Sequencing of a Wild Apple (<i>Malus baccata</i>) Genome Unravels the Differences Between Cultivated and Wild Apple Species Regarding Disease Resistance and Cold Tolerance

Abstract

<i>Malus baccata</i> is one of four wild apple species that can hybridize with the cultivated apple species (<i>Malus domestica</i>). It is widely used in high-latitude apple-producing areas as a rootstock and breeding resource because of its disease resistance, and cold tolerance. A lack of a reference genome has limited the application of <i>M. baccata</i> for apple breeding. We present a draft reference genome for <i>M. baccata</i> The assembled sequence consisting of 665 Mb, with a scaffold N50 value of 452 kb, included transposable elements (413 Mb) and 46,114 high-quality protein-coding genes. According to a genetic map derived from 390 sibling lines, 72% of the assembly and 85% of the putative genes were anchored to 17 linkage groups. Many of the <i>M. baccata</i> genes under positive selection pressure were associated with plant-pathogen interaction pathways. We identified 2,345 Transcription factor-encoding genes in 58 families in the <i>M. baccata</i> genome. Genes related to disease defense and cold tolerance were also identified. A total of 462 putative nucleotide-binding site (NBS)-leucine-rich-repeat (LRR) genes, 177 Receptor-like kinase (RLK) and 51 receptor-like proteins (RLP) genes were identified in this genome assembly. The <i>M. baccata</i> genome contained 3978 cold-regulated genes, and 50% of these gene promoter containing DREB motif which can be induced by <i>CBF</i> gene. We herein present the first <i>M. baccata</i> genome assembly, which may be useful for exploring genetic variations in diverse apple germplasm, and for facilitating marker-assisted breeding of new apple cultivars exhibiting resistance to disease and cold stress.