| Summary: | Apple scab caused by Venturia inaequalis is one of the most prevalent and devastating diseases of apple (Malus × domestica) worldwide. Breeding programs are attempting to introgress scab resistance genes from wild apples into commercial cultivars for sustainable disease control. Most of the commercially available scab-resistant varieties rely on the Rvi6 resistance gene from Malus floribunda 821. The evolution of new pathotypes of V. inaequalis, which have caused the breakdown of Rvi6-based resistance, highlights the need for the characterization and pyramiding of different scab resistance genes for durable scab resistance. This study was performed to characterize another scab resistance locus Rvi12 from Malus baccata ‘Hansen’s baccata #2’ (HB2). The Rvi12 locus was fine-mapped to a physical interval of approximately 882 kb by the use of ‘Golden Delicious’ reference genome guided marker development and a large mapping population. Through a BAC-library-based chromosome walking, additional markers were developed and a single BAC clone spanning the Rvi12 interval was identified. Following PacBio RS II sequencing and the use of the hierarchical genome assembly process, the BAC clone sequence was assembled. The Rvi12 resistance locus was further narrowed to a 62.3 kb genomic region of the HB2 genome. Gene prediction and in-silico characterization identified five putative candidate genes showing homology to known disease resistance genes or genes involved in disease resistance signaling. Protein domain analysis and quantitative real-time PCR (qRT-PCR) of the five putative candidate genes indicated a LRR receptor-like serine/threonine kinase as the most likely candidate gene for Rvi12 resistance. Overall, the novel markers developed from this study will be useful for the marker-assisted selection of apple genotypes carrying the Rvi12 resistance. Further the identification of candidate gene for Rvi12 based scab resistance will provide the initial resources required for developing scab resistant transgenic or cisgenic apple lines with the Rvi12 resistance.
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