Functional classification, genomic organization, putatively cis-acting regulatory elements, and relationship to quantitative trait loci, of sorghum genes with rhizome-enriched expression
Functional classification, genomic organization, putatively cis-acting regulatory elements, and relationship to quantitative trait loci, of sorghum genes with rhizome-enriched expression
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DOI：
10.1104/pp.106.082891
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发表时间：
2006-11-01
期刊：
影响因子：
7.4
通讯作者：
Paterson, Andrew H.
中科院分区：
文献类型：
--
作者：
Jang, Cheol Seong;Kamps, Terry L.;Paterson, Andrew H.
根状茎是植物竞争力和入侵性的重要器官。我们已经确定了基因的表达水平显着高于根茎比其他植物部分，并探讨其功能分类，基因组组织，调控基序，并与数量性状位点（QTL）赋予根茎。富含根茎表达的基因分布在广泛的功能类别中，这一发现表明根茎植物中许多基因家族的个体成员具有一定程度的专业化。一个不成比例的份额与根茎富集表达的基因牵连在次生和激素代谢，非生物刺激和发展。高频率的未知功能基因反映了我们对这种植物器官的认识仍然有限。一个假定的寡糖基转移酶表现出最高程度的根茎特异性表达，与几个转录或调节蛋白复合物因子也表现出高（但较低）程度的特异性。根据水稻（Oryza sativa）同源基因的上游序列推断，高粱（Sorbitum bicolor）根茎顶端组织中相对高表达的基因富含嘧啶盒、TATCCA盒和CAREs盒等顺式元件，表明赤霉素参与了许多根茎特异性基因的调控。从显示根茎富集表达的cDNA克隆中，表达的序列标签形成455个重叠群，绘制在水稻基因组上，并与水稻和高粱中再生和根茎性状的QTL似然区间进行比对。高度表达的根茎基因在一定程度上丰富了根茎或再生的QTL似然区间，具体的候选人，包括一些最根茎特异性基因。一些根状茎和再生QTL被证明是潜在的相互关联的结果古老的重复，这表明长期的功能保守的潜在基因。深入了解影响根茎生长的基因和途径，为遗传和/或外源操纵根茎性以及进一步解剖根茎性的分子进化奠定了基础。
Rhizomes are organs of fundamental importance to plant competitiveness and invasiveness. We have identified genes expressed at substantially higher levels in rhizomes than other plant parts, and explored their functional categorization, genomic organization, regulatory motifs, and association with quantitative trait loci (QTLs) conferring rhizomatousness. The finding that genes with rhizome-enriched expression are distributed across a wide range of functional categories suggests some degree of specialization of individual members of many gene families in rhizomatous plants. A disproportionate share of genes with rhizome-enriched expression was implicated in secondary and hormone metabolism, and abiotic stimuli and development. A high frequency of unknown-function genes reflects our still limited knowledge of this plant organ. A putative oligosaccharyl transferase showed the highest degree of rhizome-specific expression, with several transcriptional or regulatory protein complex factors also showing high ( but lesser) degrees of specificity. Inferred by the upstream sequences of their putative rice ( Oryza sativa) homologs, sorghum ( Sorghum bicolor) genes that were relatively highly expressed in rhizome tip tissues were enriched for cis-element motifs, including the pyrimidine box, TATCCA box, and CAREs box, implicating the gibberellins in regulation of many rhizome-specific genes. From cDNA clones showing rhizome-enriched expression, expressed sequence tags forming 455 contigs were plotted on the rice genome and aligned to QTL likelihood intervals for ratooning and rhizomatous traits in rice and sorghum. Highly expressed rhizome genes were somewhat enriched in QTL likelihood intervals for rhizomatousness or ratooning, with specific candidates including some of the most rhizome-specific genes. Some rhizomatousness and ratooning QTLs were shown to be potentially related to one another as a result of ancient duplication, suggesting long-term functional conservation of the underlying genes. Insight into genes and pathways that influence rhizome growth set the stage for genetic and/or exogenous manipulation of rhizomatousness, and for further dissection of the molecular evolution of rhizomatousness.