中国农业大学赖锦盛研究小组在《细胞》发表研究，通过对3,367个玉米基因组进行深度测序，揭示稀有变异对农艺性状的重要贡献。

稀有变异数量极为丰富，但其对植物农艺性状的全基因组贡献仍不清楚。在此，研究人员对3,367个多样化的优良玉米自交系进行了深度全基因组测序，发现了7,530万个变异，其中79.2%为稀有变异。总体而言，研究人员鉴定出10个农艺性状的411个独立关联信号，其中359个归因于整体稀有变异，且稀有变异的效应大小约为常见变异的2.4倍。频率分层的基于基因组的限制性最大似然分析表明，稀有变异在受强适应选择的性状中捕获了相当大比例的的表型方差，这与性状相关变异的等位基因频率从热带玉米中的常见变为温带玉米中的稀有相一致。作为对传统变异水平全基因组关联研究的补充，基于基因的检验额外鉴定出94个候选基因-性状关联。该研究凸显了稀有变异作为玉米复杂农艺性状遗传结构的重要组成部分，并为未来功能研究和育种提供了亟需的资源。

附：英文原文

Title: Deep sequencing of 3,367 maize genomes uncovers substantial contribution of rare variants to agronomic traits

Author: Liangliang Huang, Chao Bian, Beibei Xin, Xuecai Zhang, Qiong Lu, Yang Yue, Yingshuang Li, Rong Zeng, Xinxiang Liu, Xingming Fan, Tianyu Wang, Yanbo Wang, Jingsheng Cao, Jianguo Zhang, Jianyu Wu, Zhongwei Lin, Jiuran Zhao, Weidong Cheng, Shibin Gao, Yanhui Chen, Yuncai Lu, Junpin Yang, Wenguo Liu, Zehui Chen, Haiyan Sun, Xiaomin Lu, Jiquan Xue, Shuhua Yang, Qiujie Liu, Jian Chen, Hainan Zhao, Haiming Zhao, Weibin Song, Jinsheng Lai

Issue&Volume: 2026-10-27

Abstract: Rare variants are highly abundant, yet their genome-wide contributions to agronomic traits remain elusive in plants. Here, we performed deep whole-genome sequencing of 3,367 diverse elite maize inbred lines, uncovering 75.3 million variants, of which 79.2% were rare. Overall, we identified 411 independent association signals for 10 agronomic traits, including 359 attributable to globally rare variants, with rare variants showing effect sizes approximately 2.4 times those of common variants. Frequency-stratified genome-based restricted maximum likelihood (GREML) analyses indicated that rare variants captured a substantial proportion of phenotypic variance for traits under strong adaptive selection, consistent with the allele frequencies of trait-associated variants shifting from common in tropical to rare in temperate maize. Complementing conventional variant-level genome-wide association studies (GWAS), gene-based tests identified an additional 94 candidate gene-trait associations. Our study highlights rare variants as important components of the genetic architecture of complex agronomic traits in maize and provides much-needed resources for future functional studies and breeding.

DOI: 10.1016/j.cell.2026.09.063

Source:https://www.cell.com/cell/abstract/S0092-8674(26)01209-2