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Objective 4 – breeding lines Over the five years of this project, over 1100 individuals (pre-screened in the glasshouse and nursery) from 58 different scion progenies were transferred to the fruiting assessment plots for industry evaluation funded by the APBC. Rootstock selections SR8-59 and SR8-104 (AR10-2-5 x AR86-1-22) looked promising in orchard trial and are being propagated for possible commercialisation by the APBC and the new EMRC. Eleven further EMR rootstock selections that have shown promise in trials have been propagated for potential commercialisation. Three pear x apple hybrids were propagated to provide interstems that might allow pear cultivars to be propagated on to dwarfing apple rootstocks. These have also been transferred to the new EMRC for evaluation. The rootstock M.116 that was created in previous Defra-funded work and released recently via the APBC has excited interest among UK cider growers as it is resistant to crown rot, which can be a problem in the wetter climate of the West Country, and is well anchored enough to allow mechanical harvesting of fruit. Rooted liners of M.116 were provided in February 2008 for trialling by the Department of Agriculture and Rural Development for Northern Ireland. A survey of more recent literature on rootstock breeding/germplasm indicated several accessions to add to our parent collection including derivatives of M. robusta that may utilise water more efficiently. Seven more ‘exotic’ apple rootstocks were added to the parent collection, four Hashabi of Middle Eastern origin thought to be adapted to warm winters and dry summers and three from the Geneva New York programme reported to have multiple resistances. Progeny M255 (SA580-10 x SA912-12), which was raised to study the interaction of genes for red fruit flesh (Fig. 2) and had been selected for columnar habit, was scored for intensity of flesh colour. Two selections had exceptionally dark flesh, giving juice remarkably resistant to browning and these have been propagated for evaluation of agronomic characters and possible commercial merit. A small trial was planted of two further columnar apple selections for commercial assessment. 
Figure 2: Red-fleshed individuals from progeny M255 showing a range of intensity of colour A series of crosses were made to develop pyramided resistance. Major gene scab (V. inaequalis) resistance was combined with both major gene and polygenic resistance to mildew (P. leucotricha) in backgrounds of good fruit quality. A cross was also made between ‘Saturn’ (Vf scab resistance) and a selection that was reputed to contain the Vr/Vx scab resistance genes with a view to developing pyramided resistance for apple scab. Two crosses were made to introduce resistance to scab and mildew into cider apples, using a regular cropping, late, full bittersweet variety and a regular cropping, mid-season, bittersweet variety. Two cultivars with low winter chill requirements, ‘Dorsett Golden’ and ‘Ein Shemer’ were identified and ‘Dorsett Golden’ from the National Fruit Collection at Brogdale was used in the crossing programme for 2007. Other crosses that will generate novel breeding lines are mentioned under objectives 1 & 2. Discussion and implications The completion and publication of the ‘Fiesta’ x ‘Totem’ map (Fernández- Fernández et al., 2008) which is the most saturated published SSR map of apple to date provided an excellent reference resource for mapping individual traits, and the map proved to be a useful starting point to select primers for the development of the M432 rootstock map. The wealth of experience gained through participating in HiDRAS not only benefited this project but has also had direct benefits to other Defra-funded projects. The development of the SSR multiplexes for fingerprinting the National Fruit Collections (GC0139 ‘Fingerprinting the National Fruit Collection - a demonstration study on pear’ and GC0140 ‘Fingerprinting the National Apple and Pear Collections’) was based on techniques optimised during this work. EMR’s HiDRAS multiplexes were also successfully used in distinguishing cultivars for a commercial fruit distribution company that was concerned over possible mixing of supplies. New markers have been mapped in apple that are linked to virescence, woolly apple aphid resistance, self-compatibility, columnar habit, weeping habit and susceptibility to the strobilurin fungicide Amistar which will be useful tools for breeding programmes. However the status of the ‘precursor’ gene for resistance to rosy apple aphid remains uncertain. We have also successfully mapped the first marker for aphid resistance in pear. A series of new QTLs have also been mapped that are linked to fruit quality traits within the HiDRAS project. Industry-funded staff have been trained in DNA extraction and the use of markers for pre-selection. They have used a number of markers to confirm the presence or absence of key traits in advanced selection and parental material from the apple breeding programme. New progenies and breeding lines developed with sustainability as a target have been passed to the industry-funded project for evaluation. The specific focus on rootstocks has lead to a renewed interest from the UK fruit and cider industries and consequently improved links with the Horticulture Development Council (HDC). Our broadening of the genetic base of the rootstock collection may be useful in responding to climate change. The two rootstock mapping progenies M430 and M432 have been developed as hard-pruned ‘hedge’ trees to enable the production of the replicated material necessary for the recording of the phenotypic data for QTL identification in further projects. The long-term nature of this work was recognised at the beginning of this project when it was agreed with the project officer that these hedged progenies would be produced. Possible future work The new Defra-funded project WU0115 ‘Genomics tools for pre-selection of water-use efficiency (WUE) in top fruit rootstocks’ is due to start on 1.4.08 will take forward the work on the M432 progeny focusing on the identification of markers linked to WUE. A replicated planting of the progeny is planned which will enable further rootstock-controlled characters over and above WUE to be mapped, e.g. tree vigour and crop yield. The amount of molecular and phenotypic data held within the HiDRAS database is vast. The partnership has already initiated discussions on the most appropriate way forward to develop further projects to mine the data. Discussions on a European level have also been initiated with ERGI (the European Rosaceous Genomics Initiative) and on a wider scale with HortResearch, New Zealand, University of the Western Cape, South Africa and members of the US-based GDR (Genome Database for Rosaceae). The indications of stretches of synteny between the apple genome and those of Fragaria and/or Prunus identified in the rosaceous genomics project HH3724SSF are not just of theoretical interest. Where such regions include agronomic traits, marker information from one crop can provide a short cut to characterising the homologous gene in another crop. Comparative mapping is currently the focus of much attention by ERGI. Actions arising including presentations, industry interaction and IP This project benefited from close links not only with the APBC and the EU Framework V project HiDRAS but also with the Defra-funded project on rosaceous genomics HH3724SSF. Current issues affecting the UK and international fruit industry that could be addressed through breeding and identification of markers were frequently discussed at the bi-annual APBC meetings. Refereed publications are listed in Section 9. Further non-peer reviewed publications, specific presentations and meetings (scientific, industry-orientated and with the general public) are listed below. Publications (non-peer reviewed) FERNÁNDEZ-FERNÁNDEZ, F., CLARKE, J.B., TOBUTT, K.R. (2004) Preferential amplification of microsatellite alleles: an example in apple. Acta Horticulturae, 663:87-90 JAMES, C.M., EVANS, K.M. (2004) Identification of molecular markers linked to the mildew resistance genes Pl-w and Pl-d in apple. Acta Horticulturae, 663:123-128 PARISI, L., FOUILLET, V., SCHOUTEN, H., GROENWOLD, R., LAURENS, F., DIDELOT, F., EVANS, K., FISCHER, C., GENNARI, F., KEMP, H., LATEUR, M., PATOCCHI, A., THISSEN, C., TSIPOURIDIS, C. (2004) Variability of the pathogenicity of Venturia inaequalis in Europe. Acta Horticulturae, 663:107-114 TOBUTT, K.R. (2004) Mapping top fruit. Plant It! (Defra R & D Newsletter), 6:7 PARISI, L., LAURENS, F., DIDELOT, F., EVANS, K., FISCHER, C., FOUILLET, V., KEMP, H., LATEUR, M., PATOCCHI, A., SCHOUTEN, H, TARTARINI, S,. TSIPOURIDIS, C. (2006) Geographical distribution of V. inaequalis strains virulent to the Vf gene in Europe. IOBC Bulletin, 29:49-52 KOUASSI, A.B., DUREL, C.E., MATHIS, F., LAURENS, F., GIANFRANCESCHI, L., KOMJANC, M., MOTT, D., PATOCCHI, A., GOBBIN, D., FERNÁNDEZ-FERNÁNDEZ, F., DUNEMANN, F., BOUDICHEVSKAJA, A., STANKIEWICZ, M., VAN