New genomics resources and local adaptation GWAS in wild Malus angustifolia reveal genetic regions for enhancing abiotic resiliency in apple

Authors: MANSFELD, BEN - Washington University; MIGICOVSKY, ZOE - Acadia University; BROCK, JORDAN - Washington University; HEWENS-HIGGINS, BLAKE - Acadia University; Burchard, Erik; YOCCA, ALAN - Hudsonalpha Institute For Biotechnology; OU, SHUJUN - Ohio University; WHITT, LAUREN - Former ARS Employee; DHINGRA, ANURADHA - Washington University; Gottschalk, Christopher; HARKESS, ALEX - Hudsonalpha Institute For Biotechnology; Gutierrez, Benjamin; VAN NOCKER, STEVE - Michigan State University; Tang, Lisa

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/21/2026
Publication Date: 7/31/2026
Citation: Mansfeld, B., Migicovsky, Z., Brock, J., Hewens-Higgins, B., Burchard, E.A., Yocca, A., Ou, S., Whitt, L., Dhingra, A., Gottschalk, C.C., Harkess, A., Gutierrez, B.L., Van Nocker, S., Tang, L. 2026. New genomics resources and local adaptation GWAS in wild Malus angustifolia reveal genetic regions for enhancing abiotic resiliency in apple. Horticulture Research. https://doi.org/10.1093/hr/uhag336.
DOI: https://doi.org/10.1093/hr/uhag336

Interpretive Summary: Apple (Malus domestica Borkh) production faces many challenges stemming from abiotic stresses such as extreme temperatures, droughts, and spring frosts. The introduction of resiliency traits from wild Malus relatives that originate from high stress environments could offer new genetic solutions to a changing climate. Use of wild Malus relatives in breeding is constrained by the lack of genomic resources and base knowledge of genetics associated with abiotic stress. To address this gap, we used a combination of the latest genome sequencing and resequencing approaches to assemble a high-quality reference genome for Malus angustifolia, a native apple to the Southeastern U.S., and resequence its germplasm to enable genome wide association study to identify regions and structural variants associated with abiotic stresses. We used climate data from the origin of each resequenced sample as a phenotype to identify 144 regions of the genome of M. angustifolia that were significantly associated with abiotic stresses such as seasonal precipitation and maximum seasonal temperature. These results will enable identification of resilient M. angustifolia accessions along with targeted genetics for use in breeding of climate resilient apples.

Technical Abstract: Apple (Malus domestica Borkh) production faces many challenges stemming from abiotic stresses such as extreme temperatures, droughts, and spring frosts. The introduction of resiliency traits from wild Malus relatives that originate from high stress environments could offer new genetic solutions to a changing climate. Use of wild Malus relatives in breeding is constrained by the lack of genomic resources and base knowledge of genetics associated with abiotic stress. To address this gap, we used a combination of the latest genome sequencing and resequencing approaches to assemble a high-quality reference genome for Malus angustifolia, a native apple to the Southeastern U.S., and resequence its germplasm to enable genome wide association study to identify regions and structural variants associated with abiotic stresses. We used climate data from the origin of each resequenced sample as a phenotype to identify 144 regions of the genome of M. angustifolia that were significantly associated with abiotic stresses such as seasonal precipitation and maximum seasonal temperature. These results will enable identification of resilient M. angustifolia accessions along with targeted genetics for use in breeding of climate resilient apples.