Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China.
Nat Commun. 2024 Aug 24;15(1):7291. doi: 10.1038/s41467-024-51854-0.
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.
串联重复（TRs）是指在重复数量上串联变化的基因组区域，通常是多等位基因的。它们的特征及其对水稻基因表达和数量性状的贡献在很大程度上是未知的。在这里，我们基于 231 个基因组组装和水稻泛基因组图来调查水稻 TR 变异。我们确定了 227391 个多等位基因 TR 基因座，其中包括 54416 个在日本晴参考基因组中不存在的 TR 变异。只有 1/3 的 TR 变异与附近的双等位基因变异（SNP、Indels 和 PAV）表现出强连锁。使用 193 个穗和 202 个叶片转录组数据，我们分别揭示了 485 和 511 个 TR 作为 QTL，独立于附近基因表达的其他双等位基因变异。以株高和粒宽为例，我们鉴定并验证了 TR 对水稻农艺性状变异的贡献。这些发现将增强我们对多等位基因变异功能的理解，并有助于水稻的分子育种。