DE WEG, E., BINK, M. (2007) Pedigree –based QTL mapping for fruit firmness in apple using Markov Chain Monte Carlo methods and Bayesian inferences Proceedings of the XI QTL for MAS workshop. Toulouse (published on-line) TobUtt, K.R., Evans, K.M. (in press) ECPGR Fruit Network – Microsatellite workshop – December 2006. ECPGR Newsletter VAN DE WEG, W.E., JANSEN, J., VOORRIPS, R.E., DUREL, C.E., LAURENS, F., PATOCCHI, A., DUNEMANN, F., EVANS, K., GUERRA, W., KOMJANC, M., LATEUR, M., ANTOFIE, A., KELLERHALS, M., SANSAVINI, S., TOMALA, K., ZURAWICZ, E., GIANFRANCESCHI, L., BINK, M. (2008) QTL Mapping in multiple, pedigreed populations: proof of concept delivered by results from 27 progenies for quantitative fruit quality traits in apple. Plant & Animal Genomes XVI Conference. http://www.intl-pag.org/16/abstracts/PAG16_W25_204.html EVANS, K.M. (in press) Introduction to molecular markers & DNA fingerprinting. DNA Day EMRA Members Day report FERNÁNDEZ- FERNÁNDEZ, F. (in press) An introduction to mapping for marker-assisted selection in fruit crops. DNA Day EMRA Members Day report EVANS, K.M., FERNÁNDEZ- FERNÁNDEZ, F., GOVAN, C. (submitted) Harmonising fingerprinting protocols to allow comparisons between germplasm collections - Pyrus. Proceedings of Eucarpia Fruit Breeding & Genetics Symposium 2007. Zaragoza PATOCCHI, A., FERNÁNDEZ-FERNÁNDEZ, F., EVANS, K., SILFVERBERG-DILWORTH, E., MATASCI, C.L., GOBBIN, D., REZZONICO, F., BOUDICHEVSKAIA, A., DUNEMANN, F., STANKIEWICZ-KOSYL, M., MATISSE, F., SOGLIO, V., GIANFRANCESCHI, L., DUREL, C.E., TOLLER, C., COVA, V., MOTT, D., KOMJANC, M., BARBARO, E., COSTA, F., VOORRIPS, R.E., RIKKERINK, E., YAMAMOTO, T., CEVIK, V., GESSLER, C., VAN DE WEG, W.E. (submitted) Development of a set of apple SSRs markers spanning the apple genome, genotyping of HiDRAS plant material and validation of genotypic data. Proceedings of Eucarpia Fruit Breeding & Genetics Symposium 2007. Zaragoza Presentations K. Evans described the top fruit breeding programme at East Malling Research to the delegates of the Worshipful Company of Fruiterers Top Fruit Conference during a plot walk at EMR, 25 June 2003 F. Fernández-Fernández, J. Clarke and K. Tobutt presented a poster entitled ‘Preferential application of microsatellite alleles – an example in apple’ at the Eucarpia Symposium, Angers, September 2003 C. James and K. Evans presented the paper ‘Identification of molecular markers linked to the mildew resistance genes Pl-w and Pl-d in apple’ at the Eucarpia Symposium, Angers, September 2003 K.R. Tobutt and R. Maxted described the East Malling apple breeding programme to the HDC ‘Apple and Pear Variety Day’ delegates at EMR, 23 September 2003 K. Tobutt gave a talk entitled ‘Breeding fruit, broadleaved timber trees and woody ornamentals’ to visitors attending the EMR launch, 17 March 2004 F. Fernández-Fernández gave a talk on apple breeding at EMR to Phosyn and a group of Chinese customers, 4 July 2005 K. Tobutt described progress in the project to the Apple & Pear Breeding Club at Pépinières du Valois on 7 September 2005 K. Tobutt presented work to date of this project to the Defra review panel at Defra, London on 21 September 2005 F. Fernández-Fernández presented work on apple mapping and markers and K. Tobutt and C. Govan presented apple and pear breeding at the EMR Open Day on 22 September 2005 K. Tobutt made a presentation on ‘Understanding the incompatibility system in apple and related genera’ to the East Malling Trust, Bradbourne House, on 9 January 2006 K. Tobutt gave a talk on aspects of perennial plant breeding relevant to the Biology A level syllabus to pupils of Sutton Valence School, at EMR on 21 February 2006 F. Fernández and C. Govan demonstrated and explained some areas of DNA technology and the food chain to groups of visiting school children during Science weeks in 2005, 2006 and 2007 K. Tobutt gave a talk on ‘Molecular markers for fingerprinting and marker-assisted selection in fruit’ to the RHS Fruit & Vegetable Committee, Vincent Square, 11 April 2006 K. Evans presented ‘Current world resources in Rosaceous fruit breeding programmes’ at the National Fruit Show, 19 October 2006 K. Evans gave an EMR site seminar entitled ‘HiDRAS (High quality Disease Resistant Apples for Sustainable agriculture) – European apple genomics’, describing this joint EU/Defra project, 20 March 2007 K. Tobutt and K. Evans presented talks to the public on apple breeding at EMR at the EMR ‘Apple Day’ weekend and manned a stand with further information available (September 2007) Meetings