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1. 14 3 Getting started with upload of host resistance information 15 4 Trial manager fais secccisccscocetssvenecuscnencedsssccsusuessenasevenecssuesd setssuencess ness seiseonecenses sdussesescsisancseugaseseaceseaseceness 16 5 Field test for foliage blight 18 5 1 Edit Info Field test for foliage blight nasus 18 5 2 Edit Data Field test for foliage blight 0 eee cseensecnseceseceseenseeeseesseessneseaeesaeesaaecaaesnaeens 22 53 Show Info Field test for foliage blight asas 24 54 Show data Field test for foliage blight cece cseecnecseeceseeeseeeeeeeeaeeeaeecsaecsaecaecsaeeaeeees 24 55 Export data Filed test for foliage blight 0 0 eee cssecsseceseceseceseeeseeeseeeseecsaecaaecsaecsaeenseeees 26 5 6 Corrections of data after uploading oe eee eeeeeseeereeenceceecseceseceseceseceeeeeeeseeeseaeeeaeesaaecaaessaeens 27 6 Detached leaf test for foliage blight resistance 28 61 Edit Info Detached leaf test for foliage blight resistance 28 62 Edit Data Detached leaf test for foliage blight resistance
2. 30 63 Show Info Detached leaf test for foliage blight resistance 32 6 4 Show data Detached leaf test for foliage blight resistance 32 7 Field CeSt for maturity u u wS h i qu am osaa Soo EEES N SESER OSEE TOSTAE KESS 33 7 1 EditInto EFieldt stf rmatfugyul un teoriiston akatae etaeun e Ee eiea asi 33 7 2 Edit Data Field test for maturity uN aq n ioei tenie eii nianse 34 7 3 Show Info Field test for maturity eee eeeeseeeseesseceseceseceseceseesseeseaeeeaeeeseeesaecaecaecsaeenseeess 36 7 4 Show data Field test for Maturity cece eseeseesseecseeceseceaecesecsseceseeeseeseeeseaeesaeesaaeeaaessaeens 36 8 Whole tuber test for tuber blight resistance 38 8 1 Edit Info Whole tuber test for tuber blight resistance 38 82 Edit Data Whole tuber test for tuber blight resistance 40 83 Show Info Whole tuber test for tuber blight resistance 42 8 4 Show data Whole tuber test for tuber blight resistance 42 9 Tuber slice test for tuber blight resistance
3. EUCABLIGHT files download area Trial name 2005_DK_01_05_TEST 1 Left click with the mouse on the file name below 2 Excel will open and show the content of your predefined Excel spreadsheet 3 Save the file on your hard disk as Microsoft Excel format 4 Enter your results and send your file to TG1 for quality control If Excel does not open csv format might not be associated with Excel on your computer then right click with the mouse and save the original esv file on your harddisk Then import this file to Excel You are not allowed to change the filename 2005 DK 01 05 TEST csv Fields and buttons Step 1 Step 2 Step 3 Explanation When you select Edit data on the Trial manager main page a new page opens for entrance of 1 Number of varieties and or genotypes in the trial experiment 2 Number of replicates in the trial experiment 3 Enter the number of tubers per cultivar and per replicate in the experiment This information is used for generation of the Excel spreadsheet for entrance of your primary data for tuber disease assessments When you have entered your numbers of varieties replicates and dates select Update to go to next step Select cultivar names from the Select drop down box To find a cul tivar name among the 4000 names in the list you can search via the Search box Write B and the list will start at cultivar name Ba banki Write Bi and th
4. 44 9 1 Edit Info Tuber slice test for foliage blight resistance a 44 9 2 Edit Data Tuber slice test for foliage blight resistance a 46 93 Show Info Tuber slice test for foliage blight resistance a 48 9 4 Show data Tuber slice test for foliage blight resistance a aa 49 10 Field test for tuber blight resistance 50 10 1 Edit Info Field test for tuber blight resistance naa 50 10 2 Edit Data Field test for tuber blight resistance a 54 10 3 Show Info Field test for tuber blight resistance a asassssssss 56 10 4 Show data Field test for tuber blight resistance n 56 ff ROCHON COS E A 57 12 Host resistance database tables and diagram 1 Introduction to host resistance information 1 1 Late blight Late blight caused by the oomycete pathogen Phytophthora infestans first occurred in Euro pean potatoes in 1845 when P infestans was imported from its centre of origin which is thought to be the Toluca Valley in Mexico The disease was first noted in Belgium and spread rapidly to The Netherlands France
5. 56 11 References Bourke P M A 1964 Emergence of potato blight 1843 46 Nature 203 805 808 Drenth A Tas I C Q amp Govers F 1994 DNA fingerprinting uncovers a new sexually re producing population of Phytophthora infestans in the Netherlands European Journal of Plant Pathology 100 97 107 Focke W O 1881 Die Pflanzenmischlinge Ein Beitrag zur Biologie der Gew chse Contri bution to the Biology of Crop Plants Verlag von Gebriider Borntraeger Berlin 567 pp Fry W E Goodwin S B Matuszak J M Spielman L J Milgroom M G amp Drenth A 1992 Population genetics and intercontinental migrations of Phytophthora infestans An nual Review of Phytopathology 30 107 129 Hansen J G Koppel M Valskyte A Turka I amp Kapsa J 2005 Evaluation of foliar re sistance in potato to Phytophthora infestans based on an international field trial network Plant Pathology 54 169 179 Jiihlke 1849 Beitrag zu dem Solanum utile von Klotzsch Contribution to Klotzsch s Sola num utile Allgemeine Gartenzeitung 17 356 Lindley J 1848 Notes on the wild potato Journal of the Royal Horticultural Society 3 65 72 M ller K O amp Black W 1952 Potato breeding for resistance to blight and virus diseases during the last hundred years Zeitschrift f r Pflanzenz chtung 31 305 318 Wastie R L 1991 Breeding for resistance In Phytophthora infestans the cause of late blight of potato D S
6. Internal Report Entry and transfer of host resistance information to the EUCABLIGHT database User manual Jens Grenbech Hansen Poul Lassen amp Leontine Colon P a MEA DA aa INTERNAL REPORT PLANT PRODUCTION e NO 1 JANUARY 2006 Ministry of Food Agriculture and Fisheries Danish Institute of Agricultural Sciences INTERNAL REPORT e PLANT PRODUCTION e NO 1 JANUARY 2006 Entry and transfer of host resistance information to the EUCABLIGHT database User manual Jens Grenbech Hansen amp Poul Lassen Danish Institute of Agricultural Sciences Department of Agroecology Research Centre Foulum DK 8830 Tjele Denmark Leontine Colon Plant Research International B V Biodiversity and Breeding Droevendaalsesteeg 1 P O Box 16 6700 AA Wageningen The Netherlands Internal reports contain primarily research results and reports on experiments and are intended mainly for DIAS employees and collaborators The reports can also be used as supporting documents for project meetings The reports can also describe internal relationships and guidelines for DIAS Price per report non subscribers Up to 50 pages 55 DKK 50 pages 85 DKK Please apply to Danish Institute of Agricultural Sciences PO Box 50 8830 Tjele Denmark Tel 45 8999 1028 www agrsci dk Printing www digisource dk Foreword This user manual was produced in the frame of the EUCABLIGHT concerted action 2003 2006 Only 10
7. Scroll and find the correct name If a variety in your trial is not in the list then con tact TG1 to include this in the list For breeding line names write the code name directly in the text box for Genotype name In the final step the EUCABLIGHT database has now generated a csv file that you should use for entrance of your primary disease data Right click with the mouse on the file name If your default Windows separator is set to semicolon then Excel will auto matically open and read the file Select Save as change the file format to Excel enter the file name as given on the files download area web page and then save the file on your harddisk If the file is not opened correctly then save the csv file to your harddisk via left click on the file name Then import the file to Excel and save as Ex cel format Sort your original data according to the format in the EUCABLIGHT Excel file and copy and past your data into the EU CABLIGHT Excel spreadsheet Finally send this Excel with your data to the TG1 group for quality control You will then be an nounced via an e mail when your data have been uploaded to the database Ok in Trial overview table 31 6 3 Show Info Detached leaf test for foliage blight resistance Trial information Name 2005_DK_04_02_TEST DH Print this page Trial type Detached leaf test Trial responsible Jens Gr nbech Hansen Trial institution Danish Institute of Agricultural Sciences Tri
8. Britain and Ireland where it was responsible for causing famine in 1845 1848 Bourke 1964 In the 160 years since this introduction P infestans has remained one of the most devastating potato pathogens in Europe Almost immediately after the appearance of late blight attempts were made to solve the prob lem using host resistance in the form of Solanum demissum a Mexican relative of the potato S tuberosum This wild species was used as alternative crop Lindley 1848 Jiihlke 1849 and without much success as a source of major resistance genes in potato breeding programs around 1850 Focke 1881 It was used again between 1909 and 1950 with the first resistant cultivars appearing on the market around 1930 Miiller amp Black 1952 Figure 1 Symptoms of late blight caused by Phytophthora infestans on a potato leaf Unfortunately virulent strains of the pathogen overcame this resistance as early as 1849 J hlke 1849 and have continued to do so Virulence is usually a recessive trait and Euro pean P infestans strains are often polyploid which allows them to store large numbers of unexpressed virulence genes in their genetic background without fitness costs Virulent strains originating from this hidden reservoir have an enormous capacity to multiply rapidly and spread over long distances Strains with virulence for all 11 R genes from S demissum occur worldwide although some virulence factors are less frequent such as Avr8 an
