The genome sequence of Ciherang, an Indonesian rice mega variety, revealed the footprints of modern rice breeding

Ciherang is an Indonesian rice mega variety that was developed from IR64. To study the extent of genetic exchange on IR64 genome during Ciherang development and to identify the effects of those genomic changes, whole-genome sequencing and analyses were conducted on Ciherang and IR64. Ciherang genome sequencing generated reads that are >24 times the size of rice genome and 98.6% of those sequences could be mapped to the Nipponbare reference genome. Variant calling showed that IR64 and Ciherang had 3,015,867 (0.8%) and 2,954,801 (0.79%) sequence differences to Nipponbare, respectively, while Ciherang and IR64 only differed by 0.13%. There were 493,298 sequence variations between Ciherang and IR64, and 434,890 of them were single nucleotide polymorphisms (SNPs) while the remaining 58,408 were insertions/deletions (indels). Sequence differences are prominent in chromosomes 8, 10, and 12, indicating that many introgressions from the donor parents were retained in those chromosomes. There are 1,007 high impact mutations in Ciherang that are polymorphic to IR64, and some of them were found in genes affecting panicle and seed characteristics like Os01g0588900 and Os02g0154200. These discoveries will aid breeding programs that utilize IR64 or Ciherang and can serve as the basis for intellectual property rights management for future varieties.