Open Access Research article

Putative resistance gene markers associated with quantitative trait loci for fire blight resistance in Malus ‘Robusta 5’ accessions

Susan E Gardiner1*, John L Norelli2, Nihal de Silva3, Gennaro Fazio4, Andreas Peil5, Mickael Malnoy6, Mary Horner7, Deepa Bowatte1, Charmaine Carlisle1, Claudia Wiedow1, Yizhen Wan8, Carole L Bassett2, Angela M Baldo4, Jean-Marc Celton9, Klaus Richter10, Herb S Aldwinckle11 and Vincent GM Bus7

Author Affiliations

1 The New Zealand Institute for Plant & Food Research Limited (PFR) Palmerston North, Private Bag 11600, Manawatu Mail Centre, 4442, Palmerston North, New Zealand

2 USDA-ARS, Appalachian Fruit Research Station, 2217 Wiltshire Rd., Kearneysville, WV, 25430, USA

3 PFR Mt Albert, Private Bag 92169, Auckland Mail Centre, 1142, Auckland, New Zealand

4 USDA-ARS, Plant Genetic Resources Unit, 630W. North St., Geneva, NY, 14456, USA

5 Julius Kühn-Institut (JKI), Institute for Breeding Research on Horticultural and Fruit Crops, Pillnitzer Platz 3a, D-01326, Dresden, Germany

6 Foundation E. Mach - Istituto Agrario San Michele all'Adige, Via E. Mach 1, 38010, San Michele all'Adige, TN, Italy

7 PFR Hawke’s Bay, Private Bag 1401, 4157, Havelock North, New Zealand

8 Apple Research Center, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China

9 UMR Génétique et Horticulture (GenHort), INRA ⁄ Agrocampus-ouest ⁄ Université d’Angers, Centre Angers-Nantes, 42 rue Georges Morel – BP 60057, 49071, Beaucouze´ Cedex, France

10 JKI, Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Str. 27, D-06484, Quedlinburg, Germany

11 Department of Plant Pathology and Plant-Microbe Biology, Cornell University, 630W. North St., Geneva, NY, 14456, USA

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BMC Genetics 2012, 13:25  doi:10.1186/1471-2156-13-25

Published: 3 April 2012

Additional files

Additional file 1 :

Putative fire blight resistance genes. Selection of candidate resistance genes for fire blight and their mapping by: SNP (NZsn) or SSR (NZms) markers in ‘Malling 9’ x ‘Robusta 5’ or ‘Royal Gala’ x A689-24 populations (worksheet ‘A: mapped in populations’), or bin-mapping in either of above populations (worksheet ‘B: bin mapped’), or by physical positioning within the whole genome sequence of ‘Golden Delicious’ with 200kbp gaps inserted between scaffolds [104] (worksheet ‘C: physical position”). Columns A = EST GenBank accession number; B = Description: Source of EST (project, cultivar derived from, response to Erwinia amylovora ( Ea) challenge); followed by annotation (sequence description [Genbank accession number, BLASTx similarity]); C = Selection criteria including citation for inference from scientific literature, D = Marker name; E = PCR primer sequences of marker; and F = Genetic map location and physical position in WGS. Followed by Footnotes and Literature Citations.

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Additional file 2 :

Fire Blight Unigenes. Unique contigs (fire blight unigenes) assembled from 5,395 apple ESTs identified from Ea-challenged leaves of moderately resistant ‘Red Delicious’ and highly resistant ‘Geneva 41’ apple rootstock [47]. Worksheet ‘ad file 2’ Columns A = contig number, B = bp length of contig, C = number of EST sequences in contig, D = average EST sequence length and E = contig consensus sequence. Worksheet ‘Fasta’ can be used to assemble sequences in FASTA format.

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Additional file 3 :

Predicted coding regions within fire blight resistance QTL on Linkage Group 7 of ‘Robusta 5’ (R5-US) accession. Homologues of predicted coding regions within fire blight (fb) resistance QTL on Linkage Group 7 of R5-US and their detection in fb transcript profiling data. Key to row fill color: gray = could play a role in host-pathogen interactions based upon annotation, light-orange = detected in at least one fb transcript profiling experiment, mid-orange = fb candidate resistance gene based upon annotation and detection, dark-orange = likely fb candidate resistance gene based upon multiple lines of evidence. Columns: A = Predicted coding sequence ID (WGS MDP#); B-E = WGS physical location in Genome Database for Rosaceae (GDR) G-Browse: B = Scaffold #, C = transcript start, D = transcript stop, E = transcript length; F = number of fb transcript profiling databases detected in; G = transcript database detected in; H-L = best functional annotation determined from GDR ‘Malus_x_domestica.v1.0_gene_pep_function_101210.formated.xls’; M-Q = Arabidopsis homologue determined from GDR ‘Malus_x_domestica.v1.0_predicted Arabidopsis homologs.xls’; R-V = Swiss Prot homologue determined from GDR ‘Malus_x_domestica.v1.0_gene_pep_uniprot_sprot_blastp_100610.formated.xls’; W-AA = TREMBL homologue determined from GDR ‘Malus_x_domestica.v1.0_gene_pep_uniprot_trembl_blastp_100610.formated.xls’. In all cases, GDR annotation columns list match ID, organism, protein description, percent identity and BLASTP E value. Column shading denotes data from different GDR annotation databases.

Format: XLS Size: 249KB Download file

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