9. Edit data Trial name 2005_DK_04_01_TEST Name Jens Gr nbech Hansen Institution Danish Institute of Agricultural Sciences Trial type Field test foliar blight Trial site Trial site 1 Prepare database table for dataset 2005_DK_04_01_TEST Enter the number of cultivars and or genotypes in the trial 2 Enter the number of replicates in the trial 2 Enter the number of dates of observations in the trial 2 Update Cultivar Genotype names Trial name 2005_DK_04_01_TEST Select cultivar names from drop down box or enter genotype names as e g BPU311 Search Select Cultivar Genotype Agria Insert selected cultivar Bintje Insert selected cultivar Update Bintj Bintje Dates of observation Trial name 2005_DK_04_01_TEST Enter observation dates via the calendar button Observation dates in the trial 09 06 2004 A 24 06 2004 liil Update EUCABLIGHT files download area Trial name 2005_0K_04_01_TEST 1 Left click with the mouse on the file name below 2 Excel will open and show the content of your predefined Excel spreadsheet 3 Save the file on your hard disk as Microsoft Excel format 4 Enter your results and send your file to TG1 for quality control If Excel does not open csv format might not be associated with Excel on your computer then right click with the mouse and save the original csv file on your harddisk Then import this file to
10. Excel You are not allowed to change the filename 2005 DK 04 01 TEST csv Fields and buttons Step 1 Step 2 Step 3 Step 4 Explanation When you select Edit data on the Trial manager main page a new page opens for entrance of 1 Number of varieties and or genotypes in the trial experiment 2 Number of replicates in the trial experiment 3 Number of dates of observations in the trial experiment This information is used for generation of the Excel spreadsheet for entrance of your primary data for disease assessments When you have entered your numbers of varieties replicates and dates select Update to go to next step Select cultivar names from the Select drop down box To find a cul tivar name among the 4000 names in the list you can search via the Search box Write B and the list will start at cultivar name Ba banki Write Bi and the list will start with Biason Scroll and find the correct name Some varieties may be hard to find for example Mira is under S as Sarpo Mira and Timo is under H as Hankkijan Timo If a variety in your trial is not in the list then contact TG1 to include this in the list For breeding line names write the code name directly in the text box for Genotype name Select the Calendar button and select the dates of observations in the trial This information is used for generation of the Excel spread sheet for entrance of your primary data for disease assessments Us ing the Calenda
11. events Fry et al 1992 adaptive response to new resistance genes or agrochemicals intro duced to combat the pathogen Wastie 1991 and the recent occurrence of sexual reproduc tion in several parts of the European continent Drenth et al 1994 Many studies on the structure and evolution of these populations have been undertaken but there is still a lack of general understanding of the mechanisms involved including for instance the extent of meta population structures and the impact of local and long scale migrations The collation of the available data by EUCABLIGHT into a harmonised and readily accessi ble database will allow breeders and geneticists to compare or exploit sources of resistance in their breeding programmes Other target groups are farmers and advisers using Decision Sup port Systems who need reliable information about the aggressiveness of the late blight popu lation and the level and stability of resistance in the potato cultivars in their region 1 2 EUCABLIGHT The European Concerted Action on Blight or EUCABLIGHT A Late Blight Network for Europe www EUCABLIGHT org as it will be known is co ordinated by the Scottish Crop Research Institute in Dundee Scotland and will run for 3 years 2003 2006 The EU CABLIGHT consortium consists of a group of 24 European partners from 14 European coun tries with varied expertise in both host and pathogen research The European Union s Concerted Actions are intended to
12. region Arhus Obligatory Planting date 20 February 2004 Inoculum date Not relevant Soil type Loamy sand N Fertilization 150 kg N ha Overhead irrigation frequency Twice a week Overhead irrigation total amount 50 100 mm Standard cultivars included Alpha Bintje Eesterling Escort Gloria Robijn Sarpo Mira SASA differntials planted 13233343 536 7 8 9 10 11 SASA differentials scored compatible in early epidemic Not known SASA differentials scored compatible in late epidemic Supplementary Late blight in the region 24 June 2004 Late blight at the trial site 01 July 2004 Emergence date 30 May 2004 Number of plants per plot 5 9 Previous crop Barley Inoculum source Natural infection and spreader plants Inoculated part of trial Not relevant Inoculum density sp ml x 1000 Not relevant Zoospores sporangia in inoculum Not relevant Organic No Comments Several organic fields are grown in the area When you select Show Info in the Trial manager it shows all information you have entered via Edit Info 5 4 Show data Field test for foliage blight Show graphics Year 2005 Country Denmark Region Nordjylland Number of cultivars 46 Nurnber of dates 14 Number of replicates 3 Responsibilty Poul Lassen Sarpo Mira 212 7 0 03 0 01 aliant 1 850 3 0 27 0 01 0 15 0 01 0 94 I Aviala 2 800 1 0 41 0 01 0 20 0 02 0 94 Robijn 2 941 2 154 3 0 43 0 02 0 14 0 01 0 87 024 001 Escort 3 318 4 1104 0 48 0 02
13. send the file to the data base manager 27 6 Detached leaf test for foliage blight resistance 6 1 Edit Info Detached leaf test for foliage blight resistance Trial information Detached leaf test Trial name 2005_DK_04_02_TEST Update Obligatory Leaves from Field v Inoculation date 01 03 2005 FA Scoring date 01 03 2005 Standard cultivars included Alpha Bintje Eersteling Escort Gloria Robijn Sarpo Mira Virulence in inoculum 6 7 8 9 10 11 Not known V 102 304 Single isolate or mix Single O Mixture Supplementary Plant age in weeks ii 24 Inoculum density sp ml x 1000 Unknown wl Zoospores sporangia in inoculum Unknown Number of droplets per leaflet 1 O2 Comments Update 28 Fields and buttons Leaves from Inoculation date Scoring date Standard cultivars included Virulences in inocu lum Single isolate or mix Plant age in weeks Inoculum density Zoospores sporangia in inoculum Number of droplets per leaflet Comment Explanation Select via the drop down box if leaves were taken from the field green house or climate chamber Press the calendar button and enter the date of inoculation Press the calendar button and enter the date of scoring for disease Mark in the checkboxes which of the stand
14. the available data into a harmo nised and readily accessible database so as to allow breeders and geneticists to compare or exploit sources of resistance in their breeding programmes 1 4 Data collection and transfer to EUCABLIGHT database Protocols for assessing biological pathogenic and genetic diversity vary between laboratories engaged in host resistance and population analyses of P infestans worldwide but also in Europe These differences make the comparison of data collected by different teams difficult and sometimes downright impossible Furthermore technologies for the analysis of genetic and phenotypic diversity evolve rapidly Therefore one of the main objectives of EU CABLIGHT is to collate formalise assess and recommend the most suitable protocols through the collective work of its members These protocols are available through a dedicated section of the EUCABLIGHT website The overall aim is to provide reliable standardised methodologies generating readily comparable data and to facilitate the use and adoption of improved protocols for future work The incorporation of seven standard cultivars into trials is a major requirement of the proto cols The standard cultivars have been chosen on the basis of their availability and the ex pected durability of the resistance and represent the extremes of susceptibility and resistance in the three maturity classes first early Eersteling and Gloria maincrop Bintje and Es c
15. 0 35 0 04 0 94 i I Bilbo 3 374 0 142 1 0 49 0 02 0 17 0 01 0 87 o O o oO Fi Fi o Fi El n Tivoli 3 441 0 104 1 0 35 0 03 0 97 I j e I 24 When you select Show Data in the Trial manager it shows results derived from the disease progress curves There will be a link to documentation of all methods applied to the data 100 80 60 c 2 40 kal B 20 0 n O 10 20 30 40 50 60 Calculation of AUDPC and logistic Days after inoculation transformation for calculation of R slope and Delay of symptoms Logistic transformation severity data divided by 100 Taken from the documentation file Only data from 0 5 to 99 are used In y 1 y Wes Y 570 0 24Xx t r 0 998 0 10 20 3 40 50 60 X t Days after inoculation 25 5 5 Export data Filed test for foliage blight 3 EUCABLIGHT Microsoft Internet Explorer Eier Rediger vis Foretrukne Funktioner Hj lp s Tibage x a Aso Foretrukne Medier S Br E gt adresse fa http www eucablight org Host Host asp FileName TrialManager asp z P Hyperlinks izj Wel 28 July 2005 Bent J Nielsen euca EUCABLIGHT Ral my Potato Late Blight Network For Europe Trial overview Trial manager Cultivars Export data Trial name 2004_DK_09_01 Download your primary data mean disease data by date or derived statistics from the disease progress curve AUDPC AIR Delay etc The
