SGER: A genome-based approach to discover MADS box genes

Yale University, New Haven CT

Investigators

Abstract

The completion of the Arabidopsis genome sequence has led to the very real possibility of translating genome level information from this model system to many non-model species of agronomic interest. However, this can be hampered by inaccurate or incomplete comparisons between species. In particular, it is vital to accurately assess orthology (genes in different species originating from a single gene in the last common ancestor of the species) versus paralogy (genes arising from a gene duplication event). In general, this requires identifying all related gene family members in the species being compared. Because gene functions are often conserved between orthologs, the assessment of orthology versus paralogy has important implications for hypothesizing gene functions in crop species where traditional forward or reverse genetic techniques are not easily employed This SGER proposal seeks to develop a redundant oligonucleotide hybridization and PCR-based method to comprehensively identify all members of a gene family in a target crop species for which only BAC resources exist. Having this information will enable robust phylogenetic comparisons of such gene families between species, and identify genes that are likely to confer useful traits. This proposal focuses on identifying all members of the large type 2 MADS box gene family from Lycopersicon esculentum (tomato) to carry out detailed studies of gene family diversification. If successful, the strategy described in this proposal should be generally applicable to most genes families from virtually any species for which a high quality BAC library exists.