PT  - JOURNAL ARTICLE
AU  - Guotian Li
AU  - Rashmi Jain
AU  - Mawsheng Chern
AU  - Nikki T. Pham
AU  - Joel A. Martin
AU  - Tong Wei
AU  - Wendy S. Schackwitz
AU  - Anna M. Lipzen
AU  - Phat Q. Duong
AU  - Kyle C. Jones
AU  - Liangrong Jiang
AU  - Deling Ruan
AU  - Diane Bauer
AU  - Yi Peng
AU  - Kerrie W. Barry
AU  - Jeremy Schmutz
AU  - Pamela C. Ronald
TI  - The Sequence of 1504 Mutants in the Model Rice Variety Kitaake Facilitates Rapid Functional Genomic Studies
AID  - 10.1101/111237
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 111237
4099  - http://biorxiv.org/content/early/2017/02/23/111237.short
4100  - http://biorxiv.org/content/early/2017/02/23/111237.full
AB  - The availability of a whole-genome sequenced mutant population and the cataloging of mutations of each line at a single-nucleotide resolution facilitates functional genomic analysis. To this end, we generated and sequenced a fast-neutron-induced mutant population in the model rice cultivar Kitaake (Oryza sativa L. ssp. japonica), which completes its life cycle in 9 weeks. We sequenced 1,504 mutant lines at 45-fold coverage and identified 91,513 mutations affecting 32,307 genes, 58% of all rice genes. We detected an average of 61 mutations per line. Mutation types include single base substitutions, deletions, insertions, inversions, translocations, and tandem duplications. We observed a high proportion of loss-of-function mutations. Using this mutant population, we identified an inversion affecting a single gene as the causative mutation for the short-grain phenotype in one mutant line with a small segregating population. This result reveals the usefulness of the resource for efficient identification of genes conferring specific phenotypes. To facilitate public access to this genetic resource, we established an open access database called KitBase that provides access to sequence data and seed stocks, enabling rapid functional genomic studies of rice.One-sentence summary We have sequenced 1,504 mutant lines generated in the short life cycle rice variety Kitaake (9 weeks) and established a publicly available database, enabling rapid functional genomic studies of rice.