16. 0 copies will be hard copied due to expected updates This version or an up dated version of the user manual will also be available on the EUCABLIGHT web site http www EUCABLIGHT org Foulum 6 January 2006 Jens Grgnbech Hansen Poul Lassen and Leontine Colon blight EUCABLIGHT Contents OATU A AE A A E EN E E R sevens osesboosaveds 5 1 Introduction to host resistance information 7 1 11 ate blehtu 2 uuu sanawaanqaqu u bole doa sl akecetii betestelsdacasted ssces Slataeethase test sts EE E EN s 7 1 2 BUGCABLIGH E I ie Sa kh S a fetes ees hase ive ete ote dite 9 13 Why sampling host resistance information 0 ee eee esecsseceeceseceseceseceseeseeeeseeseneseaeesaeesaeesaaeenaees 9 14 Data collection and transfer to EUCABLIGHT database a 9 Le Cultivar databases u am ma u S tes iets ees bes oth cava ak eine Mana dete espe es 11 1 6 Data handling and StatISI6S ua naa au hians sages isd E a EEEE E EE EREN 11 17 Overviews of results in EUCABLIGHT 0 ee eee eeecscecsseceseeeeeseeeseeeeeaeeeaeeeaeecsaecsaecaecnaeenseenes 11 1 8 Intellectual Property RIPBt _ nasua Bapa u i 12 1 9 Howto participate y u san Sun g Sauna a n a sa 12 1 10 Quality Control E esien Santi hu a a Ea aaan aan tuhuspatihu sisata h tisto 13 2 Software and hardware requirements
17. 2004_DK_09_01 Bent J Nielsen O Data Data Data Date I Info Info Info 2004 Field test maturity Flakkebjerg 2004_DK_09_02 Bent J Nielsen C pata Data Data I Info Info Info Update E udf rt agp nmtemet 16 Fields and buttons Trial Manager Trial ID Public Data Public Info Edit Data Edit Info Show Data Show Info Export data Explanation The Trial manager is your personal area for preparing Excel spread sheets for primary data upload for showing and exporting primary and derived data and for editing and showing your trial backeround information When you log into EUCABLIGHT and select the menu Results Host resistance the Trial Manager including the trial IDs for your trial will be available Information about Year Trial type Trial site name and Trial name were provided by EUCABLIGHT TG1 based on infor mation from you see section 1 9 Averages and other statistics of your secondary data are public by default because the value of the database les in sharing our results However you have the possibility not to show these on the public side by unselecting this checkbox Unselect this checkbox to keep your background data only available after login Select Edit Data to prepare an Excel spreadsheet for entrance of your primary data Select Edit Info to enter background information about your trial Select Show Data to show your primary data that were uploaded to the EUCABLIGHT d
18. 7 2004 Harvest date 03 08 2004 Pa Scoring date 11 08 2004 Sail type Claytype gt 20 clay v N fertilization 150kgN ha Standard cultivars included Alpha Bintje Eersteling Escort Gloria Robijn Sarpo Mira Virulence in inoculum i1MzM3s04M5s06M708 O23 Mio M11 D Not known O Supplementary Previous crop Wheat Inoculum density sp ml x 1000 g 10 v Zoospores sporangia in inoculum Sporangia Comments Update 44 Fields and buttons Planting date Harvest date Inoculation date Scoring date Soil type N fertilization Standard cultivars Included Previous crop Inoculum density Zoospores sporangia in inoculum Comments Update Explanation Press the calendar button and select the planting date of the potatoes Press the calendar button and select the harvest date of the potatoes Press calendar button and select the date of inoculation of the tuber slices Press the calendar button and select the scoring date of the potatoes Select via drop down box the soil type in the trial Select the total amount of N fertilization applied Mark in the checkboxes which of the standard cultivars were in cluded in the trial Write in the text box the name of the previous crop Select the inoculum density used for inoculation Select the type of inoculum If unknown then select Unknown Write comments about the
19. Enter your results and send your file to TG1 for quality control If Excel does not open csv format might not be associated with Excel on your computer then right click with the mouse and save the original csv file on your harddisk Then import this file to Excel You are not allowed to change the filename 2005 DK 01 04 TEST csv Fields and buttons Step 1 Step 2 Step 3 Explanation When you select Edit data on the Trial manager main page a new page opens for entrance of Number of varieties and or genotypes in the trial experiment Number of replicates in the trial experiment Enter the number of tubers per replicate in the experiment eee s Enter the number of slices per tuber in the experiment This information is used for generation of the Excel spreadsheet for entrance of your primary data for tuber disease assessments When you have entered your numbers of varieties replicates and dates se lect Update to go to next step Select cultivar names from the Select drop down box To find a cul tivar name among the 4000 names in the list you can search via the Search box Write B and the list will start at cultivar name Babanki Write Bi and the list will start with Biason Scroll and find the cor rect name Some varieties may be hard to find for example Mira is under S as Sarpo Mira and Timo is under H as Hankkijan Timo If a variety in your trial is not in the list then contact TG1 to include this in the
20. IR_01_01 Leslie J Dowley Show Show 2004 Poland Mazowieckie 28 g 2 2004_PL_O7_01 Beata Tatarowska Show Show 2004 Poland Podkarpackie 28 6 2 2004_PL_09_01 Beata Tatarowska Show Show 2004 Poland Podkarpackie 28 6 2 2004_PL_09_03 Beata Tatarowska Show Show 2004 Scotland South Ayrshire 20 4 2 2004_SC_27_01 Ruth Solomon Blackburn 2004 Slovakia Presovsky 36 5 2 2004_SK_07_01 Jan Held k nasaq nna L adal 2 412 Da sit ani Dauid ch z Ei Internet Trial overview table in EUCABLIGHT 15 4 Trial manager 3 EUCABLIGHT Microsoft Internet Explorer Eler Rediger vis Foretrukne Funktioner Hj lp Tibage a ET Foretrukne Medier g Br E gt Adresse http www eucablight org Host Host asp FileName TrialManager asp Os Hyperlinks me alx A ENEE euca EUCABLIGHT EJ 28 July 2005 Potato Late Blight Network For Europe Trial overview Trial manager Cultivars Trial manager Print this page The trials registered by EUCABLIGHT based on your login name are in this table To enter new data please select Edit Data and follow the guide Ticking the Public checkbox means that secondary data derived from your primary data will be available on the public side of the website Primary data will only be accessible to you the owner For new users please read Help Year Trial type Trial site name Trial name Responsibility Public Edit Show Export 2004 Field test foliar blight Flakkebjerg
21. Ingram P H Williams eds Advances in Plant Pathology 7 193 224 Academic Press London Zimnoch Guzowska E amp Flis B 2002 Evaluation of resistance to Phytophthora infestans A survey In Lizarraga C ed Proceedings of the Global Initiative on Late Blight GILB Conference 11 13 July 2002 Hamburg Germany CIP Lima Peru 37 47 57 12 Host resistance database tables and diagram The database field names and tables cover all trial types Most of the database fields are iden tical between trial types but certain field names are only associated with a specific trial type i e PlantingDateEarly PlantingDateMedium and PlantingDateLate is only for tuber field test None of the database fields concerning inoculation with P i are included in maturity test Each field name is associated with a trial type via the trial type ID number Table 1 hst_Trial Database field names explanation field type ID numbers and options of host resistance data in the EUCABLIGHT database A combination of the four key variables results in a unique identification of the trial VARIABLES IN DA EXPLANATION FIELD ID NUMBERS AND TABASE FIELD TYPE OPTIONS NAMES Trial year Integer CountrylD String 2 RegionID Integer TriallD Integer TrialName String 50 TrialSite Public or not String 50 TrialTypelD Integer suis l PublicData Name of the field Boolean 0 Public 1 Restricted PublicInfo Number ID of foci Boolean N
22. Plot PreviousCrop InoculumSource InoculumTrialPart InoculumDensity IsolateComposition LeafSource IsolateType PlantWeekAge Droplet PlantingDateEarly PlantingDateMidEarly PlantingDateLate Organic HarvestDate ContainsData Comment hst_TrialType TrialTypeID TriallypeName hst_Trial irulence Trialear CountryID RegionID TrialID Trial irulenceID Trial irulenceTest Trialvirulencev alue hst_TrialDate OF TrialYear TrialDateID TrialDate Figure 2 Host resistance database diagram of tables 62 hst_TrialStandardCultiv TrialYear CountryID RegionID TrialiD TrialstdCultivarID TrialStdCultivarvalue hst_TrialCultivar Trialvear CountryID RegionID TrialID TrialCultivarID TrialCultivarName v hst_TrialDbservation TrialYear CountryID RegionID TrialID TrialCultivarID TrialDateID TrialReplicateID TrialObseryvation
23. Sporangia Both mixed Unknown Field Greenhouse Single Mixture 1 2 3 5 5 6 7 8 9 10 1 2 NE a au EH RO SRR Ee eo sami suan NES Oe Oh 59 Table 2 hst_TrialType Database field names explanation field type ID numbers and op tions of host resistance data in the EUCABLIGHT database VARIABLES IN DA TABASE FIELD EXPLANATION FIELD ID NUMBERS AND TYPE OPTIONS NAMES TrialtypelD Key Trial type ID Integer TrialTypeName Name of the trial String 50 Table 3 hst_Trial Virulence Database field names explanation field type ID numbers and options of host resistance data in the EUCABLIGHT database VARIABLES IN DA TABASE FIELD EXPLANATION FIELD ID NUMBERS AND TYPE OPTIONS NAMES Trial year CountryID RegionID TriallD TrialVirulencelD Key variables TrialVirulenceTest TrialVirulenceValue a _ _ Region ID number Integer Trial ID number Trial virulence ID Differentials Included Boolean 1 True 2 False Compatible test result Boolean 1 True 2 False Table 4 hst_TrialStandardCultivar Database field names explanation field type ID numbers and options of host resistance data in the EUCABLIGHT database VARIABLES IN DA TABASE FIELD NAMES Trial year CountrylD RegionID TriallD TrialStdCultivarID TrialStdCultivarValue n oO is a 8 gt gt o z 60 EXPLANATION ID NUMBERS AND OPTIONS Count
