Yiwang Zhong, Liying Feng, Huidong Deng, Xiaohao Ji, Jing Zhang, Yangyang Sun, Peifan Lin, Yang Qiao, Shenghua Xie, Haibo Wang, Lijun Guo, Xuejie Feng

Commun Biol.; 2025 Aug 23; 8(1):1273. doi: 10.1038/s42003-025-08715-3.

Abstract

Durio zibethinus Murr. is a tropical fruit crop of growing global importance, prized for its unique flavor and nutritional value. Yet only a narrow genetic base has been utilized in breeding efforts. We performed whole-genome resequencing of 114 diverse durian accessions collected in China, identifying over 39 million high-quality SNPs across the genome, revealing genome-wide patterns of diversity. Population structure analysis revealed three major genetic clusters, supported by PCA, phylogenetic analysis, and STRUCTURE modeling. Genome-wide scans identified candidate selective sweeps, and several genes potentially under selection. From the 114 accessions, we further identified a core collection of representative durian germplasms capturing the majority of the species' genetic diversity. This subset includes both elite cultivars and genetically distinct individuals. Our study provides insights into the genetic diversity and population structure of cultivated durian. The defined core collection and genomic variation map establish a valuable resource for durian breeding and germplasm conservation. These findings will facilitate the identification of superior alleles for important traits and guide future durian improvement programs.

See https://pubmed.ncbi.nlm.nih.gov/40849519/

Figure 1: Distribution of LTR and SNPs on the genome and transposable element landscape characterization.

A. a Gene Density.

B. Distribution of Copia transposons. 

C. Distribution of Gyspy transposons. 

D. SNP Density in the POP1 population. 

E. SNP Density in the POP2 population. 

F. SNP Density in the POP3 population. B Phylogenetic tree of full-length Gypsy and Copia LTR retrotransposons based on RT domain amino acid sequences. Major clades are labeled according to known superfamilies or lineages. C Boxplot showing the insertion time distribution (Mya) of the top 10 most abundant LTR retrotransposon families in the durian genome. Horizontal lines within boxes indicate the median values, and dots represent outliers. RLC retrotransposon, LTR Copia, RLG retrotransposon, LTR Gypsy.