Breve descripcion del Proyecto

Transcripción

1 United Natins Develpment Prgramme mm ma Reprte Final de A vance y LOgfOS de Pfyect* Prject Title Plant Genmics and Capacity Building in Latin America Fecha de entrega al PNUD Semestte Realizad pr Primer Semestre 2009 Gisella Orjeda Award ID Prject 10 UNDAFOutcme(s); Expected CP Outeme(s); Expected Output(s): (INT08K Frtalecimient y mejramient del desarrll de mercads sstenibles de prduccin, capital y trabaj, cn enfasis en las areas de exclusin. Disei'i y aplicaci6n de esquemas para el desarrll de micr finanzas en apy a pequei'ias y micr empresas, cnsiderand el aprvechamient de las pteneialidades lcales. Transferir la tecnjgia desarrllada pr el cnsrci internacinal de investigadres de America Latina y para refrzar ls vinculs ent re ls cientifics senir y j6venes de America Latina que partieipan en el pryeet de la papa. Implement ing Partner: Respnsible Parties; Award Start Date Award End Date Ttal Award Amunt Universidad Peruana Cayetan Heredia Universidad Peruana Cayetan Heredia 04/02/ /03/2009 USs 38,000 Breve descripcin del Pryect The main bjective f the prpsal is t enhance the capacity in Genmics and Biinfmatics Research in Latin America by netwrking and replicating training exercises. This is ging t be dne in the framewrk f the Internatinal Ptat genme-sequencing cnsrtium int which all the participating cuntries are already invlved. (See: lmvw.ptatgenme.net). The whle prject aims t increase the flw f infrmatin between the three cuntries. What we intend with the present prpsal is t transfer the technlgy develped by the internatinal cnsrtium researchers t Latin America and t re-enfrce the links amng the senir and yung Latin-American scientists invlved in the ptat prject. In the first place, the main yung researchers assisting in the ptat genme prject will be trained fr 2 mnths in bth, biinfrmatics and wet-lab prcedures. The 6 trainees will receive training in grups f tw frm different cuntries t stimulate partnership and develp persnal cntact. Once the main research assistants are trained, we need t begin planning a wrkshp in lima fr the partners f the prject. The bjective is t transfer the latest technlgy invlved in the Ptat Genme sequencing prject t the maximum number f peple. Fr this reasn befre the wrkshp begins, it is necessary fr the Peruvian crdinatrs t d a study travel f 10 days t the University f Waeninen in Hlland t be uddated n the latest develdments

2 and t planily all the tpics 01 the wrkshp. The wrkshp will be carried ut at the Universidad Peruana Cayetan Heredia hwever it wuld be ideal t have the tw main biinfrmaticians f the Internatinal cnsrtium t be trainers in Lima. It is expected that the training activities and the cntacts that this fund will prduce, will imprve the flw f infrmatin amng participating cuntries and will allw fr a Latin American success sequencing the genme f ne f the mst imprtant crps f ur regin. I) PRINCIPALES LOGROS DEL PROVECTO descripcin de ls principal_s lgrs del pry,et durante el semestre A Wrkshps was carried ut at the Genmics Research U nit f Labr~"':O;'i~O'~d;'::I~",~'~"~ig~,~,Ci6C"Cy"0~'C,C"C,O"'C'"("LI~0~),"FC,Cw'ItCyC7f ~S,Ci,C"C,C,,~,----I Unlversidad Peruana Cayetan Heredia. The tile f the wrkshp was: Ptat Genme Sequencing Cnsrtium, Biinfrmatics Wrkshp. It was held between the 2 6 February All the members f the Latin American Ptat Cnsrtium and participants f this project attended. A detailed reprt, presentatins, phts and a cmplete list f participants is attached t the present reprt. 1 Chilean scientists attended a meeting and cngress in Ireland and stijyed at TEAGASC, Ireland with ne f the Internatinal Ptat Genme Rquencing cnsrtium memb!rs fr training after the meetin9, A detailed reprt is attached. 2 BrCll ilian scientists attended a meeting and cngress in 1 Eurpean cuntries and received training at Wageningen UniverSity, anther f the Internatinal members f the cnsrtium. A detailed reprt is attached. 2

