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

拟南芥基因组序列的完成使得将该模式系统的基因组水平信息翻译到许多具有农艺兴趣的非模式物种成为可能。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，准确评估同源性（不同物种的基因源自物种最后共同祖先的单一基因）与同源性（基因源于基因复制事件）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物之间通常是保守的，因此对同源物与同源物的评估对于假设作物物种的基因功能具有重要意义，而传统的正向或反向遗传技术不容易采用。SGER提案旨在开发一种基于冗余olig核苷酸杂交和pcr的方法，以全面识别目标作物物种中只有BAC资源存在的基因家族的所有成员。有了这些信息，就可以在物种之间对这些基因家族进行强有力的系统发育比较，并识别可能赋予有用特征的基因。本课题拟重点鉴定番茄2型MADS大盒基因家族的所有成员，开展基因家族多样化的详细研究。如果成功，本文所描述的策略应该普遍适用于几乎任何存在高质量BAC文库的物种的大多数基因家族。

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.