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Background  The mechanism underlying the interaction between host plant and host-selective toxin (HST)-producing  Alternaria alternata  during infection is of particular interest for sustainable crop production. Alternaria blotch of apple ( Malus  ×  domestica  Borkh.) caused by  A. alternata  apple pathotype is a major disease particularly in East Asia, which is the largest producer of apples globally. A single dominant gene,  Alt , controls the susceptibility of the apple cultivar ‘Delicious’ to Alternaria blotch. In this study, we fine mapped the  Alt  locus and characterized three potential candidate genes.    Results  We used 797 F 1  individuals derived from 15 crosses between apple accessions susceptible ( Alt / alt ) and resistant ( alt / alt ) to Alternaria blotch to construct physical and genetic maps of the  Alt  locus located on the top of chromosome 11. Susceptible accessions were derived from ‘Delicious.’ To fine map the  Alt  locus, we constructed a BAC library of ‘Starking Delicious,’ a sport of ‘Delicious,’ and used graphical genotyping to delimit the  Alt  locus to a region of 43 kb. Three genes predicted within the candidate  Alt  region were potentially involved in plant defense response, among which the gene encoding a coiled coil-nucleotide binding-leucine rich repeat (CC-NB-LRR) type disease resistance protein was the most promising. Moreover, a 12-bp insertion was uniquely identified in the 5′ untranslated region of the  Alt -associated allele of this gene, the presence or absence of which co-segregated with the susceptibility or resistance to  A. alternata  apple pathotype, respectively, among 43 tested cultivars including old ones and founders of modern apple breeding.    Conclusion  A disease resistance protein has been suggested as a determinant of susceptibility/resistance to HST-producing  A. alternata  for the first time. Our finding provides new insight into the mechanism of HST-mediated disease control used by  A. alternata  against host plants.    Electronic supplementary material  The online version of this article (10.1186/s12870-019-1737-7) contains supplementary material, which is available to authorized users.

Identification of candidate genes responsible for the susceptibility of apple (Malus × domestica Borkh.) to Alternaria blotch