attended K. Tobutt and K. Evans attended the Apple and Pear Breeding Club policy group meetings at Pépinières du Valois, France (2005 and 2006) and EMR (2003, 2004, 2005, 2006 and 2007) K. Evans attended the HiDRAS Workpackage 7 meeting in April 2004 at Warsaw Agricultural University, Poland K. Tobutt and K. Evans attended the RHS Fruit Conference on 6 October 2004 in London K. Evans, K. Tobutt and C. Gutteridge attended a meeting at Defra with the HDC to discuss EMR’s apple and pear breeding programme (11 April 2005) K. Evans and F. Fernández-Fernández attended the annual HiDRAS meetings in Zurich, Switzerland, in 2004, Warsaw Agricultural University, Poland, in 2005, CRA-Gembloux, Belgium, in 2006, Wageningen, N.L., in 2007 and the final meeting in Zaragoza, Spain, also in 2007 F. Fernández-Fernández attended the HiDRAS Work-Package 2 meeting in April 2005 at BAZ-Dresden, Germany K. Evans attended the National Fruit Collection Advisory Committee meetings at Brogdale in 2004, 2005, 2006, 2007 and 2008 K. Tobutt attended the meetings of the Plant Genetic Resources ABC Stakeholders meeting at Wisley on 10 October 2005 and meetings of the UK Plant Genetic Resources Group in 2004, 2005, 2006 and 2007 K. Tobutt attended a meeting on ‘Safeguarding the National Fruit Collections’ organised by Defra at the QEII Conference Centre on 15 December 2005 K. Tobutt attended the inaugural meeting of a new COST action (864) ‘PomeFruitHealth’ as one of the UK members of the management committee in Belgium in January 2006 K. Tobutt chaired the Fruit Coordinating Network at a meeting of ECP/GR’s Coordinating Networks in Bonn, March 2006 K. Evans, K. Tobutt and F. Fernández-Fernández attended a presentation on new software (Chiasma) to manage breeding and genetic data by John Purse (ex-Shell Eucalyptus breeder) at EMR in March 2006 F. Fernández-Fernández and D. Sargent attended the HiDRAS training course on FlexQTL mapping software in Wageningen (September 2006) K. Tobutt, K. Evans, F. Fernández-Fernández, J. Clarke and C. Govan organised and hosted a two-day meeting of international experts on microsatellite fingerprinting of tree-fruit behalf of the ECPGR at EMR (December 2006) K. Tobutt and K. Evans hosted a visit from Prof. Cameron Peace (Washington State University) to discuss possible future collaborations between the USA and UK apple molecular biology teams (April 2007) F. Fernández-Fernández visited Dr Susan Brown (Cornell University - USA) and discussed breeding objectives for apple scions (July 2007) F. Fernández-Fernández discussed the use of automated software to score AFLP markers and the suitability of these markers for rootstock mapping with Yiz Lem Wan (Cornell University - USA) (July 2007) F. Fernández-Fernández visited Prof. Vladislav Ognjanov's apple breeding plots in Novi Sad (Serbia) and discussed breeding objectives for apple scions (August 2007) K. Tobutt and K. Evans discussed pear breeding and cultivation with visitors to EMR from the Zhengzhou Institute of Pomology, China (September 2007) K. Evans and J. Clarke attended the Symposium of the fruit section of Eucarpia in Zaragoza, Spain and presented two posters in September 2007 K. Tobutt, K. Evans, F. Fernández-Fernández, J. Clarke and C. Govan hosted a visit from Dr Gennaro Fazio (the apple rootstock breeder and geneticist from the USDA ARS at Cornell University, Geneva, USA) in September 2007. Advances in mapping rootstocks were discussed K. Tobutt, K. Evans, F. Fernández-Fernández, J. Clarke and C. Govan organised and hosted a two-day international meeting on ‘Molecular genetics of rosaceous plants’ with colleagues from the Rosaceous Genomics project (HH3724SSF) at Aylesford Friars (December 2007) F. Fernández-Fernández attended the 'Cornwall Fruit Focus' event organised by the Eden Project (Boldeva - Cornwall) in December 2007. Apple cultivation in Cornwall, opportunities for organic fruit production and the use of molecular markers for fingerprinting local germplasm were discussed K. Evans attended the HDC Tree Fruit Panel meeting at Bradbourne House, East Malling to discuss the new EMR Rootstock Club (January 2008) K. Evans hosted a visit from Dr Alessio Martinelli (International New Varieties Network) and Andrew Tinsley (HDC) to negotiate the contract and objectives for the new EMRC (January 2008)
9. This section should be used to record links (hypertext links where possible) or references to other published material generated by, or relating to this project.
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