A super pan-genomic landscape of rice

Pan-genomes from large natural populations can capture genetic diversity and reveal genomic complexity. Using de novo long-read assembly, we generated a graph-based super pan-genome of rice consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African rice. Our pan-genome reveals extensive structural variations (SVs) and gene presence/absence variations. Additionally, our pan-genome enables the accurate identification of nucleotide-binding leucine-rich repeat genes and characterization of their inter- and intraspecific diversity. Moreover, we uncovered grain weight-associated SVs which specify traits by affecting the expression of their nearby genes. We characterized…

• UD
  U.S. Department of Agriculture
• NN
  National Natural Science Foundation of China

  Awards: 32188102, 31961143015, 31925029, 31822029, 91735304, 32101718
• CA
  China Agricultural University
• CA
  Chinese Academy of Sciences
• CP
  China Postdoctoral Science Foundation

  Awards: 2020 M672903, 2020M672903, BX2020372, BX201600151
• CA
  Chinese Academy of Agricultural Sciences
• UO
  University of Chinese Academy of Sciences
• AR
  Agricultural Research Service
• AS
  Agricultural Science and Technology Innovation Program
• BA
  Basic and Applied Basic Research Foundation of Guangdong Province

  Award: 2020B1515120086
• IO
  Institute of Genetics