Abstract
Fire blight, a bacterial disease caused by Erwinia amylovora, is the most devastating disease of apples and a major threat to apple production. Most commercial apple cultivars are susceptible to fire blight, driving the need to develop fire-blight-resistant cultivars. Although several major fire blight resistance QTLs have been identified from wild species of Malus, the challenges of breeding apples due to long juvenile phase and heterozygosity greatly limit their use. M. sieversii, the primary progenitor of domesticated apples, is one of the wild Malus species that is sexually compatible with M. domestica and has some favorable fruit quality traits. In this study, we performed QTL analysis on two F1 apple populations of M. domestica cv. “Royal Gala” × M. sieversii (GMAL4591 and GMAL4592) to identify fire blight resistance QTL. Parental linkage maps were constructed for each family using marker sets of approximately 20K GBS-SNPs. Phenotype data was collected from parents and progeny through controlled fire blight inoculations in the greenhouse for two subsequent years. A significant (P < 0.0001) moderate-effect fire blight resistance QTL on linkage group 7 of GMAL4591 was identified from the paternal parent M. sieversii “KAZ 95 17-14” (Msv_FB7). Msv_FB7 explains about 48–53% of the phenotyping variance across multiple years and time points. Additionally, a significant (P < 0.001) minor effect QTL explaining 18% of the phenotypic variance was identified in population GMAL4592 on LG10 from “Royal Gala.” We developed diagnostic SSR markers flanking the Msv_FB7 QTL to use in apple breeding. These findings have the potential to accelerate the development of fire-blight-resistant cultivars.
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Data availability
The genotype by sequencing SNP data sets for GMAL4591 and GMAL4592 to construct genetic maps are made available on the Dryad database (10.5061/dryad.15dv41p3c).
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Acknowledgements
This research was funded by the New York State Department of Agriculture & Markets, Apple Research & Development Program (ARDP). We would like to acknowledge the USDA (United States Department of Agriculture) Plant Genetic Resources Unit (PGRU) in Geneva, New York, for providing the plant material. We would like to recognize Dr. Julliany Pereira Silva for helping establish and maintain the mapping populations in the greenhouse and to collect the first year of phenotype data.
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A.K. conceptualized, designed, and managed the project. R.T. and D.C-S. performed the experiments. R.T. performed all analysis and interpretation as well as drafted the manuscript. R.T., D.C-S., G-Y.Z., and A.K. revised and finalized the manuscript. All authors read and approved the final version.
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Supplementary Information
Supplementary Figure 1.
A-D) Linkage map plots showing the centiMorgan (cM) distance per chromosome of the four parental linkage maps constructed for populations GMAL4591 (A-B) and GMAL4592 (C-D). E) A marker density plot for the paternal linkage map of GMAL4591 (B) showing regions in blue having lower density and regions in red having a higher density ranging from 0.9cM to 30cM. F) A regression plot showing the correlation of physical position in the Golden Delicious Double Haploid Genome (y-axis) and the cM genetic position of the paternal markers from GMAL4591 (x-axis). (PNG 7.13 mb)
Supplementary Figure 2.
The logarithm of the odds (LOD) plots to display regions of the four parental linkage maps that are significantly (P<0.0001) associated with the percent shoot lesion length (PSLL) across two years of fire blight infection data in two F1 populations (GMAL4591, GMAL4592). The x-axis shows the centimorgan position of the marker on the linkage map and the y-axis shows its LOD value from composite interval mapping (CIM) analysis on 17 linkage groups. The red threshold line represents the LOD cutoff of significance given P<0.0001. In the legend from top to bottom, the red line is the results from the area under the disease progress curve from the 2020 data, the orange is PSLL from 2018, the green is PSLL from 2019, light blue is PSLL (7dai) from 2020, purple is PSLL2 (10dai) from 2020, and pink is PSLL3 (15dai) from 2020. (PNG 1.54 mb)
Supplementary Figure 3.
Biplots of the fire blight percent shoot lesion length (PSLL1-3) and area under the disease progress curve of percent shoot lesion length (AUDPC PSLL) of 2020 plotted against PSLL 2019 for two F1 mapping populations (GMAL4591-top; GMAL4592-bottom). The blue line represents the regression of phenotypic values with the Pearson correlation value and p-value above each plot. For 2020 data, PSLL1, PSLL2, and PSLL3 represent the phenotypic value taken on 7, 10, and 15 dai, respectively. For 2019, PSLL 2019 was taken on 7 dai. (PNG 147 kb)
Supplementary Figure 4.
Q-Q plots of the residual values of fire blight percent shoot lesion length (PSLL1-3) and area under the disease progress curve of percent shoot lesion length (AUDPC PSLL) of 2020 and the PSLL of 2019 for two F1 mapping populations (GMAL4591-top; GMAL4592-bottom). The red line represents the reference line for a normal distribution. For 2020 data, PSLL1, PSLL2, and PSLL3 represent the phenotypic value taken on 7, 10, and 15 dai, respectively. For 2019, PSLL 2019 was taken on 7 dai. The data were transformed using the Box-Cox transformation, using an optimal lambda value of 0.6. (PNG 980 kb)
Supplemental Table 1.
Phenotypic variation for two years of fire blight inoculation data for the F1 apple populations GMAL4591 and GMAL4592. The mean, standard deviation and broad sense heritability (H2) are shown for the leaf length (LL), shoot length (SL), percent shoot lesion length (PSLL), and the area under the disease progress curve of the percent shoot lesion length (AUDPC PSLL). (DOCX 16 kb)
Supplemental Table 2.
Primer sequences and melting temperature (Tm) of the SSR markers linked to Msv_FB7 fire blight resistance QTL on linkage group (LG) 7 developed in this study for marker-assisted selection in apple breeding programs. The top sequence is the forward primer with the M13 tail in bold and underlined while the reverse primer is just below. (DOCX 13 kb)
Supplemental Table 3.
Table of the SSR marker name, genotype name, PI numbers, species, SSR fragment sizes in base pairs (bp) without the M13 tail, information on known fire blight resistance QTL for eight apple genotypes. Genotypes with multiple fragments have different fragment lengths separated by a slash. PI number is the plant introduction (unique identifier) from USDA-GRIN database. (DOCX 17 kb)
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Tegtmeier, R., Cobb-Smith, D., Zhong, GY. et al. Identification and marker development of a moderate-effect fire blight resistance QTL in M. sieversii, the primary progenitor of domesticated apples. Tree Genetics & Genomes 19, 50 (2023). https://doi.org/10.1007/s11295-023-01626-6
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DOI: https://doi.org/10.1007/s11295-023-01626-6