Abstract
Wild species of domesticated crops provide valuable genetic resources for resistance breeding.Prunus davidiana,a wild relative of peach with high heterozygosity and diverse stress tolerance,exhibits high resistance against aphids.However,the highly hetero-zygous genome of P.davidiana makes de-termining the underlying factors influencing re-sistance traits challenging.Here,we present the 501.7 Mb haplotype-resolved genome as-sembly of P.davidiana.Genomic comparisons of the two haplotypes revealed 18,152 struc-tural variations,2,699 Pda_hap1-specific and 2,702 Pda_hap2-specific genes,and 1,118 allele-specific expressed genes.Genome com-position indicated 4.1％of the P.davidiana genome was non-peach origin,out of which 94.5％was derived from almond.Based on the haplotype genome,the aphid resistance quan-titative trait locus(QTL)was mapped at the end of Pda03.From the aphid resistance QTL,PdaWRKY4 was identified as the major domi-nant gene,with a 9-bp deletion in its promoter of the resistant phenotype.Specifically,PdaWRKY4 regulates aphid resistance by pro-moting PdaCYP716A1-mediated anti-aphid metabolite betulin biosynthesis.Moreover,we employed a genome design to develop a breeding workflow for rapidly and precisely producing aphid-resistant peaches.In con-clusion,this study identifies a novel aphid re-sistance gene and provides insights into ge-nome design for the development of resistant fruit cultivars.
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