文献类型： 外文期刊

作者： He, Huiying ¹ ; Leng, Yue ¹ ; Cao, Xinglan ¹ ; Zhu, Yiwang ¹ ; Li, Xiaoxia ¹ ; Yuan, Qiaoling ¹ ; Zhang, Bin ¹ ; He, Wenchuang ¹ ; Wei, Hua ¹ ; Liu, Xiangpei ¹ ; Xu, Qiang ¹ ; Guo, Mingliang ¹ ; Zhang, Hong ¹ ; Yang, Longbo ¹ ; Lv, Yang ¹ ; Wang, Xianmeng ¹ ; Shi, Chuanlin ¹ ; Zhang, Zhipeng ¹ ; Chen, Wu ¹ ; Zhang, Bintao ¹ ; Wang, Tianyi ¹ ; Yu, Xiaoman ¹ ; Qian, Hongge ¹ ; Zhang, Qianqian ¹ ; Dai, Xiaofan ¹ ; Liu, Congcong ¹ ; Cui, Yan ¹ ; Wang, Yuexing ⁶ ; Zheng, Xiaoming ⁷ ; Xiong, Guosheng ⁸ ; Zhou, Yongfeng ¹ ; Qian, Qian ¹ ; Shang, Lianguang ¹ ;

作者机构： 1.Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Guangdong Lab Lingnan Modern Agr, Genome Anal Lab,Minist Agr & Rural Affairs,Shenzhe, Shenzhen 518120, Peoples R China

2.Henan Univ, Sch Life Sci, State Key Lab Crop Stress Adaptat & Improvement, Kaifeng 475004, Peoples R China

3.Henan Univ, Shenzhen Res Inst, Shenzhen 518000, Peoples R China

4.Fujian Acad Agr Sci, Inst Biotechnol, Fujian Prov Key Lab Genet Engn Agr, Fuzhou 350003, Peoples R China

5.Yazhouwan Natl Lab, Sanya 572024, Peoples R China

6.China Natl Rice Res Inst, State Key Lab Rice Biol, Hangzhou 310006, Peoples R China

7.Chinese Acad Agr Sci, Natl Key Facil Gene Resources & Genet Improvement, Inst Crop Sci, Beijing 100081, Peoples R China

8.Nanjing Agr Univ, Acad Adv Interdisciplinary Studies, Plant Phen Res Ctr, Nanjing 210095, Jiangsu, Peoples R China

期刊名称：NATURE COMMUNICATIONS （ 影响因子：15.7； 五年影响因子：17.2 ）

ISSN：

年卷期： 2024 年 15 卷 1 期

页码：

收录情况： SCI

摘要： 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 multiallelic variants and facilitate rice molecular breeding. Tandem repeats (TRs) have unique ability to drive a range of phenotype variations. Here, the authors survey rice TR variations based on 231 genome assemblies and the rice pan-genome graph, identify TR variations associated with expressed genes, and reveal expression TRs contributed to rice agronomic trait variations.