24. al site Trial site 2 Trial year 2005 Trial country Denmark Trial region Arhus Obligatory Leaves from Field Inoculation date 08 June 2005 Scoring date 16 June 2005 Standard cultivars included Alpha Bintje Eesterling Escort Virulence in inoculum 1 2 5 8 10 Single isolate or mix Single Supplementary Plant age in weeks 5 6 Inoculum density sp ml x 100 10 20 Zoospores sporangia in inoculum Both mixed Number of droplets per leaflet 2 Comments When you select Show Info in the Trial manager it shows all information you have entered via Edit Info 6 4 Show data Detached leaf test for foliage blight resistance Trial data Trial name 2005_DK_04_02_TEST Plant stage sporulation and Necrotic area means per cultivar Cultivar Plant stage Sporulation Necrotic area Bintje Kuras Screen dump currently not available When you select Show data in the Trial Manger it shows results derived from the disease scores on the 1 9 lesion size scale and the 1 3 sporulation scale Lower averages indicate lar ger lesions and more sporulation 32 7 Field test for maturity 7 1 Edit Info Field test for maturity Trial information Field test for maturity Trial name 2005_DK_04_03_TEST Update Obligatory Planting date 20 04 2005 7 Soil type Sandy loam v N fertilization 150 kg N ha w Overhead irrigation Total amount 150 100 mm x Standard cultivars included Alpha v Bintje V Eersteling M Esco
25. ames Select cultivar names from drop down box or enter genotype names as e g BPU311 Search Trial name 2005_DK_04_03_TEST Select Cultivar Genotype fe Fecula lt Anco Insert selected cultivar Fecula Insert selected cultivar Update Dates of observation Enter scoring dates via the calendar button Scoring dates in the trial 21 07 2005 a 29 07 2005 ia Update Trial name 2005_DK_04_03_TEST EUCABLIGHT files download area Left click with the mouse on the file name below Excel will open and show the content of your predefined Excel spreadsheet Save the file on your hard disk as Microsoft Excel format Enter your results and send your file to TG1 for quality control Dune Trial name 2005_DK_04_03_TEST If Excel does not open csv format might not be associated with Excel on your computer then right click with the mouse and save the original csv file on your harddisk Then import this file to Excel You are not allowed to change the filename 2005 DK 04 03 TEST csv Fields and buttons Step 1 Step 2 Step 3 Step 4 Explanation When you select Edit data on the Trial manager main page a new page opens for entrance of 4 Number of varieties and or genotypes in the trial experiment 5 Number of replicates in the trial experiment 6 Number of dates of maturity scorings in the trial experiment This information is used for gen
26. ard varieties were included in the trial Mark in the checkboxes which of the virulences are present in the inocu lum Mark if a single isolate or a mixture of isolates were used for inoculation Select via the drop down box the age of the plants in weeks Select via the drop down box the density of inoculum sporangia ml x 1000 Select via the drop down box if inoculum contains zoospores sporangia or a mixture Alternatively select Unknown Mark the number of droplets per leaflets used for inoculation Write additional information about the experiment in the comment text box 29 6 2 Edit Data Detached leaf test for foliage blight resistance Step 1 Step 2 Step 3 30 Edit data Name Jens Gr nbech Hansen Institution Danish Institute of Agricultural Sciences Trial type Detached leaf test Trial site Trial site 2 Prepare database table for dataset 2005_DK_04_02_TEST Enter the number of cultivars and or genotypes in the experiment Enter the number of replicates in the experiment Enter the number of leaflets per cultivar and per replicate in the experiment 2 2 2 Trial name 2005_DK_04_02_TEST Cultivar Genotype names Select cultivar names from drop down box or enter genotype names as e g BPU311 Cultivar Genotype Update Search Trial name 2005_DK_04_02_TEST Select Bintje v Bintje Insert selected cultivar Kuras In
27. atabase Select Show Info to show background information entered about your trial Select Export data to download your primary data mean disease data by date or derived statistics from the disease progress curve AUDPC AIR Delay etc The files are in csv semicolon sepa rated format that easily can be imported into Excel or any software that can read text files 17 5 Field test for foliage blight 5 1 Edit Info Field test for foliage blight Trial information Field test for foliage blight resistance Update Obligatory Planting date 20 02 2004 fA Inoculation date 01 01 2005 A Soil type Loamy sand v N fertilization 150kgN ha Overhead irrigation Frequency Twiceaweek v Total amount 50 100 mm Y Standard cultivars included Alpha V Bintje VZ Eersteling VZ Escort VZ Gloria M Robijn M Sarpo Mira SASA differentials planted Mz v 3 M4 Ms M 6 v z v 8 v 9 v 10 M 11 Z Not known O SASA differentials scored compatible in early epidemic 11 12 13 Dla Dl s Ll e D1z Dl 8 0 9 0 10 0 11 D Not known O SASA differentials scored compatible in late epidemic 1 0203 040580607 0 8 0 9 0 10 0 11 0 not known O Supplementary Late blight in the region 24 06 2004 JE Late blight at the trial site 01 07 2004 No late blight C Crop emergence date 30 05 2004 a Number of plants per plot 5 9 Prev
28. ckboxes if late blight symptoms appeared in each of the SASA s differentials If none of these clones were planted then select Not known Press the calendar button and select the date when late blight ap peared in the region 5 10 square km radius Press the calendar button and select the date when late blight ap peared at the trial site Press the calendar button and select the date of crop emergence Select the number of plants per plot via the drop down box Write in the text box the name of the previous crop 19 Inoculum source Inoculated part of trial Inoculum density Zoospores sporangia in inoculum Organic Comments Update 20 Select the source of inoculum via the drop down box Select the part of the trial that was inoculated If natural infection then select Whole trial Select the inoculum density used for artificial inoculation If natural infection then select lt 5 sp ml x 1000 Select the type of inoculum If unknown or natural infection then select Unknown Select via radio button if the trial was grown organic or not Write comments about the trial i e use of fungicide type etc if a primary attack was observed uneven disease development or any thing special When you have entered all information then select Update to store your information in the EUCABLIGHT database 21 5 2 Edit Data Field test for foliage blight Step 1 Step 2 Step 3 Step 4 22
29. d Avr5 or rare such as Avr9 As a result breeders have turned to new sources of major genes such as the Mexican species S bulbocastanum or the South American species S microdontum using both direct gene transfer and traditional breeding methods The implementation of strategies for the integrated control of potato late blight with reduced inputs of fungicides would benefit if durable blight resistance were more common in com mercial potato cultivars This includes both foliage and tuber resistance since the pathogen also attacks tubers Durable resistance often termed field resistance or race non specific or horizontal resistance does exist However in potato this is usually associated with late ma turity and is selected against in breeding because breeders highly favour early genotypes Many sources of late blight resistance exist in wild and primitive potatoes and developed cul tivars but the nature of that resistance is often poorly understood The current European data on host resistance are fragmented and the methods used to collect this data are often not well documented The effective deployment of resistant commercial cultivars creates a moving target for P infestans but such a strategy can only be effective if we understand the existing pathogen population structure and can predict its ongoing evolution Phytophthora infestans popula tions have undergone many significant changes since 1845 with several major migration
30. da tabase via special web pages based on Trial ID and trial type The primary disease data and the background data are merged in the database based on the trial Ids You need a PC Excel a browser and Internet connection for these operations 14 3 Getting started with upload of host resistance information 1 After login to the EUCABLIGHT web site then open your personal Trial Manager via Results Host Enter background information for your trial via Edit Info in the Trial manager 2 Select Edit Data to generate an Excel file for storage of primary results 4 Send your Excel file with primary data to the host resistance technical TG1 group for quality control 5 After quality control your data will be uploaded to the database You will be announced via e mail 6 Select Show Data to see your results as graphs of disease progress curves tables with mean disease data by date or derived statistics from the disease progress curve AUDPC AIR Delay etc Additionally you can analyse your data via the Graphic analysis tool and you can compare your results with results from other similar trials 7 Select Export data to download your results in Excel files E EUCABLIGHT Microsoft Internet Explorer l x Filer Rediger Vis Foretrukne Funktioner Hj lp HTba gt gt O A 3 seg Foretrukne EFmedier Q Gh C gt Adresse E http www eucablight orgiHost Host asp FleName TrialOverview asp z G8 Hyperinks gt b
