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

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 (CoERs) and drive rice centromere expansion and evolution. Furthermore, high-quality genome assembly and complete T2T reference genome enable us to obtain more centromeric genome information despite the mapping and cloning of centromere genes is challenging. We investigated the association between structural variations (SVs) and gene expression in the rice centromere. A centromere gene, OsMAB, that positively regulates rice tiller number, was further confirmed by eQTL, haplotype analysis and CRISPR/Cas9 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. This article is protected by copyright. All rights reserved.