Haplotype‐Resolved Genome Assembly and Population Genomics Reveal Evolutionary History and Agronomic Traits of Mulberry
Journal
Plant Biotechnology Journal
Journal Issue
Online Version of Record before inclusion in an issue
ISSN
1467-7644
1467-7652
Date Issued
2025-11-26
Author(s)
Wang, Zhifeng
Liu, Peigang
Jiao, Chengzhi
Zhang, Yazhou
Xu, Zilong
Lin, Tianbao
Zhu, Yan
Jing, Xin
Huang, Yuan
Chao, Nan
Zhao, Mengjie
Liu, Yan
Liu, Huizi
Sun, Bo
Zhang, Fen
Li, Quanzi
Lv, Zhiqiang
Sun, Xuepeng
Wei, Jia
Abstract
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.
Subjects
ancient mulberry trees
bulked segregant analysis
disease resistance
genome-wide association study
haplotype genomes
Publisher
Wiley
Type
journal article