31. e list will start with Biason Scroll and find the correct name Some varieties may be hard to find for example Mira is under S as Sarpo Mira and Timo is under H as Hankkijan Timo If a variety in your trial is not in the list then contact TG1 to include this in the list For breeding line names write the code name directly in the text box for Genotype name In the final step the EUCABLIGHT database has now generated a csv file that you should use for entrance of your primary disease data Right click with the mouse on the file name If your default Windows separator is set to semicolon then Excel will auto matically open and read the file Select Save as change the file format to Excel enter the file name as given on the files download area web page and then save the file on your harddisk If the file is not opened correctly then save the csv file to your harddisk via left click on the file name Then import the file to Excel and save as Ex cel format Sort your original data according to the format in the EUCABLIGHT Excel file and copy and past your data into the EU CABLIGHT Excel spreadsheet Finally send this Excel with your data to the TG1 group for quality control You will then be an nounced via e mail when your data have been uploaded to the data base Ok in Trial overview table 4 8 3 Show Info Whole tuber test for tuber blight resistance Trial information Name 2005_DK_01_05_TEST Trial type Trial
32. e potatoes 51 Previous crop Inoculum density Zoospores sporangia in inoculum Organic Comments Update Write in the text box the name of the previous crop Select the inoculum density used for artificial inoculation If natural infection then select lt 5 sp ml x 1000 Select the type of inoculum If unknown or natural infection then select Unknown Select via radio button if the trial was grown organic or not Write comments about the trial i e use of fungicide type etc if a primary attack was observed uneven disease development or any thing special When you have entered all information then select Update to store your information in the EUCABLIGHT database 52 53 10 2 Edit Data Field test for tuber blight resistance Step 1 Step 2 Step 3 Step 4 54 Edit data Trial name 2005_DK_01_06_TEST Name Poul Lassen Institution Danish Institute of Agricultural Sciences Trial type Field test tuber blight Trial site Trial site 6 Prepare database table for dataset 2005_DK_01_06_TEST Enter the number of cultivars and or genotypes in the trial 5 Enter the number of replicates in the trial 3 Update Cultivar Genotype names Trial name 2005_DK_01_06_TEST Select cultivar names from drop down box or enter genotype names as e g BPU311 Search Select Cultivar Genotype kur Kura
33. eration of the Excel spreadsheet for entrance of your primary data for disease assessments When you have entered your numbers of varieties replicates and dates select Update to go to next step Select cultivar names from the Select drop down box To find a cul tivar name among the 4000 names in the list you can search via the Search box Write B and the list will start at cultivar name Babanki Write Bi and the list will start with Biason Scroll and find the cor rect name If a variety in your trial is not in the list then contact TG1 to include this in the list For breeding line names write the code name directly in the text box for Genotype name Select the Calendar button and select the dates of observations in the trial This information is used for generation of the Excel spreadsheet for entrance of your primary data for maturity scorings Using the Calendar button you can shift between years lt lt September 2005 gt and between months lt lt September 2005 gt gt Select Update to go to next step In the final step the EUCABLIGHT database has now generated a csv file that you should use for entrance of your primary disease data Right click with the mouse on the file name If your default Windows separator is set to semicolon then Excel will automatically open and read the file Select Save as change the file format to Excel enter the file name as given on the files download area web page and then sa
34. files are in csv semicolon separated format that easily can be imported into Excel or any software that can read text files On your computer the csv format might be associated with Excel When you left dobble click on the filename then data will be shown in Excel in separate coloumns If data are not shown in separate coloumns you have to right click on the filename and download the file to your harddisk Then open the file and specify format of the csv file as requested by Excel If you need to update your primary data in the Eucablight database please download the primary data file fram this page edit your data and send the file to the database manager Original data including replications in the format as generated by the Eucablight database using Edit 2004 DK 09 01 csv data in the Trial manager Mean disease assessments by date 2004 DK 09 01 MeanDisease csy Statistics derived from the disease progress curves i e AUDPC rAUDPC AIR and Delay of 1 2004 DK 09 01 AUDPC csv disease Depending on your settings for date and decimal character in Windows you might need to change the dates or decimal characters in the data you have downloaded Intellectual property rights Only the owner of data has access to download of data In this respect the owner is the person registered as responsible for the trial and has login to Eucablight If somebody wants to use data for publications analysis etc they should make a request to the
35. he trial Early Crop emer gence Mid early Crop emergence Late Crop emer gence Explanation Press the calendar button and select the planting date of early pota toes Press the calendar button and select the planting date of mid early potatoes Press the calendar button and select the planting date of late pota toes Press calendar button and select the date of artificial inoculation in the trial If inoculum source was natural infection then select the date when first symptoms occurred in the trial Select via drop down box the soil type in the trial Select the total amount of N fertilization applied Select the frequency of irrigation If irrigation was carried out only a few times irregularly then select Less as required Select the total amount of irrigation as close as possible to options available Mark in the checkboxes which of the standard cultivars were in cluded in the trial Press the calendar button and select the date when late blight ap peared in the region 5 10 square km radius Alternatively mark No late blight Press the calendar button and select the date when late blight ap peared at the trial site Alternatively mark No late blight Press the calendar button and select the date of crop emergence for early potatoes Press the calendar button and select the date of crop emergence for mid early potatoes Press the calendar button and select the date of crop emergence for lat
36. ia left click on the file name Then import the file to Excel and save as Excel format Sort your original data according to the format in the EUCABLIGHT Excel file and copy and past your data into the EUCABLIGHT Excel spread sheet Finally send this Excel with your data to the TG1 group for quality control You will then be announced via e mail when your data have been uploaded to the database Ok in Trial overview table 55 10 3 Show Info Field test for tuber blight resistance Trial information Name 2005_DK_01_06_TEST Trial type TrialTypeName Trial responsible Poul Lassen Trial institution Danish Institute of Agricultural Sciences Trial site Trial site 6 Trial year 2005 Trial country Denmark Trial region Nordjylland Obligatory Early planting date 02 March 2005 Mid early planting date 02 March 2005 Late planting date 02 March 2005 Inoculation date 02 March 2005 Soil type Sand N Fertilization 0 kg Nha Overhead irrigation frequency No irrigation Overhead irrigation total amount No irrigation Standard cultivars included virulence in inoculum Not known Supplementary Late blight in the region 02 March 2005 Late blight at the trial site 02 March 2005 Emergence date 02 March 2005 Previous crop Inoculum density sp ml x 1000 Unknown Zoospores sporangia in inoculum Unknown Organic No Comments Bj Print this page 10 4 Show data Field test for tuber blight resistance Screen dump currently not available
37. ious crop Barley Inoculum source Natural infection and spreader plants Inoculated part of trial Unknowr Inoculum density sp ml x 1000 J w nkno Zoospores sporangia in inoculum j Organic wo Oves 18 Trial name 2005_DK_04_01_TEST Fields and buttons Planting date Inoculation date Soil type N fertilization Frequency of irriga tion Amount of irrigation Standard cultivars Included SASA diff Planted SASA diff Scored Compatible Late blight in the Region Late blight in the trial Crop emergence Number of plants per plot Previous crop Explanation Press the calendar button and select the planting date of the potatoes Press calendar button and select the date of artificial inoculation in the trial If inoculum source was natural infection then select the date when first symptoms occurred in the trial Select via drop down box the soil type in the trial Select the total amount of N fertilization applied Select the frequency of irrigation If irrigation was carried out only a few times irregularly then select Less as required Select the total amount of irrigation as close as possible to options available Mark in the checkboxes which of the standard cultivars were in cluded in the trial Mark in the checkboxes which of the SASA s differentials were planted If none of these clones were planted then select Not known Mark in the che
