Genome Sequencing and Comparative Analysis of the Early Flowering Rice Variety Kitaake


Rashmi Jain, Guotian Li, Jerry Jenkins, Shengqiang Shu, Dario Copetti, David Kudrna, Mawsheng Chern, Nhan T Pham, Tong Wei, Joel Martin, Phat Duong, Wendy Schackwitz, Anna Lipzen, Eda Karaagac, Randy Ruan, Kerrie W Barry, Rod Wing, Jeremy Schmutz,
Pamela Ronald

Kitaake, an early flowering rice cultivar, is emerging as a preferred model for rice genetic analysis. Compared with the Japonica rice variety, Nipponbare, and the Indica rice variety, 93-11, the Kitaake rice variety has a smaller stature, much shorter life cycle (ca. 9 weeks vs. 6 months) and is easier to transform. To facilitate the use of Kitaake, we conducted a whole genome assembly of Kitaake using PacBio sequencing supplemented with Illumina sequencing. The estimated genome size of Kitaake is 382 Mb arranged in 12 chromosomes and some unmapped scaffolds. We annotated high quality 35,596 non-transposable element protein coding genes in Kitaake and identified genetic variations between Kitaake and Nipponbare. There are 265,377 SNPs and 66,329 INDELs (<30 bp) comparing with Nipponbare. The genomic variations identified in this study are important for future functional genomics studies of important rice traits, such as early flowering of Kitaake. The Kitaake genome is available online at the JGI Phytozome. The Kitaake genome and the previously established whole-genome sequenced mutant population provide powerful resources in rice functional genomics studies.

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