3 11) PERFORMANCE DEl PROYECTO Indicar el grad de avance de las actividades prgramadas en el Prdc durante el semestre Resultad.1 linea de base M.ta Indicadr 6 MSc level scientists trained in biinfrmatics and wet-lab genmics MSc level scientists trained in biinfrmatics and wet-lab.genmi(s Enhance the capacity in Genmics and Biinfmatics Research in Latin America by netwrking and replicating training exercises Number f scientist trained Actividad.1..1 Meta Indicadr %delgr Training n biinfrmatics f 1 junir scientists frm each cuntry (Brazil, Chile and Peru) 3 scientists trained Number f scientists trained fr 2 mnths, University f Wageningen, The Netherlands 100% Cmentaris Actividad.1.2 Meta Indicadr %de lgr Training n wet lab genmics f 1 junir scientists frm each cuntry (Brazil, Chile and Peru) 3 scientists trained Number f scientists trained fr 2 mnths <University f Wageningen, The Netherlands> Cmentaris 2009, semestre.1/2 Cmentaris.100% %ttal de Igr del Resultad 1 Prmedi % de lgr actividades en elsemestre "'0" It has been very difficult t identify yung SCientists with the netessary backgrund In Chile a call fr 2 pstdctral psitins had been annunced fr a mnth in the main newspapers and n ne has applied fr the psitins. Finally they have identifi ed ne persn Resultad 2. linea de base Meta Indicadr Three Peruvian crdinatrs ready t rganize a training wrkshp in Latin America and prvide supprt t the varius Latin-American participating scientists Only ne crdinatr has e)(perience in High thrughput genmics latest technlgy invlved In the Ptat Genme sequencing project transferred t the ma)(imum number f peple Crdinatr visit t Wageningen t crdinate the wrkshp and Wrkshp e)(penses and Wrkshps reprt Actividad 2.1 Meta Indicadr %de lgr Study visit f 3 Senir Peruvian scientists fr 2 weeks <University f Scientist prepared t rga nise,) Wrkshp In ptat genmlcs and biinfrmati(s 3 Numberf visits t the University f 10 0% Wageningen by Peruvian scientists

4 Wageningen, The Netherlands> Cmentaris 2 Peruvian scientists have participated f the Ptat genme sequencing cnsrtium meeting in April 2008, One f them als participated in the steering cmmittee meeting f the Internatinal Cnsrtium in representatin f the latin American COlleagues. Further t this 3 day meeting they have stayed fr ne mre week t di5(uss the wrk t be dne, and crdinate a wrkshp that will be earned ut in September this year in lima. One Peruvian scientist is the crdinatr f the latin American Ptat genme sequencing cnsrtium and she will g again in Octbert Wageningen and Clgne where the Slanacea cnference SOL2008 will be carried ut Als she will participate in the steering cmmittee meeting f the Ptat genme %ttal de lgr del Resultad , semestre 1/2 Cmentari05 Prmedi% de lgr actividades en el semestre ","" Activity finished befre this perid. Resultad 3 Linea de base Meta Indicadr E ight peple, trained in lima in biinfrmatics fr structuralgenmics N peple trained in structural genmics Imprve the flw f infrmatin amng participating cuntries Wrkshp expenses, Wrkshp held Actividad 2.1 Meta Indicadr %de lgr Ten day wrkshp in lima. PI frm each cuntry and varius representatives f Brazil, Chile and Peru fr a Blinfrmatics pipeline set up '00% Wrkshp expenses, Wrkshp held hands n Wrkshp carried ut. wrkshp n the techniques f the prject <Universidad Peruana Cayetan Heredia> Cmentaris The server and cmputers have been installed and the biinfrmatics pipeline has been set up. The Server is being accessed nrmally and used every day by ur Chilean, Argentinean and Brasilean partners. The wrkshp was carried ut succesfully. A detailed reprt in Spanish is attached. %ttal de lgr del Resultad 2 Prmedi % de lgr activldades en el semestre 2008, semestre 1/2 Cmentaris '" Very successful Wrkshp. Yu may see the results lking in Genebak fr ptat genmic sequences prduced by us and the partners using ur server and the knwledge btained during the wrkshp. Perfrmance del Pryect en el semestre 2008, semestre 1/2 Cmentaris Ttal % de lgr de resultads ' 00 We thank the help f Mr. Albert Suppa and Ms. Sharn Lu fr the succes f the prject III) PRINCIPALES PROBLEMAS Y OBSTACULOS EN LA IMPLEMENTACION Describir ls principales bstaculs experimentads durante la implementacin. Incluir las medidas que han sid adptadas para enfrentar las dificultades. 4

