A haplotype resolved chromosome-scale assembly of North American wild apple Malus fusca and comparative genomics of the fire blight Mfu10 locus

Authors: MANSFELD, BEN - Donald Danforth Plant Science Center; YOCCA, ALAN - Auburn University; OU, SHUJUN - The Ohio State University; HARKNESS, ALEX - Auburn University; Burchard, Erik; Gutierrez, Benjamin; VAN NOCKER, STEVE - Michigan State University; Gottschalk, Christopher

Submitted to: bioRxiv
Publication Type: Pre-print Publication
Publication Acceptance Date: 3/24/2023
Publication Date: 3/24/2023
Citation: Mansfeld, B., Yocca, A., Ou, S., Harkness, A., Burchard, E.A., Gutierrez, B.L., Van Nocker, S., Gottschalk, C.C. 2023. A haplotype resolved chromosome-scale assembly of North American wild apple Malus fusca and comparative genomics of the fire blight Mfu10 locus. bioRxiv. https://doi.org/10.1101/2023.03.22.533842.
DOI: https://doi.org/10.1101/2023.03.22.533842

Interpretive Summary: The domesticated apple has many wild relatives that could offer unique genetics to be used by breeders to improve cultivated varieties. However, these wild relatives are understudied and lack genomic resources. Here, we sequenced and assembled a genome for apple’s wild relative Malus fusca (the Pacific crabapple). M. fusca is unique in that it originated in the Pacific Northwest of North America, which was isolated from the Asiatic origins of the domesticated apple. To assemble the genome, we used long-read sequencing technology and high-throughput chromatin conformation sequencing coupled with scaffolding using genetic maps. In addition, we sourced a vast amount of public transcript sequencing data to identify genes and annotate the genome. Our genome for M. fusca represents one of the highest-quality apple genomes generated to date. Using the assembled genome, we explored genetic variations between the two haploid genomes that make the diploid M. fusca that was sequenced and compared our genome assembly with other high-quality apple genomes. We identified thousands of variations, including large inserts/deletions between the haploid assembled and regions of high synteny with other apple species. These analyses allowed us to further investigate a known region of the M. fusca genome that contributes to resistance to the major apple pathogen, Erwinia amylovora, that is responsible for the disease fire blight. Within that region, we found that M. fusca contains more copies of a candidate gene, which is hypothesized to confer resistance, compared to susceptible domesticated apple cultivars. Insights gained from the assembly of a M. fusca genome will be invaluable as a tool to facilitate genetic-informed breeding and improved rootstock and scion cultivars.

Technical Abstract: The Pacific crabapple (Malus fusca) is a wild relative of the commercial apple (Malus x domestica). With a range extending from Alaska to Northern California, M. fusca is extremely hardy and disease resistant. The species represents an untapped genetic resource for development of new apple cultivars with enhanced stress resistance. However, gene discovery and utilization of M. fusca has been hampered by the lack of genomic resources. Here, we present a high-quality, haplotype-resolved, chromosome-scale genome assembly and annotation for M. fusca. The genome was assembled using high-fidelity long-reads and scaffolded using genetic maps and high-throughput chromatin conformation capture sequencing, resulting in one of the most contiguous apple genomes to date. We annotated the genome using public transcriptomic data from the same species taken from diverse plant structures and developmental stages. Using this assembly, we explored haplotype structural variation within the genome of M. fusca, identifying thousands of large variants. We further showed high sequence co-linearity with other domesticated and wild Malus species. Finally, we resolve a known quantitative trait locus associated with resistance to fire blight (Erwinia amylovora). Insights gained from the assembly of a reference-quality genome of this hardy wild apple relative will be invaluable as a tool to facilitate DNA-informed introgression breeding.