Accurate Gene Models, a Catalog of Natural Variation, and a Comprehensive LORE1 Mutant Collection Facilitate Lotus japonicus Functional Genomics

Characterization of monogenic symbiotic mutant phenotypes found by forward genetic screens has been instrumental for establishing the framework of genes coordinating nodule formation in the model legumes Lotus japonicus and Medicago truncatula. To complement this approach it is now important to investigate more complex traits governing symbiosis. We are in the process of transforming the genomic resources of the model legume L. japonicus to allow QTL and genome-wide association studies of multigene inherited traits to be combined with efficient validation by reverse genetics. These approaches require a complete and well-annotated genome, a catalog of natural variation, and a comprehensive mutant collection. We have produced accurate gene models using a hierarchical selection scheme that combines mRNA-seq data, ab initio modeling and homology information. Using these models, we have annotated the effects on gene structure and coding sequence of SNPs detected by full genome re-sequencing of 30 natural L. japonicus accessions. The new models were also used to annotate more than 200,000 LORE1 retrotransposon insertions, allowing us to identify knockout alleles for the majority of L. japonicus protein coding genes. The LORE1 mutant lines can be ordered at http://carb.au.dk/resources/ and http://www.kazusa.or.jp/lotus/LORE1/index.html.