38. light EUCABLIGHT Ea 28 July 2005 Potato Late Blight Network For Europe Trial overview Cultivars a Trial overview Print this page Select Show Info to see trial background information Select Show Data to see results Field test for foliage blight resistance Info Data Year Country Region Number of Number of Number of Trial name Responsibility cultivars dates replicates 2005 Germany Mecklenburg Vorpomrnern 0 0 0 2005_GE_21_01 Ulrich Darsow 2005 Scotland South Ayrshire 0 0 0 2005_SC_27_01 Ruth Solornon Blackburn 2005 Slovakia Presovsky 28 5 2 2005_SK_07_01 J n Heldak 2004 Austria NiederOsterreich 95 5 2 2004_4U_05_01 Bodo Trognitz Show Show 2004 Denmark vejle 14 8 2 2004_DK_05_01 Hanne Grethe Kirk Show Show 2004 Denmark Vestsj lland 46 14 3 2004_DK_09_01 Bent J Nielsen Show Show 2004 Estonia J geva 30 19 3 2004_EE_05_01 Mati Koppel Show show 2004 Finland Etel Pohjanmaa 14 3 4 2004_FI_14_01 Asko Hannukkala Show Show 2004 Finland Kanta H me 24 10 4 2004_FI_05_01 Asko Hannukkala Show Show 2004 Finland Kanta H me 18 33 4 2004_FI_05_02 Asko Hannukkala Show Show 2004 Finland Pohjois Pohjanmaa 14 16 3 2004_FI_17_01 Asko Hannukkala Show Show 2004 France Garonne Haute 48 8 2 2004_FR_31_01 Roland Pell Show Show 2004 Germany Mecklenburg Vorpommern 25 18 3 2004_GE_21_01 Ulrich Darsow 2004 Hungary K z p Dun nt l 0 0 0 2004_HU_02_01 Istvan Wolf Show Show 2004 Ireland Carlow 27 7 4 2004_
39. list For breeding line names write the code name directly in the text box for Genotype name In the final step the EUCABLIGHT database has now generated a csv file that you should use for entrance of your primary disease data Right click with the mouse on the file name If your default Windows separator is set to semicolon then Excel will automatically open and read the file Select Save as change the file format to Excel enter the file name as given on the files download area web page and then save the file on your harddisk If the file is not opened correctly then save the csv file to your harddisk via left click on the file name Then import the file to Excel and save as Excel format Sort your original data according to the format in the EUCABLIGHT Excel file and copy and past your data into the EUCABLIGHT Excel spread sheet Finally send this Excel with your data to the TG1 group for quality control You will then be announced via e mail when your data have been uploaded to the database Ok in Trial overview table 47 9 3 Show Info Tuber slice test for foliage blight resistance Screen dump not currently available Fields and buttons Explanation Show Info When you select Show Info on the Trial Manager main page the background information for your trial will be shown You can al ways edit your background information 48 9 4 Show data Tuber slice test for foliage blight resistance Screen dumps curren
40. mary data into a predefined Excel spreadsheet we import and then process your data You can now compare your own primary results as RAUDPC apparent infection rate number of days till first symptoms 1 9 scale values etc with similar results from other regions and years in Europe Primary data and primary results will only be available for the owner of the data The collection of primary data makes it possible to evaluate the results using several statistical methods including new ones generated by the EUCABLIGHT project Secondly the evalua tion of primary results from previous years may be a contribution to the discussion how dis crepancies in resistance scores for the same varieties are due to the historical use of different methods for resistance evaluation At the web site you will find a documentation of all statis tical methods applied 1 7 Overviews of results in EUCABLIGHT The data will be presented as genotypic averages for each of the seven protocols used Users will be able to see these averages by country or region and by year Users will not be able to extract the primary data The averages will be accompanied by statistical information such as standard error and number of replicates 11 The user will be able to choose if the information will be presented in tables or graphs The unique feature of the EUCABLIGHT database is that it also contains information about the late blight populations in the regions and years of resista
41. n select Region menu and find region name and ID for your trial OO eS a A description of the trial including comments if your trial setup is different than recom mended in the EUCABLIGHT protocols especially if some or all of the standards are missing or if you have less than 5 disease assessments over time If your trial is accepted by TG1 your trial ID information is sent to the EUCABLIGHT man ager for upload to the EUCABLIGHT database The trial ID will be associated with your 12 EUCABLIGHT member ID When you log into EUCABLIGHT and select Host menu your trial will be visible via the Trial overview table and in your personal Trial Manager If you are not a EUCABLIGHT member username and password will be sent to you via e mall How to use the Trial Manager is explained in section 3 and 4 1 10 Quality control The following points will be taken into account e For foliage field trials Do you have enough disease assessments over time and do they include the relevant part of the epidemic e Areall the standards 7 varieties 11 R gene differentials included e Is the number of missing values acceptable 13 2 Software and hardware requirements Based on trial information EUCABLIGHT generates a text file with identification of trial data This file is imported into Excel where the primary results are entered and sent to EU CABLIGHT for storage in the database Background trial information is entered into the
42. nce testing This will allow correla tion of resistance genes in the host with virulence genes in the pathogen and predictions of durability of resistance There is no limit to the amount of data the database can handle Reliability and informativity will of course be better if more primary data are available New varieties can be added at any time and their data will be linked to earlier data of the yet unnamed breeding line 1 8 Intellectual Property Rights Primary data will remain the exclusive intellectual property of and will only be available to the owner of the data The summarising information in the database generated from several at least 50 primary datasets is in the public domain and freely available for use Such information would for example be the average foliage resistance level of a certain variety to natural infections across Europe in the years 2004 2014 Publication of this summarising information is only possible when proper reference is made to the EUCABLIGHT website as the source of the informa tion 1 9 How to participate TG1 Leontine Colon Bent Nielsen Ulrich Darsow is the quality control body to decide which trial results can be uploaded Please offer your trial to TG1 by E mail For each trial you need to E mail us this information Trial type foliage field foliage detached leaf etc Trial responsible person s RP name Trial institution Trial site name Trial year Trial country Trial regio
43. near regression and extrapolation 36 37 8 Whole tuber test for tuber blight resistance 8 1 Edit Info Whole tuber test for tuber blight resistance Trial information Whole tuber test for tuber blight resistance Trial name 2005_DK_01_05_TEST Update Obligatory Planting date 20 04 2004 E Harvest date 20 07 2004 E Inoculation date 97 97 2004 E Scoring date 04 08 2004 E Soil type Sandy loam N fertilization 100 kgN ha Standard cultivars included Alpha Bintje o Eersteling M escort O Gloria O Robijn Sarpo mira O Virulences in inoculum 10203040506 07 08 09 M 10 M 11 C Not known O Supplementary Previous crop Barley Inoculum density sp ml x 1000 5 10 Zoospores sporangia in inoculum Sporangia Comments O 7 SOs 38 Fields and buttons Planting date Harvest date Inoculation date Scoring date Soil type N fertilization Standard cultivars Included Previous crop Inoculum density Zoospores sporangia in inoculum Comments Update Explanation Press the calendar button and select the planting date of the potatoes Press the calendar button and select the harvest date of the potatoes Press calendar button and select the date of inoculation of the tubers Press the calendar button and select the scoring date of the potatoes Select via dro
44. ort and late Alpha and Robijn Sarpo Mira was added to represent the highest resistance class although the durability of its resistance has yet to be established To facilitate the dis semination of the seven standards they have been distributed as seed potatoes They are also being made available from the Scottish Agricultural Science Agency SASA in East Craigs as in vitro cultures In addition to these standards the inclusion of SASA s 11 single R gene differentials R1 R11 is also recommended to ensure that high resistance scores are not only the result of a simple pathogen race structure The protocols were compiled by members of the host and pathogen technical groups of EUCABLIGHT and discussed during project meetings before validation as EUCABLIGHT Recommended protocols The following type of data will be collected in the frame of EU CABLIGHT Foliage test field resistance Maturity field assessment Detached leaflet assay Whole tuber lab test Tuber slice test Tuber field test Glasshouse whole plant PON Pu Ou Please find protocols for these trials under the Protocols section on the EUCABLIGHT web site The protocols will be used from the 2004 season onwards Only data collected using these methods will be included in the EUCABLIGHT database In this way the data will be fully comparable across years and locations Additionally we will collect data from trials carried out in previous years in Europe The pro
45. owner of the data Then the owner has to provide the data personally Nobody else than the owner of data can download either primary data or derived statistics from Eucablight a Fi interne 26 Download your primary data mean disease data by date or derived statistics from the disease progress curve AUDPC AIR Delay etc The files are in csv semicolon separated for mat that easily can be imported into Excel or any software that can read text files On your computer the csv format might be associated with Excel When you left double click on the filename then data will be shown in Excel in separate columns If data are not shown in sepa rate columns you have to right click on the filename and download the file to your harddisk Then open the file and specify format of the csv file as requested by Excel Only the owner of data has access to download of data In this respect the owner is the person registered as responsible for the trial and has login to EUCABLIGHT If somebody wants to use data for publications analysis etc they should make a request to the owner of the data Then the owner has to provide the data personally Nobody else than the owner of data can download either primary data or derived statistics from EUCABLIGHT 5 6 Corrections of data after uploading If you need to update your primary data in the EUCABLIGHT database please download the primary data file from the Export data web page edit your data and
