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

Yang Lv ¹Congcong Liu ²Xiaoxia Li ²Yueying Wang ³Huiying He ²Wenchuang He ²Wu Chen ²Longbo Yang ²Xiaofan Dai ²Xinglan Cao ²Xiaoman Yu ²Jiajia Liu ²Bin Zhang ²Hua Wei ²Hong Zhang ²Hongge Qian ²Chuanlin Shi ²Yue Leng ²Xiangpei Liu ²Mingliang Guo ²Xianmeng Wang ²Zhipeng Zhang ²Tianyi Wang ²Bintao Zhang ²Qiang Xu ²Yan Cui ²Qianqian Zhang ²Qiaoling Yuan ²Noushin Jahan ³Jie Ma ³Xiaoming Zheng ⁴Yongfeng Zhou ²Qian Qian ⁵Longbiao Guo ³Lianguang Shang⁶

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作者信息

1. State Key Laboratory of Rice Biology,China National Rice Research Institute,Hangzhou 310006,China;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
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. State Key Laboratory of Rice Biology,China National Rice Research Institute,Hangzhou 310006,China
4. Yazhouwan National Laboratory,No.8 Huanjin Road,Yazhou District,Sanya City 572024,China;National Key Facility for Crop Gene Resources and Genetic Improvement,Institute of Crop Science,Chinese Academy of Agricultural Sciences,Beijing 100081,China
5. State Key Laboratory of Rice Biology,China National Rice Research Institute,Hangzhou 310006,China;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;Yazhouwan National Laboratory,No.8 Huanjin Road,Yazhou District,Sanya City 572024,China
6. 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;Yazhouwan National Laboratory,No.8 Huanjin Road,Yazhou District,Sanya City 572024,China
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Abstract

Rice(Oryza sativa)is a significant crop worldwide with a genome shaped by various evolutionary factors.Rice centromeres are crucial for chromo-some 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 com-prising both cultivated and wild species of Asian and African rice.We showed that rice cen-tromeres 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.Fur-thermore,high-quality genome assembly and com-plete telomere-to-telomere(T2T)reference genome enable us to obtain more centromeric genome in-formation despite mapping and cloning of cen-tromere genes being challenging.We investigated the association between structural variations and gene expression in the rice centromere.A centromere gene,OsMAB,which positively regu-lates 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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基金项目

centers of Agricultural Genomics Institute at Shenzhen()

highperformance computing centers of China National Rice Research Institute()

National Natural Science Foundation of China(32188102)

National Natural Science Foundation of China(32372148)

Innovation Program of Chinese Academy of Agricultural Sciences()

Youth Innovation of Chinese Academy of Agricultural Sciences(Y20230C36)

Guangdong Basic and Applied Basic Research Foundation(2023B1515020053)

Youth Program of Guangdong Basic and Applied Research(2021A1515111123)

出版年

2024

植物学报(英文版)

中国植物学会

植物学报(英文版)

CSTPCDCSCD

影响因子：0.921

ISSN：1672-9072

参考文献量51

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