5 Descripcin Medid.u adptadas The main difficulty has been t identify the A new call fr psitins was carried ut. And the right peple t be trained as they need t call will included nt nly natinals resident in have a particular backgrund and Chile but als Chileans living abrad qualificatins t be able t prfit f the tw mnths in Wageningen The budget envisaged fr living expenses in Eurpe was t small t be real Tw scientists traveled instead f three. IV) lecciones APPRENDIDAS.* Describir brevemente las leccines aprendidas durante el perid cnsiderad. Oescripcin 1 If high level training is invlved it is desirable t have the peple t be trained already identified when applying fr funding. 1 Calculate expenses in a mre realistic way 3.* EI presente mdel de Reprte Anual de Pryect tiene que ser lienad en tdas sus partes que representan requisits mfnims. EI reprte puede ser cmplementad cn infrmacin adicinal a discreci6n del pryect. l as leccines aprendidas se refieren a aqueljs aprendizajes, psitivs y negativs, basads en la experiencia, relativs a frmas de reslver prblemas y/ maneras de ilevar adelante actividades que puedan servir a trs actres en prcess simi lares. las leccines aprendidas del lfp pdriln servir cm insum para las evaluacines de pryect, as! cm para cm partir cn ls demas pryects que se implementan en cnjunt cn el Gbiern. 5

6 Reprte de Event Internacinal Ptat Genme Sequencing Cnsrtium Biinfnnatics Wrkshp Genmics Research Unit Labratris de Investigaci6n y Desarrll (LI D), Faculty f Sciences Universidad Pcruana Cayetan Heredia 2-6 February 2009 EI presente reprte infrma sbre la realizaci6n de un event de entrenamient para cientifics peruanas de la UNSCH, INIA Y UPCH al cual tambien asistiern 2 cientffics chilens, 2 brasilers y 2 argentinas financiads par sus prpias agendas de financiamient. EI event tuvq cm instructres a ls Drs. Jan de Ber de la Universidad de Wageningen, Hlanda y al Sf. Michael Geffry de la Universidad del Estad Michigan en Estads Unids. EI event cmenz6 el 2 de febrer y termin el 6 de febrer sin embarg. La Unidad de genmica recibi6 ads cientifics de la Universidad Nacinal de Huamanga en Ayacuch y a trs cientifics Peruans, del Centr internacinal de la Papa, del institut nacinal de Innvacin Agraria y participantes del pryect en UPCH para darles entrenamient previ al event cn el bjetiv que puedan aprvechar al maxim el taller. Asimism recibims a un jven cientific argentin durante un mes para entrenarl previa mente al taller. Objetivs 1. Realizaci6n de un taller de entrenamient en tecnicas biinfrmaticas y de labratri que seran utilizadas en el prgrama de secuenciamient de la papa. A cntinuaei6n sc prcscnta el crngrama del taller tal cm rue entregad a ls part iei pantcs Ptat Genme Sequencing Cnsrtium Biinfrmatics Wrkshp Genmics Research Unit Labratris de Investigaci6n y Desarrll (LID), Faculty f Sciences

7 Universidad Peruana Cayetan Heredia 2-6 February 2009 Mnday 2 February 9:15-9:30 am Presentacin de Taller: Gisella Orjeda Each participant will present him-herself. Indicating their institute and their participatin in the PGSC. 9:30-9:50 am Michael Trres Server functinality thrugh putty-xming and thrugh Fedra. 9:50-10:40 Jan de Ber, Wageningell University, The Netherlands AFLP markers; the UI-ID genetic map II :00-13:00 AFLP markers; the UHD genetic map Dems: mapping markers n the UHD map llsing Atari sftware finding AFLP markers in BAC sequences llsing Atari sftware 13:00-14:00 Lunch. Cafeteria UPCH 14:00-16:00 Jan de Ber The BAC library and physical map; FISH Dem: mapping AFLP markers n the physical map view ing fingerprint cntigs with Atari sftware 16:00-16:30 Cffe Break 16:30-17:30 Jan de Ber Exercise: finding markers and anchred BACs n the physical map website viewing fingerprint cntigs n physical map website (Gelsynth) Tuesday 3 February 9: 15-10:30 Jan de Ber Use f FPC; BAC selectin and tiling path extensin 2

