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

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 identify regions and structural variants associated with abiotic stress resistance. The resulting genome assembly exhibited scaffold N50 of >40 Mb and BUSCO scores >98.7% complete for both haplotype assemblies. We used climate data from the origin of each resequenced sample as a phenotype to identify 242 regions including SNPs and structural variants (deletions, duplications, and inversions) of the genome of M. angustifolia that were significantly associated with abiotic factors such as seasonal precipitation and maximum seasonal temperature. These results will enable identification of resilient M. angustifolia accessions and genetic loci for use in breeding of climate-resilient apples.