Candidate gene mapping identifies genomic variations in the fire blight susceptibility genes HIPM and DIPM across the Malus germplasm

Abstract

Development of apple (Malus domestica) cultivars resistant to fire blight, a devastating bacterial disease caused by Erwinia amylovora, is a priority for apple breeding programs. Towards this goal, the inactivation of members of the HIPM and DIPM gene families with a role in fire blight susceptibility (S genes) can help achieve sustainable tolerance. We have investigated the genomic diversity of HIPM and DIPM genes in Malus germplasm collections and used a candidate gene-based association mapping approach to identify SNPs (single nucleotide polymorphisms) with significant associations to fire blight susceptibility. A total of 87 unique SNP variants were identified in HIPM and DIPM genes across 93 Malus accessions. Thirty SNPs showed significant associations (p < 0.05) with fire blight susceptibility traits, while two of these SNPs showed highly significant (p < 0.001) associations across two different years. This research has provided knowledge about genetic diversity in fire blight S genes in diverse apple accessions and identified candidate HIPM and DIPM alleles that could be used to develop apple cultivars with decreased fire blight susceptibility via marker-assisted breeding or biotechnological approaches.

Genomic Analysis Highlights Putative Defective Susceptibility Genes in Tomato Germplasm

“…The distribution of these SNPs was studied among the 10 S-genes (Figure 2). .5 Despite differences in the number and type of genes considered, recent analyses on the nucleotide diversity of S-genes in other species such as apple [39,40] and grape [41] have been conducted. The number and density of SNPs observed in grape (V. vinifera) was ~15 SNPs per Kb (1SNP every 66 bp), while in both wild species and hybrid/wild Vitis species, it was 18 SNPs per Kb (1 SNP every 55 bp) [41]; in apple (M. domestica), in Mlo-like genes, values of ~41 SNPs per Kb and 1SNP every 24 bp were observed [39].…”

Contributions of Reduced Susceptibility Alleles in Breeding Apple Cultivars with Durable Resistance to Fire Blight

“…Van Schie and Takken [66] reviewed possible applications of targeting S genes when breeding for disease resistance in plants. In a recent study, Tegtmeier et al [67] investigated genomic diversity of candidate fire blight S genes (HIPM and DIPM genes) in Malus germplasm. Tegtmeier et al [67] argued that targeting S genes might be a more durable approach to breeding apple cultivars with low susceptibility to fire blight.…”

“…In a recent study, Tegtmeier et al [67] investigated genomic diversity of candidate fire blight S genes (HIPM and DIPM genes) in Malus germplasm. Tegtmeier et al [67] argued that targeting S genes might be a more durable approach to breeding apple cultivars with low susceptibility to fire blight. To identify candidate genes for the Chrs.…”