8 10:30- II :00 CCCe Break 11:00-13:00 Jan de Ber Exercise: verify ing sequenced BACs with BAC cnd tl cntig extensin with BAC end tl cntig extensin with FPC 13:00-14:00 Lunch. CaCeteria UPCH 14:00-16:00.Ian de Ber a Influence fhctcrzygsity n physical map and sequencing Finding BACs in BAC pls 16:00-16:30 CCCe Break 16:30-17:30 Jan de Ber a Use f tmat BAC sequence data (relaxed BAC end tl) Exercise: cntinuatin with practicing FPC Wednesday 4 February 9:15-10:30 Jan de Ber Sequencing (principles f Sanger and 454 sequencing) => will be very general 10:30- II :00 CCCe Break II :00-13:00 Jan de Ber Overview r the PGse BAC registry web site Submitting sequences t the PGSC: multifasta frmat Exercise: Mummer and Blast alignments "Manual" rdering f BAC sequence fragments 13:00-14:00 Lunch. CaCeteria UI'CH 14:00-16:00 Michael Trres: Sequence assembly prcess (frm Sanger data - Phrcd, Phrap; Cn sed) 3

9 16:00-16:30 Cffe Break 16:30-17:30 Tur Gcnmics Research Unit UPCH-Labratris Investigacin y Desarrll -Facultad de cicncias Thursday 5 February 9:15-10:30 - Michael Geffry, Michigan State University, USA Bambus and Extending 8acs 10:30-11:00 Cffe Break 11:00-13:00 Michael Geffry Bambus and Extending I3acs 13:00-14:00 Lunch. Cafeteria VPCH 14:00-16:00 - Michael Geffry Assembly exercise 16:00-16:30 Cffe Break 16:30-17:30 Michael Geffry Assembly exercise Friday 6 February - 9:15-10:30 - Michael Geffry Michigan State University Practical exercise using chrmsme 111 sequenced SAcs 10:30-11:00 Cffe Break II :00-13:00 Michael Geffry 4

10 Assembly Scafflding and Extensin 13:00-14:00 LUllch_ Cafeteria UPC11 14:00-17:30 (always cffe break ala. 16:00) Participants in general: Free t practice and t ask questins t instructrs. Cnsrtium meeting -rm I LID: Gisella Orjcda, Sergi Feingld, Paul de Mel, Bris Sagred, (thers with invitatin). 19:30 Ccktail at G. Orjcda's huse: Pasc de la Republica 5868, Miraflrcs 5

11 departu Cun try Fundi"!:! A1!cncy arrival Htel Infrmatin fli!?ht "... arriv~~"'.., flight-'" dep- ~ "'8hl Prcisur Othe,- sfi a.chacrla'rcisur.n.!. uv airline. time number,... time number. Status Jan de Hlland Bc< Jan.deBerfci wur.nl 3 1-Jan 07- Feb Casa andia KI.M 16: : OK Michael USA Geffry Qeffrvfii'msu.edu 04-Feb 07-Feb Casa andina DELTA A 23:55 34" 01 : OK Paul Brazil de Mel nedcmelf@j lb_cm Ol-Feb [ I-Feb Casa andina TAM 10:35 JJ :45 JJ 8067 OK QrLenil Brazil Bnfim Jr., rz~nij. u ni~n.lb r:.ap.a.br 3 J-Jan 07-Feb Casa adina raea 21:00 TA :15 TA 131 OK Rbert Brazil Tgawa 10 >awa!ffceanten.embr.lpili 31-Ja 07-Feb Casa andina I"A('". 21:0~ IA :15 IA 131 OK Leandr Hspedaje Argentina Barreir lebarreir8zi'uholmai l.cm 14-Jan 07-Feb UPCH I.A~ A 22: : OK Sergi Argentina Feingld s fei II >ldfiilba1carce. i III a.!lov.ar Ol-Feb 07-Feb Casa andi na AR 22: ~ : OK I Bris Chile Sagred bs:l2red!{j)i 0 ia.ci Ol-Feb 07-Feb Casa andina LAN 22:50 I.A :30 l.a053 1 OK I Annette Chile Fahrenkrg a f ahrenkrl:!lli'i nia,d Ol-Feb 07-Feb Casa undina I.AN 22:50 la :30 LA053 1 OK Pilar Taca Uruguay Zrri lla zrri tlatffdasteur.cdu_ 1\ Ol-Feb 10 Feb Casa andina TACA 09:40 Taca045 21:40 m Pabl I.aca'" Uru~uay Peraza r ern7..afii'i nia.r.uv Ol-Feb 08-Feb Casa andina lj:,\c" 119:40 Jacan.s ' I : OK 6