46. p down box the soil type in the trial Select the total amount of N fertilization applied Mark in the checkboxes which of the standard cultivars were in cluded in the trial Write in the text box the name of the previous crop Select the inoculum density used for inoculation Select the type of inoculum If unknown then select Unknown Write comments about the trial i e use of fungicide type etc if a primary attack was observed uneven disease development or any thing special When you have entered all information then select Update to store your information in the EUCABLIGHT database 39 8 2 Edit Data Whole tuber test for tuber blight resistance Step 1 Step 2 Step 3 40 Edit data Trial name 2005_DK_01_05_TEST Name Poul Lassen Institution Danish Institute of Agricultural Sciences Trial type Whole tuber test Trial site Trial site 5 Prepare database table for dataset 2005_DK_01_05_TEST Enter the number of cultivars and or genotypes in the experiment 2 Enter the number of replicates in the experiment 2 Enter the number of tubers per cultivar and per replicate in the experiment 2 Update Cultivar Genotype names Trial name 2005_DK_01_05_TEST Select cultivar names from drop down box or enter genotype names as e g BPU311 Search Select Cultivar Genotype Aamisepa Varajane he Aamisepa Varajane Insert selected cultivar Aamissep Insert selected cultivar Update
47. r button you can shift between years lt lt Septem ber 2005 gt gt and between months lt September 2005 gt gt Select Update to go to next step In the final step the EUCABLIGHT database has now generated a csv file that you should use for entrance of your primary disease data Right click with the mouse on the file name If your default Windows separator is set to semicolon then Excel will auto matically open and read the file Select Save as change the file format to Excel enter the file name as given on the files download area web page and then save the file on your harddisk If the file is not opened correctlyly then save the csv file to your harddisk via left click on the file name Then import the file to Excel and save as Ex cel format Sort your original data according to the format in the EUCABLIGHT Excel file and copy and past your data into the EU CABLIGHT Excel spreadsheet Finally send this Excel with your data to the TG1 group for quality control You will then be an nounced via e mail when your data have been uploaded to the data base Ok in Trial overview table 23 5 3 Show Info Field test for foliage blight Trial information Name 2005_DK_04_01_TEST DB Print this page Trial type Field test foliar blight Trial responsible Jens Gr nbech Hansen Trial institution Danish Institute of Agricultural Sciences Trial site Trial site 1 Trial year 2005 Trial country Denmark Trial
48. responsible Trial institution Trial site Trial year Trial country Trial region Obligatory Planting date Harvest date Inoculation date Scoring date Soil type N Fertilization Standard cultivars included Virulence in inoculum Supplementary Previous crop Comments Fields and buttons Show Info 8 4 Show data Whole tuber test for tuber blight resistance Whole tuber test Poul Lassen Danish Institute of Agricultural Sciences Trial site 5 2005 Denmark Nordjylland 20 April 2004 20 July 2004 01 July 2004 04 August 2004 Sandy loam 100 kg N ha Alpha Eesterling Robijn 1 5 9 10 Barley Inoculum density sp ml x 1000 5 10 Zoospores sporangia in inoculum Sporangia Explanation Print this page When you select Show Info on the Trial Manager main page the background information for your trial will be shown You can al ways edit your background information Screen dump currently not available 42 Fields and buttons Show data Explanation When you select Show Data on the Trial Manager main page your primary data as mean per variety genotype will be shown in a table 43 9 Tuber slice test for tuber blight resistance 9 1 Edit Info Tuber slice test for foliage blight resistance Trial information Tuber slice test for tuber blight Trial name resistance 2005_DK_01_04_TEST Update Obligatory Planting date 21 04 2004 Inoculation date 15 0
49. rt V Gloria v Robijn M Sarpo Mira o Supplementary Overhead irrigation Frequency Weekly v Comments No further comments Update Fields and buttons Planting date Soil type N fertilization Amount of irrigation Standard cultivars Included Frequency of irriga tion Comment Explanation Press the calendar button and select the planting date of the potatoes Select via drop down box the soil type in the trial Select the total amount of N fertilization applied Select the total amount of irrigation as close as possible to options available Mark in the checkboxes which of the standard cultivars that were included in the trial Select the frequency of irrigation If irrigation was carried out only a few times irregularly then select Less as required Write additional information about the experiment in the comment text box 33 7 2 Edit Data Field test for maturity Step 1 Step 2 Step 3 Step 4 34 Edit data Name Jens Gr nbech Hansen Institution Danish Institute of Agricultural Sciences Trial type Field test maturity Trial site Trial site 3 Prepare database table for dataset 2005_DK_04_03_TEST Enter the number of cultivars and or genotypes in the trial gt Enter the number of replicates in the trial 2 Enter the number of dates of maturity scorings in the trial 2 Update Trial name 2005_DK_04_03_TEST Cultivar Genotype n
50. ry ID e g UK NL String 2 Trial ID number Standard cultivar ID Standard cultivar included or Boolean 1 True not 2 False Table 5 hst_TrialCultivar Database field names explanation field type ID numbers and options of host resistance data in the EUCABLIGHT database VARIABLES IN DA EXPLANATION FIELD ID NUMBERS AND TABASE FIELD TYPE OPTIONS NAMES Trial year J CountryID Gomy Dew UK NE ss Region Dauner mes _ mammme me saqen m racutvamame Cotran sao Key variables Table 6 hst_TrialDate Database field names explanation field type ID numbers and op tions of host resistance data in the EUCABLIGHT database VARIABLESINDA EXPLANATION FIELD ID NUMBERS AND TABASE FIELD TYPE OPTIONS NAMES Trial year Key variables Table 7 hst_TrialObservation Database field names explanation field type ID numbers and options of host resistance data in the EUCABLIGHT database VARIABLES IN DA EXPLANATION FIELD ID NUMBERS AND TABASE FIELD TYPE OPTIONS NAMES Nn D gt z 6l hst_ Trial Trialvear CountryID RegionID TrialID TrialName TrialSite TrialTypeID ResponsiblePersonID PublicData PublicInfo NumberCultivar NumberReplicate NumberDate PlantingDate InoculumDate SoilType NFertilization IrrigationFrequency IrrigationAmount LateBlightRegionDate LateBlightTrialbate EmergenceDate PlantsPer
51. s a Bintje Insert selected cultivar Calgary Insert selected cultivar Aba Insert selected cultivar Abana Insert selected cultivar Kuras Insert selected cultivar Update Dates of observation Trial name 2005_DK_01_06_TEST Enter observation dates via the calendar button Observation dates in the trial 01 03 2005 lizi 02 03 2005 E Update EUCABLIGHT files download area Trial name 2005_DK_01_06_TEST 1 Left click with the mouse on the file name below 2 Excel will open and show the content of your predefined Excel spreadsheet 3 Save the file on your hard disk as Microsoft Excel format 4 Enter your results and send your file to TG1 for quality control If Excel does not open csv format might not be associated with Excel on your computer then right click with the mouse and save the original csv file on your harddisk Then import this file to Excel You are not allowed to change the filename 2005 DK 01 06 TEST csy Fields and buttons Step 1 Step 2 Step 3 Step 4 Explanation When you select Edit data on the Trial manager main page a new page opens for entrance of e Number of varieties and or genotypes in the trial experiment e Number of replicates in the trial experiment The number of scoring dates is fixed at 2 scoring dates as indicated in the protocol This information is used for generation of the Excel spreadsheet for entrance of your primary data for disease assess ments When you ha
52. sert selected cultivar EUCABLIGHT files download area Left click with the mouse on the file name below Excel will open and show the content of your predefined Excel spreads Save the file on your hard disk as Microsoft Excel format Enter your results and send your file to TG1 for quality control RUNE heet Trial name 2005_DK_04_02_TEST If Excel does not open csv format might not be associated with Excel on your computer then right click with the mouse and save the original csv file on your harddisk Then import this file to Excel You are not allowed to change the filename 2005 DK 04 02 TEST csv Fields and buttons Step 1 Step 2 Step 3 Explanation When you select Edit data on the Trial manager main page a new page opens for entrance of 1 Number of varieties and or genotypes in the trial experiment 2 Number of replicates in the trial experiment 3 Number of leaflets per cultivar and per replicate in the experiment This information is used for generation of the Excel spreadsheet for entrance of your primary data for disease assessments When you have entered your numbers of varieties replicates and dates select Update to go to next step Select cultivar names from the Select drop down box To find a cul tivar name among the 4000 names in the list you can search via the Search box Write B and the list will start at cultivar name Ba banki Write Bi and the list will start with Biason
