Construction of a dense genetic map of the Malus fusca fire blight resistant accession MAL0045 using tunable genotyping-by-sequencing SNPs and microsatellites

Abstract

Although, the Pacific crabapple, Malus fusca, is a hardy and disease resistant species, studies relating to the genetics of its unique traits are very limited partly due to the lack of a genetic map of this interesting wild apple. An accession of M. fusca (MAL0045) of Julius Kühn-Institut collection in Germany is highly resistant to fire blight disease, incited by different strains of the causative pathogen-Erwinia amylovora. This is the most destructive bacterial disease of Malus of which most of the domesticated apples (Malus domestica) are susceptible. Using a scarcely dense genetic map derived from a population of 134 individuals of MAL0045 × 'Idared', the locus (Mfu10) controlling fire blight resistance mapped on linkage group 10 (LG10) and explained up to 66% of the phenotypic variance with different strains. Although the development of robust and tightly linked molecular markers on LG10 through chromosome walking approach led to the identification of a major candidate gene, any minor effect locus remained elusive possibly due to the lack of marker density of the entire genetic map. Therefore, we have developed a dense genetic map of M. fusca using tunable genotyping-by-sequencing (tGBS) approach. Of thousands of de novo SNPs identified, 2677 were informative in M. fusca and 90.5% of these successfully mapped. In addition, integration of SNP data and microsatellite (SSR) data resulted in a final map comprising 17 LGs with 613 loci spanning 1081.35 centi Morgan (cM). This map will serve as a template for mapping using different strains of the pathogen.

Figure 1

Integrated dense genetic map of MAL0045 comprising 560 tGBS SNPs and 53 SSR markers (highlighted in red). Total length is 1081.35 cM.

Figure 2

(a) Pairwise correlations and scatter plots for the phenotypic values of MAL0045-derived progeny. The average values for each individual for the four strains and the overall average were also used for QTL analyses. The lines represent the binominal trend line. Axes show percent lesion length (PLL). (b) LOD score plot of LG10 of MAL0045 for the four E. amylovora strains and the average value of all strains. The numbers attached after each strain name indicate the year(s) of phenotyping (e.g. Ea3049_1420 means that individuals were inoculated in 2014 and 2020).