12 Cuntry I Institute [-mail Name Pru UPCH 2riedara'uch.edu.De Gisella Orjeda Peru UPCH I.l!..uzmanfe167@vah.es Frank Guzman Peru UPCH mike.cb. a mail.cm Michael Trres P,ru UPCH rb lucia htmail.em Rbert Lzan Peru UNMSM l!:!a DOnee unmsm@vah.es Olga Pnce P,ru UNSCH labtmasevichra vah.es Tmas Miranda Peru UNSCH ~ rmano 12(@lalinmail.cm German de la Cruz P,ru CIP e.mihvilvich(fficgiar.otq. Elisa Mihvilvich CIP P," IN IA fserna@inia. Qb. pe Fernand Serna P," INIA kevivanc@qrnail. cm Kelly Vivanc INIA Peru INIA jbenavides@inia. qb. pe Jr~e Benavides INIA 7

13 Travelling reprt t Wageningen/Hlland and Stckhlm/Sweden Orzenil Bnfim and Rbert Tgawa June 2009 Prspective visit t Wageningen Genmics Facility fjune 2009 We had the pprtunity t meet the Biinfrmatic grup at Wageningen Genmics Facility. Our cntact was Dr, Reland van Ham, Cluster leader fr Applied Biinfrmatics. He intrduced their facilities and the prjects that they are invlved. Our particular interest was abut the system that was develped t perfrm SAC genme anntatins called Cyrille2 and their strategy fr the ptat genme analysis. Dr. Mark Fiers the main authr f the Cyrille2 pipeline system [1] was als present n the first day and we had the chance t discuss abut further cllabrative develpment n Cyrille2 with mre integrated mdules. The hands n was with Erwin Datema ne f the develpers and c-authr f Cyrille2. He shwed the system design architecture and the ways t use the different mdules. Als he explains hw t cnfigure and run the different prgrams n the pipeline. The practical wrk was t create a small pipeline using a BAC dwnladed frm NCBI (Ptat Chrmsme III) and anntate it. At the end we culd visualize the anntatins made by the system. Anther aspect was the need fr the use f a grid cmputing and this is imprtant fr the parallejizatin t run the anntatin prcess. They are using the Sun Grid Engine [2). The visit was very prductive and we are currently installing the Cyrille2 system in ur machines at Embrapa/Brazi1. The first step will be the installatin f the infrastructure (Sun Grid Engine) and then the actual installatin f Cyrilie2. Mark Fiers already create a repsitry fr Cyrille2 n the surcefrge website (3] t share the develpment and we are very excited t see the system wrking in ur facilities.

14 [lj Mark WEJ Fiers, Ate van der Burgt, Erwin Datema, Jst CW de Grt and Reland CHJ van Ham. High-thrughput biinfrmatics with the Cyrille2 pipeline system. BMC Biin!rmtics, 2008, 9:96. [2J / index.xml [3J liel 17th Annual Internatinal Cnference n Intelligent Systems fr Mlecular Bilgy f June th Annual Internatinal Cnference n Intelligent Systems fr Mlecular Bilgy had place at Stckhlm, Sweden, n June 27, and 28. The cnference was hsted by the Internatinal Sciety fr Cmputatinal Bilgy (ISCB) and the Eurpean Cnference n Cmputatinal Bilgy (ECCB) and prvided a frum regarding the latest develpments in biinfrmatics and pprtunities t participate in special interest grup meetings. Embrapa researchers participatin tk place at the fllwing events: - Data and Analysis Management Satellite Meeting, June 27. Oral presentatins n biinfrmatics data sharing, wrkflw develpment and reuse, tl develpment fr data mining and data warehuse, standards and infrastructure fr managing data, metadata and grid/clud cmputing. - Metagenmics, Metadata and MetaAnalysis Special Interest Grup, June 27. Oral presentatins n standards and infrastructure fr managing data and metadata twards enhanced discvery f genmic and metagenmic data. - Shrt Read Sequencing Special Interest Grup, June 28. Oral presentatins n sequence assembly frm shrt reads (sequence reads frm Next Generatin Sequencing Technlgies), SNP discvery, variatin discvery, RNA sequencing and metagenmics. Regardin g Ptat Genme Prject activities n sequence assembly and biinfrmatics analysis the cnference cntributed particularly t enhance ur knwledge

