Towards a Fully Indexed Mutant Population in the Model Rice, Kitaake, Suited for Forward and Reverse Genetics Research

We have generated a rice mutant population containing 7,000 independent (M1) lines using fast-neutron induced mutagenesis in the model rice Kitaake, a short-statured, short life-cycled, early flowering rice variety. In collaboration with the Joint Genome Institute, we aim to sequence and analyze 4,000 rice mutants in order to create a rice mutant population resource that reaches an estimated 90% coverage of total rice genes. Currently, we have sequenced over 1000 mutants. On average, each mutant contains over fifteen mutated genes. We have established a database, named KitBase, to integrate all information of this mutant population, including sequences, mutated genes, and available phenotypes. DNA sequence, gene or mutant ID, chromosome coordinates, and key words can be used to search KitBase.

Using this rice mutant population, we have conducted a forward genetic screen to identify mutants that suppress the rice immune response mediated by XA21, a pattern recognition receptor conferring robust resistance to Xanthomonas oryzae pv oryzae (Xoo). We have obtained 10 suppressors of Xa21-mediated immunity (sxi), after screening approximately 21,000 plants, and characterized 4 of the sxi mutants. We have used a comparative genome hybridization approach based on rice whole-genome tiling arrays and a whole genome resequencing approach to identify candidate mutations in each mutant. The responsible mutation that cosegregates with the sxi phenotype was identified in the backcrossed segregating F2 progeny. We have complemented mutant sxi1 with one of the candidate gene. This study demonstrates the power and usefulness of this rice mutant population.