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

Author:

Mansfeld Ben N.1ORCID,Yocca Alan2,Ou Shujun3,Harkess Alex2,Burchard Erik4,Gutierrez Benjamin5,van Nocker Steve6,Gottschalk Christopher4ORCID

Affiliation:

1. Department of Biology Washington University in St. Louis St. Louis Missouri USA

2. HudsonAlpha Institute for Biotechnology Huntsville Alabama USA

3. Department of Molecular Genetics The Ohio State University Columbus Ohio USA

4. USDA ARS Appalachian Fruit Research Station Kearneysville West Virginia USA

5. USDA ARS Plant Genetic Resources Unit Geneva New York USA

6. Department of Horticulture Michigan State University East Lansing Michigan USA

Abstract

SUMMARYThe Pacific crabapple (Malus fusca) is a wild relative of the commercial apple (Malus × 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 the development of new apple cultivars with enhanced stress resistance. However, gene discovery and utilization of M. fusca have 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 haplotypic 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.

Funder

Agricultural Research Service

National Science Foundation

Publisher

Wiley

Subject

Cell Biology,Plant Science,Genetics

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