Linking Rice, Arabidopsis and the Grasses to Explore Natural Genetic Variation

到目前为止，基于图谱的作物基因克隆和鉴定在很大程度上局限于单基因性状，如那些具有抗病能力的性状，这些性状由导致明显表型效应的单基因控制。然而，大多数重要的农艺性状，如产量和产量构成因素，都是受多基因控制并受环境影响的多基因性状。在过去的十年里，分子标记和遗传连锁图谱的应用使得基因组中控制多基因性状的特定区域被称为数量性状座位(QTL)，在所有主要作物物种中都能被识别出来。然而，尽管这些区域有丰富的位置信息，但真正克隆出的数量性状基因却很少。因此，关于这些基因的性质和功能，以及重要农艺性状遗传变异背后的分子机制的许多问题仍然没有得到回答。来自野生稻祖先(O.rufipogon)的QTL与优良栽培材料的开花时间、粒重和株高的自然变异相关的基因将被识别和表征。三个定位于水稻1号染色体的QTL将成为目标，1号染色体是第一批完全测序的水稻染色体之一。其具体目标是精细定位开花时间、粒重和株高的主效QTL，然后分离位于这些区域内的候选基因，最后通过与QTL潜在基因的转化来证明表型互补。我们将比较野生和栽培水稻、其他禾本科植物和拟南芥中目标QTL基因同源基因的序列差异，以获得进化的视角和对重要功能保守结构域的洞察。这项工作将产生与禾本科牧草重要农艺性状相关的基因的特性和功能意义的重要新信息，并将测试当目标区域有基因组序列时快速识别QTL基因的多方面策略。

To date, the map-based cloning and characterization of genes from crop species has largely been limited to monogenic traits, such as those providing disease resistance, that are controlled by single genes causing clear phenotypic effects. Most agronomically-important traits, such as yield and yield components, however, are polygenic traits controlled by multiple genes and influenced by the environment. Over the past decade, the application of molecular markers and genetic linkage maps has allowed specific regions of the genome controlling polygenic traits, called quantitative trait loci (QTLs), to be identified in all of the major crop species. In spite of the wealth of positional information for these regions, however, few genes underlying quantitative traits have actually been cloned. As a result, many questions concerning the nature and function of these genes, as well as the molecular mechanisms behind the genetic variation of agronomically-important traits, remain unanswered. The genes underlying QTLs derived from a wild rice ancestor (O. rufipogon) that are associated with natural variation for flowering time, grain weight, and plant height in elite cultivated material will be identified and characterized. Three QTLs that map to rice chromosome 1, one of the first rice chromosomes to be completely sequenced, will be targeted. The specific objectives are to fine-map major QTLs for flowering time, grain weight, and plant height, then to isolate candidate genes that are located within those regions and, finally, to demonstrate phenotypic complementation via transformation with genes underlying the QTLs. The sequence variation from orthologs of the genes underlying the target QTLs in wild and cultivated Oryza, other grasses, and Arabidopsis will be compared to gain an evolutionary perspective and insight into functionally-important conserved domains. This work will generate significant new information about the identity and functional significance of genes associated with agronomically-important traits in the grasses and will test a multi-faceted strategy for rapid identification of genes underlying QTLs when genomic sequence is available in the target region.