J Integr Plant Biol. ›› 2024, Vol. 66 ›› Issue (2): 196-207.DOI: 10.1111/jipb.13607

• Functional Omics and Systems Biology • Previous Articles     Next Articles

A centromere map based on super pan-genome highlights the structure and function of rice centromeres

Yang Lv1,2†, Congcong Liu2†, Xiaoxia Li2†, Yueying Wang1†, Huiying He2, Wenchuang He2, Wu Chen2, Longbo Yang2, Xiaofan Dai2, Xinglan Cao2, Xiaoman Yu2, Jiajia Liu2, Bin Zhang2, Hua Wei2, Hong Zhang2, Hongge Qian2, Chuanlin Shi2, Yue Leng2, Xiangpei Liu2, Mingliang Guo2, Xianmeng Wang2, Zhipeng Zhang2, Tianyi Wang2, Bintao Zhang2, Qiang Xu2, Yan Cui2, Qianqian Zhang2, Qiaoling Yuan2, Noushin Jahan1, Jie Ma1, Xiaoming Zheng3,4, Yongfeng Zhou2, Qian Qian1,2,3*, Longbiao Guo1* and Lianguang Shang2,3*   

  1. 1. State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China;
    2. 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;
    3. Yazhouwan National Laboratory, No. 8 Huanjin Road, Yazhou District, Sanya City 572024, China;
    4. National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
    These authors contributed equally to this work.
    *Correspondence: Qian Qian (qianqian188@hotmail.com); Longbiao Guo (guolongbiao@caas.cn); Lianguang Shang (shanglianguang@caas.cn, Dr. Shang is fully responsible for the distributions of all materials associated with this article)
  • Received:2023-12-19 Accepted:2023-12-28 Online:2023-12-30 Published:2024-02-01

Abstract: Rice (Oryza sativa) is a significant crop worldwide with a genome shaped by various evolutionary factors. Rice centromeres are crucial for chromosome segregation, and contain some unreported genes. Due to the diverse and complex centromere region, a comprehensive understanding of rice centromere structure and function at the population level is needed. We constructed a high-quality centromere map based on the rice super pan-genome consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African rice. We showed that rice centromeres have diverse satellite repeat CentO, which vary across chromosomes and subpopulations, reflecting their distinct evolutionary patterns. We also revealed that long terminal repeats (LTRs), especially young Gypsy-type LTRs, are abundant in the peripheral CentO-enriched regions and drive rice centromere expansion and evolution. Furthermore, high-quality genome assembly and complete telomere-to-telomere (T2T) reference genome enable us to obtain more centromeric genome information despite mapping and cloning of centromere genes being challenging. We investigated the association between structural variations and gene expression in the rice centromere. A centromere gene, OsMAB, which positively regulates rice tiller number, was further confirmed by expression quantitative trait loci, haplotype analysis and clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 methods. By revealing the new insights into the evolutionary patterns and biological roles of rice centromeres, our finding will facilitate future research on centromere biology and crop improvement.

Key words: centromere, super pan-genome, CentO satellite repeat, rice

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