A haplotype-resolved, chromosome-scale genome for Malus domestica Borkh. ‘WA 38’

Authors: ZHANG, HUITING - Washington State University; KO, ITSUHIRO - Washington State University; EAKER, ABIGAIL - Washington State University; HANEY, SABRINA - Washington State University; KHUU, NINH - Washington State University; RYAN, KARA - Washington State University; APPLEBY, AARON - Washington State University; HOFFMANN, BRENDAN - Washington State University; LANDIS, HENRY - Washington State University; PIERRO, KENNETH - Washington State University; WILLSEA, NOAH - Washington State University; Hargarten, Heidi; YOCCA, ALAN - Former ARS Employee; HARKESS, ALEX - Hudsonalpha Institute For Biotechnology; Honaas, Loren; FICKLIN, STEPHEN - Washington State University

Submitted to: G3: Genes, Genomes, Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/28/2024
Publication Date: 9/17/2024
Citation: Zhang, H., Ko, I., Eaker, A., Haney, S., Khuu, N., Ryan, K., Appleby, A., Hoffmann, B., Landis, H., Pierro, K., Willsea, N., Hargarten, H.L., Yocca, A., Harkess, A., Honaas, L.A., Ficklin, S. 2024. A haplotype-resolved, chromosome-scale genome for Malus domestica Borkh. ‘WA 38’. G3: Genes, Genomes, Genetics. 14(12). Article jkae222. https://doi.org/10.1093/g3journal/jkae222.
DOI: https://doi.org/10.1093/g3journal/jkae222

Interpretive Summary: The apple cultivar ‘WA 38’, trade marked as Cosmic Crisp ®, is one of the top 10 bestselling apple cultivars in the United States. It enjoys popularity among consumers and growers due to its attractive color, texture, flavor, cold hardiness, long term storage capabilities (> 1 year), and scab resistance. Conversely, ‘WA 38’ suffers from undesirable traits as well, such as a propensity for physiological symptoms possibly linked to mineral imbalances, maturity at harvest, and an ‘off’ flavor. This flavor issue may stem from improper picking times, crop load management, handling/packing practices, or other post harvest processes. However, there is limited knowledge regarding the genetic basis contributing to either the desirable or undesirable traits of ‘WA 38’. To gain a deeper understanding of these traits, an investigation into the genetic composition of ‘WA 38’ at the nucleotide level and on a gene-by-gene basis is warranted. Furthermore, in recent years, several apple genomes, including that of ‘Honeycrisp,’ a parent of ‘WA 38,’ have been published. This provides a unique opportunity for scientists to decode cultivar-specific traits by comparing, base-by-base, those cultivar genomes. The ‘WA 38’ genome, as detailed in our manuscript, serves as a valuable resource to the pome fruit research community. It also holds the potential to expedite and enhance future apple breeding programs.

Technical Abstract: Genome sequencing for agriculturally important Rosaceous crops has made rapid progress both in completeness and annotation quality. Whole genome sequence and annotation gives breeders, researchers, and growers information about cultivar specific traits such as fruit quality, disease resistance, and informs strategies to enhance postharvest storage. Here we present a haplotype-phased, chromosomal level genome of Malus domestica, ‘WA 38’, a new apple cultivar released to market in 2017 as Cosmic Crisp ®. Using both short and long read sequencing data with a k-mer based approach, chromosomes originating from each parent were assembled and segregated. This is the first pome fruit genome fully phased into parental haplotypes in which chromosomes from each parent are identified and separated into their unique, respective haplomes. The two haplome assemblies, ‘Honeycrisp’ originated HapA and ‘Enterprise’ originated HapB, are about 650 Megabases each, and both have a BUSCO score of 98.7% complete. A total of 53,028 and 54,235 genes were annotated from HapA and HapB, respectively. Additionally, we provide genome-scale comparisons to ‘Gala’, ‘Honeycrisp’, and other relevant cultivars highlighting major differences in genome structure and gene family circumscription. This assembly and annotation was done in collaboration with the American Campus Tree Genomes project that includes ‘WA 38’ (Washington State University), ‘d’Anjou’ pear (Auburn University), and many more. To ensure transparency, reproducibility, and applicability for any genome project, our genome assembly and annotation workflow is recorded in detail and shared under a public GitLab repository. All software is containerized, offering a simple implementation of the workflow.