Fine-Mapping and Identification of Candidate Genes for Rvi12 Based Apple Scab Resistance from Malus baccata ‘Hansen’s Baccata 2’

Apple scab is a disease caused by the fungus Venturia inequalis which leads to significant economic losses in apple production. Breeding programs are attempting to introgress scab resistance genes from wild apple varieties into commercial cultivars for the control of the disease. Even though, 18 scab resistance genes have been identified and mapped, only three have been fine-mapped and candidate resistance genes have been identified. In this study, our objectives are to fine-map and identify the candidate resistance genes for the Rvi12 apple scab resistance from Malus baccata ‘Hansen’s baccata 2’. By using a large segregating population and closely linked markers, Rvi12 has been mapped within an interval of 882kb on Golden Delicious genome sequence. A BAC library of ‘Hansen’s baccata 2’ containing approximately 36,864 clones, with a 6.7X coverage of apple genome was developed at Amplicon Express, WA, USA. By chromosome walking, contiguous clones spanning the Rvi12 interval was identified. By the use of new SSR markers developed in this study and markers designed from BAC-end sequences, the Rvi12 resistance gene interval was further narrowed down between SNP-32N11-RSP-T/C_243 and 6F11-FSP. A single BAC clone was sufficient to cover the Rvi12 mapping interval. PacBio sequencing and assembly of the BAC clone sequences were done. Following gene prediction and qRT-PCR, two candidate genes for disease resistance were identified. Further studies on complementation and validation of the role of candidates in apple scab resistance are in progress.