53. support the co ordination of RTD tasks already financed at national level where the pooling of data would facilitate common interpretation of facts and contribute to the development of harmonised standards procedures methodologies processes or common research instruments The project will be organised in three geographic regions Western Europe which will be administered by Didier Andrivon at INRA Central Europe Ewa Zimnoch Guzowska IHAR and Nordic Europe Arne Hermansen NCRI There are two themes that run across these re gions The first Characterising host resistance will be led by Leontine Colon at PRI in The Netherlands and the second Characterising pathogen variation by David Cooke at SCRI The databases and website will be implemented by Jens G Hansen and Poul Lassen at DIAS in Denmark 1 3 Why sampling host resistance information The implementation of integrated control of late blight with reduced inputs of fungicides would benefit if durable blight resistance were more common in commercial potato cultivars Many sources of resistance exist in wild primitive and developed cultivars but the nature of that resistance is often poorly understood Standardised sampling of host resistance informa tion will enable us to allow rational and objective comparisons of genetic resources The available European data on host resistance is fragmented and often the methods used to collect this data are not well documented We aim to collate
54. tly not available 49 10 Field test for tuber blight resistance 10 1 Edit Info Field test for tuber blight resistance Trial information Field test for tuber blight resistance Trial name 2005_DK_01_06_TEST Update Obligatory Early planting date 02 03 2005 fa Mid early planting date 02 03 2005 EH Late planting date 02 03 2005 A Inoculation date 02 03 2005 fa Soil type Sand v N fertilization Okg N ha v Overhead irrigation Frequency No irrigation v Total amount No irrigation Standard cultivars included Alpha Fi Bintje E Eersteling O Escort C Gloria O Robijn o Sarpo Mira o Virulence in inoculum 10203040s060708eO 8 O10 O 11 C Not known M Supplementary Late blight in the region 02 03 2005 fa Late blight at the trial site 02 03 2005 fa No late blight o No late blight F UU Early crop emergence date 01 01 2005 fal Mid early crop emergence date 01 01 2005 i Late crop emergence date 01 01 2005 fa Previous crop Inoculum density sp ml x 1000 Unknown v Zoospores sporangia in inoculum Unknown Organic wno O ves Comments Update 50 Fields and buttons Early planting date Mid early planting date Late planting date Inoculation date Soil type N fertilization Frequency of irriga tion Amount of irrigation Standard cultivars Included Late blight in the Region Late blight in t
55. tocols have been developed for foliage blight resistance tuber blight resistance and maturity These can be found on the EUCABLIGHT web site To accommodate the different types of trials that are commonly used in Europe there is more than one protocol for each trait except 10 maturity For foliage blight resistance data can be collected in the field in a whole plant greenhouse assay and in a detached leaflet test Tuber blight data can be collected either in the field or in the lab in the latter case using whole tubers or tuber slice tests Maturity was included because maturity has a strong influence on the expression of genes for foliage blight resistance especially QTLs and resistance information is meaningless without knowing the maturity type of the same variety 1 5 Cultivar database In order to monitor the resistance of a cultivar from the time of first selection the database contains data from both cultivars and breeding lines A database with details of more than 4000 cultivars will help to link the identities of breeding lines to cultivars and to avoid dupli cated entries due to misspellings This section of the EUCABLIGHT database also contains data relating to presence of R genes fertility use ware processing or starch and ploidy level of the germplasm collated from published and unpublished sources 1 6 Data handling and Statistics We are only collecting primary data including replicates When you enter your pri
56. trial i e use of fungicide type etc if a primary attack was observed uneven disease development or any thing special When you have entered all information then select Update to store your information in the EUCABLIGHT database 45 9 2 Edit Data Tuber slice test for foliage blight resistance Step 1 Step 2 Step 3 46 Edit data Trial name 2005_DK_01_04_TEST Name Poul Lassen Institution Danish Institute of Agricultural Sciences Trial type Tuber slice test Trial site Trial site 4 Prepare database table for dataset 2005_DK_01_04_TEST Enter the number of cultivars and or genotypes in the experiment 2 Enter the number of replicates in the experiment 2 Enter the number of tubers per replicate in the experiment 2 2 Enter the number of slices per tuber in the experiment Update Cultivar Genotype names Trial name 2005_DK_01_04_TEST Select cultivar names from drop down box or enter genotype names as e g BPU311 Search Select Cultivar Genotype Aamisepa Varajane k Aamisepa Varajane Insert selected cultivar Aamissep Insert selected cultivar Update EUCABLIGHT files download area Trial name 2005_DK_01_04_TEST 1 Left click with the mouse on the file name below 2 Excel will open and show the content of your predefined Excel spreadsheet 3 Save the file on your hard disk as Microsoft Excel format 4
57. umberCultivar Number ID of plant Integer j PlantingDate Datetime InoculumDate Datetime SoilType UTM zone North Integer Nfertilisation UTM zone East Integer Sand Loamy sand Sandy loam Clay type gt 20 clay Silt type gt 40 silt Peat Unknown 0 kg N ha 50 kg N ha 100 kg N ha 150 kg N Ha 200 kg N Ha 250 kg N Ha gt 300 kg N Ha asno es ros 58 VARIABLESINDA EXPLANATION TABASE FIELD NAMES IrrigationFrequency Latitude degree LateBighiRegionDate Latitude second Dmetime LateBlightTrialDate Latitude North or South Datetime EmergenceDate Longitude degree Datetime PlantsPerPlot Longitude minute Integer PrevlousCropi Prvious cop ng 150 lnoculumSource Integer InoculumTrialPart Integer InoculumDensity Integer LeafSource Integer lsolateT ype Integer PlantWeekAge Integer Droplet Integer PlantingDateEarly Datetime PlantingDateMidEarly Planting DateLate Datetime Datetime Organic Integer IlsolateComposition Integer HarvestDate Datetime ID NUMBERS AND OPTIONS No irrigation Daily Twice a week Weekly Less as required 1 4 5 9 10 50 gt 50 Natural infection without spreader plants Natural infection and spreader plants Artificial infection and spreader plants Whole trial Plot Plot leaflets Spreaders Infector plants lt 5 sp ml x 1000 5 10 10 20 20 50 gt 50 Zoospores
58. ve entered your numbers of varieties and repli cates select Update to go to next step Select cultivar names from the Select drop down box To find a cul tivar name among the 4000 names in the list you can search via the Search box Write B and the list will start at cultivar name Babanki Write Bi and the list will start with Biason Scroll and find the cor rect name If a variety in your trial is not in the list then contact TG1 to include this in the list For breeding line names write the code name directly in the text box for Genotype name Select the Calendar button and select the dates of observations in the trial This information is used for generation of the Excel spreadsheet for entrance of your primary data for maturity scorings Using the Calendar button you can shift between years lt lt September 2005 gt and between months lt lt September 2005 gt gt Select Update to go to next step In the final step the EUCABLIGHT database has now generated a csv file that you should use for entrance of your primary disease data Right click with the mouse on the file name If your default Windows separator is set to semicolon then Excel will automatically open and read the file Select Save as change the file format to Excel enter the file name as given on the files download area web page and then save the file on your harddisk If the file is not opened correctly then save the csv file to your harddisk v
59. ve the file on your harddisk If the file is not opened correctly then save the csv file to your harddisk via left click on the file name Then import the file to Excel and save as Excel format Sort your original data according to the format in the EUCABLIGHT Excel file and copy and past your data into the EUCABLIGHT Excel spread sheet Finally send this Excel with your data to the TG1 group for quality control You will then be announced via an e mail when your data have been uploaded to the database Ok in Trial overview table 35 7 3 Show Info Field test for maturity Trial information Name 2005_DK_04_03_TEST Print this page Trial type Field test maturity Trial responsible Jens Gr nbech Hansen Trial institution Danish Institute of Agricultural Sciences Trial site Trial site 3 Trial year 2005 Trial country Denmark Trial region Arhus Obligatory Planting date 20 April 2005 Soil type Sandy loam N Fertilization 150 kg Nha Overhead irrigation amount 50 100 mm Standard cultivars included Alpha Bintje Eesterling Escort Gloria Robijn Supplementary Overhead irrigation frequency Weekly Comments No further comments 7 4 Show data Field test for maturity Trial data Trial name 2005_DK_04_03_TEST Maturity scoring means per cultivar per date Cultivar Date 21 7 29 7 Anco Fecula Maturity scores are used to estimate the number of days from planting until 95 maturation by li

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