Haplotype‐Resolved Genome Assembly and Population Genomics Reveal Evolutionary History and Agronomic Traits of Mulberry

Mulberry is a representative economic tree species valued for both poverty alleviation and medicinal use. To advance the understanding of mulberry genomics and demography, we assembled high-quality haploid genomes of two widely cultivated mulberry varieties NS14 and QS1, and analysed 376 accessions from 12 countries, including 39 ancient trees to investigate their origin and spreading. Population genetic analyses revealed that mulberry originated in the Yunnan-Guizhou Plateau (YGP) and subsequently spread northward from South China to North China. This migration resulted in significant genetic differentiation between northern and southern populations, with the southern populations exhibiting higher genetic diversity. A total of 37 traits related to development and immunity were analysed in 203 accessions, and a genome-wide association study (GWAS) was used to identify 204 associated loci. Five causal gene haplotypes were pinpointed for key production traits of mulberry trees, including branch pitch, branch length, budburst timing, leaf thickness, and leaf size (leaf area, leaf width, and leaf length). To further explore loci related to disease resistance, we examined the resistance of 538 F₁ hybrids derived from NS14 (resistant) and QS1 (susceptible). Through bulked segregant analysis and GWAS, we identified a G-type RLK (receptor-like kinase) tandem gene cluster. Transcriptomic analyses revealed opposite expression trends of these RLK genes in NS14 and QS1, further supporting their role in mulberry blight resistance. Our findings provide valuable genomic and demographic insights for future multi-purpose breeding efforts in mulberry.