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该模型系统翻译到许多农艺学上感兴趣的非模型物种具有非常真实的可能性。然而，这可能会受到物种之间不准确或不完整的比较的阻碍。特别是，准确评估直系同源（不同物种中的基因起源于该物种最后一个共同祖先中的单个基因）与旁系同源（由基因复制事件产生的基因）至关重要。一般来说，这需要识别被比较物种中的所有相关基因家族成员。由于基因功能在直向同源物之间通常是保守的，因此评估直向同源物与旁系同源物对于假设传统正向或反向遗传技术不容易采用的作物物种中的基因功能具有重要意义。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，并确定可能赋予有用性状的基因。本研究旨在鉴定番茄2型MADS盒基因大家族的所有成员，以开展基因家族多样性的详细研究。如果成功的话，本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，其中存在高质量的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.