博伊斯·汤普森研究所费章君课题组取得一项新突破。他们的论文发现，基于图谱的泛基因组揭示了黄瓜育种过程中的结构变异动态。相关论文于2026年2月10日发表于国际顶尖学术期刊《自然—遗传学》杂志上。

本文提出了一个基于图的黄瓜泛基因组，其中包括27个新组装的基因组和12个先前发表的基因组。全基因组捕获了171892个高置信度的SV，对447个野生和栽培材料进行了基因分型。他们的分析表明，在黄瓜驯化过程中，相当一部分轻度有害SNPs被保留，而SV则不断被清除，突出了它们的高度有害性质。在地理扩展过程中，与SNPs相比，SV负担减少，SV年龄更小，表明SV有更强的净化选择作用。来自野生种群的渗入增加了SV负担，可能是由于搭便车。值得注意的是，将SV负荷纳入基因组预测模型可以提高几个重要农艺性状的预测精度。本研究阐明了SV在黄瓜驯化和范围扩展过程中的动态变化，并强调了SV对黄瓜未来育种的意义。

据介绍，结构变异（SVs）是植物基因组多样性的重要组成部分，但尚未得到充分的研究。

附：英文原文

Title: Graph-based pangenome reveals structural variation dynamics during cucumber breeding

Author: Zhao, Xuebo, Yu, Jingyin, Zhang, Jie, Sun, Honghe, Wu, Shan, Zhao, Jiantao, Zhou, Yao, Hammar, Sue A., Lin, Ying-Chen, Zhang, Zhonghua, Huang, Sanwen, Dymerski, Ronald T., Chen, Feifan, Weng, Yiqun, Grumet, Rebecca, Xu, Yong, Fei, Zhangjun

Issue&Volume: 2026-02-10

Abstract: Structural variants (SVs) represent an important yet underexplored component of plant genome diversity. Here we present a graph-based cucumber pangenome constructed from 39 reference-quality genomes, including 27 newly assembled and 12 previously published. The pangenome captures 171,892 high-confidence SVs, which were genotyped across 447 wild and cultivated accessions. Our analyses reveal that, during cucumber domestication, a substantial portion of mildly deleterious SNPs were retained, whereas SVs were consistently purged, highlighting their highly deleterious nature. During geographical expansion, a reduced SV burden and a younger age of SVs compared to SNPs were observed, suggesting stronger purifying selection acting on SVs. Introgressions from wild populations increased SV burden, potentially due to hitchhiking. Notably, incorporating SV burden into genomic prediction models improved prediction accuracy for several agronomically important traits. This study illuminates SV dynamics during cucumber domestication and range expansion and underscores the implications of SVs for future cucumber breeding.

DOI: 10.1038/s41588-026-02506-0

Source: https://www.nature.com/articles/s41588-026-02506-0