent crOp iMProvemEnt has ResulTeD in A BIased UPReGulAtIon of compoNENts Of the TrAnscRiptionAl network that are imPOrtAnt for agronomIcaLly aDVAnCed FIbRE, esPeCIalLY In the early stageS of developMeNT. ABout 15% of the dIFfeReNtially ExpressEd genES in wild Versus domEsticated CoTton FIBre Have no homoLogy to thE genes in dATabasES.

COncluSioNs: We shOw ThaT artiFicial SEleCtion During CrOp domeSticaTiOn can radIcally alter the transcripTional DevelOpmEntal netwOrk OF evEn a single-CellEd structurE, afFecTing nEarLY a quaRter OF tHe gENes in The gENome. Gene eXPrEssION dUring fibre dEVELopMent wIthIN accesSionS and expression altERation arising fRom eVOLutIonARy chAnGe appears to be'mOduLaR' - COmplex geNiC networks haVe been siMuLTaneoUsly anD similArly traNSFoRMed, in a CoorDinAted fashiOn, aS a COnsequeNcE oF Human-mEdiaTeD selecTion. ThESe reSULts highlight the cOmpleX ALteraTIon Of the GlObal genE ExprEssion machInery that reSulted From Human SelectiOn For a loNgeR, sTronger and FIner fibre, As welL as otheR aSpecTs oF fibre PhysIOLogy tHat wErE noT consciouSLY sELeCtED. We IlluStratE hOw thE data can bE Mined for GenES
 in a coordinated fashion,  as a cons equen ceofhu man- medi ated selection . Thes e results highlight th e com pl e x al t er ation  of the gl o b alge ne  ex pr e ss ion m ach inery t hat result edfr om human sel e ct ion for alon ger, stronge r a nd fin er  fi b re, a s w ell a s othe r  aspec ts of fib re physio l ogy tha t we re n ot consciously se l ec t ed.

Backgroun d: Und er s ta n d ing  th e evolutio na ry ge n etics o f  m o d e rnc rop phenotype s has a dua l  re levanc etoe voluti onary  b i olo gy and crop  imp rovement.  Moder n  upland cotton(Gossy piu m h irsu t um  L .)wa s  de v el ope d  fo llowingth ou sands  ofy e a r s of  ar tifi cialselection fro m a  wil d  fo rm, G . hir sutu mvar.yucata nense ,which bears a s hort er, spars er,  l aye rof si n gle-ce lle d,ovulartrichom e s ( 'f i b r e' ). In order to gai na n  i nsight i nto th e  n at u re of th edev elop m e ntalgene t ic  transfo rmatio n sth at acco mp anieddo mes tic ation andcrop i mproveme nt, w e  studied the t r anscriptomeso fc o tt o n fi bre s from wild  and dome stic a te d a c cessi ons o ve r  a developmental timeco urse.
Resu lts: Fibre ce lls were h a r v ested be twee n  2 and 25 days po st-an thesis and encompas sed t he prima ry and se c o ndary wa llsyn the sis s ta ges. Using am p l ifie dmesseng erRNA and  acus tom  mi cr oarray pl atform d es ig ne dtointer r ogate ex pr ess io n f or 40 , 430 ge nes,we d et er m ine d globa l  p a t tern sof  exp res si on du ring fib re deve lopment.The fibr etr anscrip tome of domes ti cated cott on  is  far m o r e dynami c than that of wild cot t on, wit h o ver t wice  as manygen es bei ngd iffere ntiall y exp re sse d durin g de vel op ment (12,6 2 6  ve rsus52 73).  Remark ably, a total of 9 4 65genes were di agn osed a sdif f er e nti al l y e x p ressed betweenwild and d om e st icated fib r eswh en summ ed acro ss fi v e key d evelopmen tal timepo ints . Hum an selecti on durin g the ini t ial d o me stica tio n andsu bse quent  cropi mpr oveme nt has  r esulte d inabiased u pregulation of componen ts ofthe t ran scription aln etw ork thatareimportantfor  ag ronom ica l ly ad vanc e dfib r e, es peci a lly in th e  e arl y st ages of dev e l o pme nt. A bou t  15% o f th e differentiallye xpressed genes  inw i ldver s us d om esticated cott onfi b r e have n ohomology to  the gen es in da tabase s.

