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

Cell; 2026; IF: 45.1

DOI: 10.1016/j.molp.2026.09.011

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.