15 f mst pwerful and up t date methdlgies t deal with sequencing prjects. Due t availability f sme special tls discussed in the events which researchers participated, new sftwares and appraches culd be disseminate within the Cnsrtium.

16 Reprte al Fnd Perez Guerrer Fnd Perez Guerrer pryect "Genmics and Capacity Building in Latin America. Actividad: Asistencia de 2 cienhfics chilens al Taller de Crdinacin y entrenamient del Cnsrci Internacinal de Secuenciacin del Genma de la Papa. Fecha y lugar de realizaci6n: 10 al 13 de juni 2009, Carlw, Irlanda Ls Ores. Bris Sagred y Nil Mejia, investigadres del Institut de Investigacines Agrpecuarias (INIA, Chile), especialistas en genmica vegetal asistiern representand a Chile a un Taller de crdinacin y entrenamient del Cnsrcia Internacinal de SecuenCiaCin del Genma de la papa cncid pr su siglas en ingles PGSC (Ptat Genme Sequencing Cnsrtium). Este taller y entrenamient se realizarn en el Centr de Bitechnlgy Prgramme del Crps Research del TEAGASC, Carlw, Irlanda entre ls dias de JuniO Asistiern mas de 27 investigadres, representand a ls 16 parses miembrs del PGSC. Adicinalmente, 10 investigadres se quedarn a un dia de capacitacin en el TEAGASC, actividad crdinada pr el Dr. Dan Milburne. En este infrme reprtams (I) ls alcances del taller de crdinacin que rue rientad a discutir e infrmar sabre ls avances y estad de secuenciaci6n del genma de la papa, y reprtams (II) ls detalles del entrenamient para el gentipad de alt rendimient para analisis genetics y su integracin cn recurss genmics. Se espera apjicar el gentipad de alt rendimient para lgrar una incrpracin efectiva del INIA en la publicacin del genma de la papa que estara lista para fines de este ana. I. Taller de crdinacin. Se analizarn ls principales avances en la btenci6n de la secuencia de cada un de ls 12 crmsmas que psee esta especie. Para este pryect de secuenciacin se estan utilizand ds individus dipjides, OM y RH. EI primer es un dble mnhaplide hmcigt btenid pr cultiv de gamets de un individu Slanum phureja, una especie diplide. EI segund un diplide hetercigt, que tiene un 75% de S. tubersum y un 25% de S phureja. 1.Estrategia de secuenciacn BAC x BAC (ejempl del crmsma 5) Ls principales Jgres fuern alcanzads pr el grup hlandes del WRU. Ls resultads mas relevantes se describen a cntinuacin. A partir de un mapa meitic ultra saturad (Ultra High Density Map) se lgr6 anclar clnes BAC mediante marcadres de tip AF LP psicinads en el cremsma 5, en termins del camin mas crt (Minimal tiling path) est implica 1 a 3 clnes BACs anclads pr marcadr de AFLP. A pesar de esta gran saturaci6n se detectan ds cpias de crmsmas representads pr Cntigs de FPC (Finger Printing Cntigs) debid a la hetercigcidad

