A Haplotype-resolved, chromosome-scale genome for Malus domestica ‘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; HARKESS, ALEX - Hudsonalpha Institute For Biotechnology; Honaas, Loren; FICKLIN, STEPHEN - Washington State University

Submitted to: bioRxiv
Publication Type: Pre-print Publication
Publication Acceptance Date: 4/30/2024
Publication Date: 5/29/2024
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.E., Harkess, A., Honaas, L.A., Ficklin, S. 2024. A Haplotype-resolved, chromosome-scale genome for Malus domestica ‘WA 38’. bioRxiv. https://doi.org/10.1101/2024.01.10.574953.
DOI: https://doi.org/10.1101/2024.01.10.574953

Interpretive Summary: The apple cultivar ‘WA 38’, trade marked as Cosmic Crisp ®, enjoys popularity among both 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 reported by consumers. 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 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 quality, disease resistance, and informs strategies to enhance post harvest storage. Here we present a haplotype phased, chromosomal level, genome of Malus domestica, ‘WA 38’, a new cultivar of apple released to market in 2017 as Cosmic Crisp ®. Using both short and long read sequencing our fully phased genome of ‘WA 38’ is about 650 Megabases, with a BUSCO score of 98.7% complete. The genome contains two haplomes which are composed of 17 chromosomes each. A total of 48,227 and 54,479 genes were annotated from HapA and HapB, respectively. Additionally, we provide whole genome comparisons to ‘Gala’ and ‘Honeycrisp’ and other relevant cultivars highlighting major differences. This assembly and annotation was done in collaboration with the American Campus Tree Genomes project that included ‘WA 38’ (WSU) and the ‘d’Anjou’ pear (Auburn University). Our workflow and software is preserved in a Docker container with extensive supporting documentation to ensure transparency, reproducibility, and use for any genome project.