Tandem repeats (TRs) are genomic regions that tandemly change in repeat number, which are often multiallelic. Their characteristics and contributions to gene expression and quantitative traits in rice are largely unknown. Here, we survey rice TR variations based on 231 genome assemblies and the rice pan-genome graph. We identify 227,391 multiallelic TR loci, including 54,416 TR variations that are absent from the Nipponbare reference genome. Only 1/3 TR variations show strong linkage with nearby bi-allelic variants (SNPs, Indels and PAVs). Using 193 panicle and 202 leaf transcriptomic data, we reveal 485 and 511 TRs act as QTLs independently of other bi-allelic variations to nearby gene expression, respectively. Using plant height and grain width as examples, we identify and validate TRs contributions to rice agronomic trait variations. These findings would enhance our understanding of the functions of multi-allelic variants and facilitate rice molecular breeding.

Huiying He, Yue Leng, Xinglan Cao, Yiwang Zhu, Xiaoxia Li, Qiaoling Yuan, Bin Zhang, Wenchuang He, Hua Wei, Xiangpei Liu, Qiang Xu, Mingliang Guo, Hong Zhang, Longbo Yang, Yang Lv, Xianmeng Wang, Chuanlin Shi, Zhipeng Zhang, Wu Chen, Bintao Zhang, Tianyi Wang, Xiaoman Yu, Hongge Qian, Qianqian Zhang, Xiaofan Dai, Congcong Liu, Yan Cui, Yuexing Wang, Xiaoming Zheng, Guosheng Xiong, Yongfeng Zhou, Qian Qian, Lianguang Shang