17 del gentip utilizad (RH). Oebid a la misma hetercigcidad n hmgenea, la libreria BAC establecida representa apenas un 65 % del crmsma. Esta falta de cbertura tambien se ve reflejada a nivel de las secuencias btenidas y ensambladas, 47 de 60 Mb. Esta falta de cbertura se debe a la falla de in tegraci6n entre el mapa genetic y mapa fisic en regines hmcigtas (altamente similares). Paralelamente, se abrd6 la secuenciaci6n del genma cmplet (Whle Genme Sequencing) del gentip RH, alcanzand una cbertura de 95x, sin embarg, es necesari un mejr mapa fisic (Whle Genme Prfiling) antes de integrar el mapa fisic (BACs) cn las secuencias. Finalmente se discuti6 acerca de la pertinencia de cntinuar cn ls esfuerzs de secuenciaci6n BAC x BAC dad el cambi en las tecnlgias de secuenciaci6n de alt rendimient y dadas las dificultades que representa el gentip RH. 2. Secuenciaci6n cmpleta del genma (WGS) de gentip experimental hmcigt DM. Mediante la platafrma Slexa del BGI principalmente se a alcanzad una cbertura cercana al 60x. EI ensamblad de cntigs ha permitid ensamblar megacntigs 0 scafflds que cubre el 85 % del genma, y gracias a ls BAC End Sequences de ls BACs de RH se ha lgrad ensamblar Super Scafflds. Se ha lgrad una integracin parcial entre el genma RH y el OM (hasta 95 % de idenidad entre regines genicas), hay ausencia de integraci6n en las regines ricas en elements repetitivs. Preliminarmente se han antad 22 mil genes y se ha detectad un event de duplicaci6n gen6mica II. Crdinaci6n y entrenamient para la integraci6n de la secuencia gen6mica cn el mapa geneuc. EI Centr Internacinal de la Papa, CIP, ha desarrllad una prgenie que tiene cm un de sus prgenitres al gentip experimental OM. Esta prgenie «OM x 0 1) x 01), Que cuenta cn uns 200 segregantes debera ser utilizada para mapear caracteres de interes en un mapa de alta densidad, y para integrar el mapa geneuc cn las secuencias gen6micas (Scafflds y Super Scafflds). Oadas las restriccines de tiemp principalmente, se ha decidid abrdar el mape genetic a partir de un sub cnjunt de la pblaci6n. Este nivel de mape sera instrumental para integrar el mapa genetic cn las secuencias gen6micas, per se requerira abrdar el mape de alta densidad cn lda la prgenie para analizar caracteres de interes. Para ambs bjetivs se mapearan al mens micrsatelites (SSRs) idenlificads en las secuencias gen6micas derivadas de la WGS de OM. Se recibi6 un entrenamienl te6ric para participar de este gentipad a la par de ls trs miembrs del cnsrci que tienen amplia experiencia y lgrar resultads en el mism plaz de tiemp. La realizaci6n del gentipad del sub cnjunt de la prgenie mediante tecnicas de alt rendimient invlucra principal mente el us cmbinad de electrfresis en geles de pliacrilamida denaturante (PAGE) para detectar ls micrsatelites plim6rfics en la prgenie derivida de OM, y el gentipad mediante electrfresis capilar (secuenciadr de Applied Bisystems). EI rendimienl de la electrfresis capilar se incrementara disefiand una estrategia que permita reslver ls SSRs mediante carga en

18 multiplex (usa cmbinad de hasta 4 flur6frs distints). EI bjetiv de esle entrenamient es que entre ls pafses sudamerica ns (Argentina, Chile y Peru) se alcance el bjetiv de gentipar 20 % de ls SSRs. Ademas, la infrmaci6n generada, servira para asistir a ls prgramas de mejramient genetic de las diversas institucines invlucradas. En e! cas de Chile en particular, ls invesligadres aprtaran can mas marcadres mediante la incrpraci6n del analisis de Diversity Arrays Technlgy (DArT) en ls experiments de mape de alta resluci6n. Sin embarg, esta tecnlgia es efectiva en lgrar generar infrmaci6n muy relevante para ls bjelivs estrategics de mape genelic. Resultads y lgrs: Gracias al entrenamienl, y la captaci6n de recurss e infraestructura ns sumarems al esfuerz de cnstruir capacidades en el area de la genetica gen6mica y biinfrmalica en Chile. Pr lr lad, este taller de entrenamient y crdinaci6n ns permitira participar en la elabraci6n y discusi6n del manuscrit que reprtara!s alcances de la secuenciaci6n del genma de la papa. Para hacer mas eficiente nuestra participaci6n, ls investigadres ChHens se incrprarn a ls sub grups de discuci6n de mape, biinfrmatica y difusi6n.