The pan-tandem repeat map highlights multiallelic variants underlying gene expression and agronomic traits in rice

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 () and Lianguang Shang ()
Additional contact information
Huiying He: Chinese Academy of Agricultural Sciences
Yue Leng: Chinese Academy of Agricultural Sciences
Xinglan Cao: Chinese Academy of Agricultural Sciences
Yiwang Zhu: Chinese Academy of Agricultural Sciences
Xiaoxia Li: Chinese Academy of Agricultural Sciences
Qiaoling Yuan: Chinese Academy of Agricultural Sciences
Bin Zhang: Chinese Academy of Agricultural Sciences
Wenchuang He: Chinese Academy of Agricultural Sciences
Hua Wei: Chinese Academy of Agricultural Sciences
Xiangpei Liu: Chinese Academy of Agricultural Sciences
Qiang Xu: Chinese Academy of Agricultural Sciences
Mingliang Guo: Chinese Academy of Agricultural Sciences
Hong Zhang: Chinese Academy of Agricultural Sciences
Longbo Yang: Chinese Academy of Agricultural Sciences
Yang Lv: Chinese Academy of Agricultural Sciences
Xianmeng Wang: Chinese Academy of Agricultural Sciences
Chuanlin Shi: Chinese Academy of Agricultural Sciences
Zhipeng Zhang: Chinese Academy of Agricultural Sciences
Wu Chen: Chinese Academy of Agricultural Sciences
Bintao Zhang: Chinese Academy of Agricultural Sciences
Tianyi Wang: Chinese Academy of Agricultural Sciences
Xiaoman Yu: Chinese Academy of Agricultural Sciences
Hongge Qian: Chinese Academy of Agricultural Sciences
Qianqian Zhang: Chinese Academy of Agricultural Sciences
Xiaofan Dai: Chinese Academy of Agricultural Sciences
Congcong Liu: Chinese Academy of Agricultural Sciences
Yan Cui: Chinese Academy of Agricultural Sciences
Yuexing Wang: China National Rice Research Institute
Xiaoming Zheng: Chinese Academy of Agricultural Sciences
Guosheng Xiong: Nanjing Agricultural University
Yongfeng Zhou: Chinese Academy of Agricultural Sciences
Qian Qian: Chinese Academy of Agricultural Sciences
Lianguang Shang: Chinese Academy of Agricultural Sciences

Nature Communications, 2024, vol. 15, issue 1, 1-13

Abstract: Abstract 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.

Date: 2024
References: View references in EconPapers View complete reference list from CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-024-51854-0 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-51854-0

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-024-51854-0

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().