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

拟南芥基因组序列的完成使得将基因组水平的信息从这个模式系统转换到许多具有农学意义的非模式物种上成为可能。然而，物种之间不准确或不完整的比较可能会阻碍这一点。特别是，准确评估正交学(不同物种中的基因源于该物种最后一个共同祖先的单一基因)与类比(源于基因复制事件的基因)是至关重要的。一般来说，这需要确定被比较物种中所有相关的基因家族成员。由于基因功能在同源基因之间往往是保守的，因此在传统的正向或反向遗传技术不容易采用的作物物种中，正向与同源基因的评估对于假设基因功能具有重要的意义。该SGER建议寻求开发一种冗余的寡核苷酸杂交和基于PCR的方法来综合识别仅存在BAC资源的目标作物物种中的一个基因家族的所有成员。拥有这些信息将使物种间此类基因家族的系统发育比较成为可能，并识别可能赋予有用特征的基因。这项建议的重点是从番茄中鉴定出大2型MADS box基因家族的所有成员，以开展基因家族多样性的详细研究。如果成功，这项建议中描述的策略应该普遍适用于几乎任何物种的大多数基因家族，这些物种都有高质量的BAC文库。

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 employedThis 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.