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

Huiying HeYue LengXinglan CaoYiwang ZhuXiaoxia LiQiaoling YuanBin ZhangWenchuang HeHua WeiXiangpei LiuQiang XuMingliang GuoHong ZhangLongbo YangYang LvXianmeng WangChuanlin ShiZhipeng ZhangWu ChenBintao ZhangTianyi WangXiaoman YuHongge QianQianqian ZhangXiaofan DaiCongcong LiuYan CuiYuexing WangXiaoming ZhengGuosheng XiongYongfeng ZhouQian QianLian-Guang Shang
Published in: Nature communications (2024)
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.
Keyphrases
  • genome wide
  • gene expression
  • dna methylation
  • copy number
  • body mass index
  • single cell
  • single molecule
  • mass spectrometry
  • convolutional neural network
  • rna seq
  • deep learning
  • data analysis