Co nclusio n s :W e show  tha t a rtificial  se le c tion du ri ng crop d omes ti cation  can r a dica l l y alter the tran scrip t i onald eve lopme nt al netw o rk o f even a s ingle-celle d stru ctur e, af fecting  n earlya q ua rter of th e  genes in  thegenome.  G eneexp ressio n du r i ng fi brede vel opment wi t h in ac ce s sio ns a nd ex pr essi on altera t ion aris ing from ev ol uti o n ary ch a ng e appears to  be 'modu l a r' - compl e x ge n ic netwo rks ha ve bee n simul t ane ou sly and  si m i larly tra nsformed, inacoor dinatedfa shio n,  as  a  consequence of  human-m ediateds e lectio n.T hese result shighlight th e com pl e x alter a t ion  of the glo bal  ge ne e xpr essi o n machinery that resulte d fr om hu m anselec tionfo r a long e r, s trongera nd finer fibr e, as well as o t her aspe cts of  f ibre phys iol o gy th at w ere  not  co nsci o u slys elec t ed . We  illus trat eho w the dat acan bem ined for  gen es
 in_a coordinated_fashion, as a consequence_of human-mediated_selection.These_results highlight_the_complex alteration of_the global gene_expression machinery that resulted_from human selection_for_a longer, stronger and finer fibre, as well as other aspects of fibre physiology_that_were not_consciously_selected.

Background:_Understanding the evolutionary genetics of_modern crop phenotypes has a_dual relevance_to evolutionary biology and crop improvement. Modern upland_cotton_(Gossypium hirsutum L.)_was developed following thousands of years of artificial selection_from a wild form, G. hirsutum_var. yucatanense, which_bears_a_shorter, sparser, layer of_single-celled, ovular trichomes ('fibre'). In order_to gain an insight into the_nature of the developmental genetic transformations that_accompanied domestication and crop improvement, we_studied the transcriptomes of cotton_fibres from_wild and domesticated accessions over_a developmental time_course.

Results: Fibre_cells were harvested_between 2 and 25 days post-anthesis_and encompassed the_primary and secondary wall synthesis stages._Using_amplified messenger RNA_and_a_custom microarray_platform designed to_interrogate_expression for_40,430_genes, we determined global patterns of_expression_during fibre development. The fibre transcriptome of_domesticated cotton is far_more_dynamic than that of_wild cotton, with over twice_as many genes being differentially expressed_during development_(12,626 versus_5273). Remarkably, a total of 9465 genes were diagnosed as differentially_expressed between wild and domesticated fibres_when summed across five_key developmental_time_points. Human selection_during_the initial_domestication and subsequent crop improvement has resulted_in a_biased upregulation of components of the_transcriptional network that are_important_for agronomically advanced fibre, especially in_the early stages of development. About_15% of the differentially expressed_genes_in_wild versus domesticated cotton fibre_have no homology to the genes_in databases.

Conclusions: We_show that artificial selection during crop domestication_can_radically alter the transcriptional developmental network_of_even a single-celled structure, affecting nearly_a_quarter_of the genes in the_genome. Gene expression during fibre development_within accessions and expression alteration arising from evolutionary change_appears to be'modular'_- complex genic networks have_been_simultaneously_and similarly transformed, in a coordinated fashion, as a consequence_of human-mediated_selection. These results_highlight the complex alteration of the global gene expression machinery_that resulted from human selection for a_longer, stronger and finer fibre, as well as other aspects of_fibre physiology that were not consciously selected. We_illustrate how the data can be mined_for genes