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

Authors: Norelli, John; GARDNER, SUSAN - Plant And Food Research; DE SILVA, NIHAL - Plant And Food Research; Fazio, Gennaro; PEIL, ANDREAS - Julius Kuhn Institute; MALNOY, MICKAEL - Iasma Research Center; HOMER, MARY - Plant And Food Research; BOWATTA, DEEPA - Plant And Food Research; CARLISLE, CHARMAINE - Plant And Food Research; WAN, YIZHEN - Northwest Agriculture And Forestry University; Bassett, Carole; Baldo, Angela; CELTON, JEAN-MARC - Plant And Food Research; ALDWINCKLE, HERB - Cornell University; BUS, VINCENT - Plant And Food Research

Submitted to: BMC Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/13/2012
Publication Date: 4/13/2012
Citation: Norelli, J.L., Gardner, S., De Silva, N., Fazio, G., Peil, A., Malnoy, M., Homer, M., Bowatta, D., Carlisle, C., Wan, Y., Bassett, C.L., Baldo, A.M., Celton, J., Aldwinckle, H., Bus, V. 2012. Putative resistance gene markers associated with quantitative trait loci for fire blight resistance in Malus 'Robusta 5' accessions. Biomed Central (BMC) Plant Biology. 13:25.

Interpretive Summary: Breeding of fire blight resistant apple varieties and rootstocks is a goal of several international apple breeding programs as options are limited for management of this destructive disease. An important source of fire blight resistance used in several breeding programs is a wild, small fruited apple known as ‘Robusta 5’. In this study, we identified gene markers for fire blight resistance by integrating further genetic mapping studies with analysis of DNA or gene databases. When three seedling populations, all with ‘Robusta 5’ as a common parent, from the United States, New Zealand, and Germany were challenged with different strains of the fire blight pathogen, two distinct genetic loci for fire blight resistance were detected on chromosome 3 of ‘Robusta 5’ where one had previously been mapped. Each genetic locus co-located with a distinct set of candidate resistance genes. The position of the genetic locus could shift depending upon the strain of the pathogen used in the challenge test. Other possible factors affecting the position of the genetic locus were the second parent of the population and the environment where challenge was conducted. The results suggest that the upper region of ‘Robusta 5’ chromosome 3 contains multiple genes contributing to fire blight resistance and that their contributions to resistance can vary depending upon pathogen virulence and additional factors. Additionally, a novel resistance locus was also detected on chromosome 7 of the US population; however, this resistance locus was not observed in the New Zealand or German populations. This international collaboration allowed broad evaluation of the fire blight resistance in ‘Robusta 5’ when crossed with different parents, grown under different environmental conditions, and challenged with strains of the pathogen from around the world. Molecular markers were developed for the potential fire blight resistance genes within the identified genetic loci. These markers will be made available to US tree fruit breeding programs to facilitate the development of fire blight resistant apple and pear cultivars by marker assisted selection.

Technical Abstract: Breeding of fire blight resistant scions and rootstocks is a goal of several international apple breeding programs, as options are limited for management of this destructive disease caused by the bacterial pathogen Erwinia amylovora. A broad, large effect QTL for fire blight resistance has been previously reported on linkage group 3 of Malus ‘Robusta 5’. In this study, we identified candidate gene markers for fire blight resistance by integrating further genetic mapping studies with bioinformatics analysis of transcript profiling data and genome sequence databases. When several defined Ea strains were used to inoculate three progenies from international breeding programs, all with ‘Robusta 5’ as a common parent, two distinct QTLs were detected on linkage group 3 where one had previously been mapped. In the New Zealand population, the proximal QTL co-located with SNP markers for a leucine rich repeat, receptor-like protein (MxdRLP1) candidate resistance gene and a closely linked class 3 peroxidase gene, while the QTL detected in the German population was approximately 6 cM distal to this, directly below a SNP marker for a heat shock 90 family protein (HSP90). In the US population, the position of the LOD score peak on linkage group 3 was dependent upon the pathogen strain used for inoculation. One of the five MxdRLP1 alleles identified in fire blight resistant and susceptible cultivars was genetically associated with resistance and used to develop a high resolution melting PCR marker. A novel resistance QTL was also detected on linkage group 7 of the US population that co-located with another HSP90 gene-family member and a WRKY transcription factor previously associated with fire blight resistance; however, this QTL was not observed in the New Zealand or German populations. The results suggest that the upper region of ‘Robusta 5’ linkage group 3 contains multiple genes contributing to fire blight resistance and that their contributions to resistance can vary depending upon pathogen virulence and additional factors. Candidate gene mapping has proved a useful aid in defining these QTLs and developing markers for marker assisted breeding of fire blight resistance.