Identification of rhizome-specific genes by genome-wide differential expression analysis in Oryza longistaminata.
Identification of rhizome-specific genes by genome-wide differential expression analysis in Oryza longistaminata.
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DOI：
10.1186/1471-2229-11-18
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发表时间：
2011-01-24
影响因子：
5.3
通讯作者：
Li Z
中科院分区：
文献类型：
--
作者：
Hu F;Wang D;Zhao X;Zhang T;Sun H;Zhu L;Zhang F;Li L;Li Q;Tao D;Fu B;Li Z
根茎性是许多禾草多年生的关键组成部分，有助于提高许多有害杂草的竞争力和入侵性，但可以潜在地用于为热带亚洲丘陵地区的可持续农民开发多年生谷类作物。长纵米（Oryza longistaminata）是一种具有强根茎的多年生野生水稻，已被用作根茎发育的遗传和分子解剖的模式物种，并在育种工作中将根茎相关性状转移到一年生水稻中。本研究利用Affymetrix基因芯片水稻基因组阵列（Affymetrix GeneChip Rice Genome Array）对水稻5个不同组织的全基因组组织特异性基因表达模式进行了比较分析，以期深入了解水稻根茎化性状的基因和分子机制。在5个不同组织中共鉴定出2566个组织特异性基因，其中在根尖（RT）和节间（RI）分别特异表达的基因58个和61个。与茎尖相比，RT中有162个基因上调，261个基因下调。6种不同的顺式调控元件（cacg、GCCGCC、GAGAC、AACGG、CATGCA和TAAAG）在RT中差异表达基因的启动子区域的丰度明显高于其他组织中均匀表达基因的启动子区域。许多RT和/或RI特异性或差异表达的基因位于与长叶薯蓣根茎表达、根茎丰度和根茎生长相关性状相关的QTL区域，因此是这些QTL的良好候选基因。根状茎性状的发生和发育受复杂的基因网络控制，涉及多种植物激素和调控基因、具有组织特异性的不同基因家族成员及其调控途径。生长素/IAA在根茎发育中起负调控作用，而GA在根茎发育中起激活作用。将根尖和根节间特异性表达基因与根茎性状qtl共定位，确定了大量水稻根茎形成和发育的候选基因，有待进一步证实。
Rhizomatousness is a key component of perenniality of many grasses that contribute to competitiveness and invasiveness of many noxious grass weeds, but can potentially be used to develop perennial cereal crops for sustainable farmers in hilly areas of tropical Asia. Oryza longistaminata, a perennial wild rice with strong rhizomes, has been used as the model species for genetic and molecular dissection of rhizome development and in breeding efforts to transfer rhizome-related traits into annual rice species. In this study, an effort was taken to get insights into the genes and molecular mechanisms underlying the rhizomatous trait in O. longistaminata by comparative analysis of the genome-wide tissue-specific gene expression patterns of five different tissues of O. longistaminata using the Affymetrix GeneChip Rice Genome Array. A total of 2,566 tissue-specific genes were identified in five different tissues of O. longistaminata, including 58 and 61 unique genes that were specifically expressed in the rhizome tips (RT) and internodes (RI), respectively. In addition, 162 genes were up-regulated and 261 genes were down-regulated in RT compared to the shoot tips. Six distinct cis-regulatory elements (CGACG, GCCGCC, GAGAC, AACGG, CATGCA, and TAAAG) were found to be significantly more abundant in the promoter regions of genes differentially expressed in RT than in the promoter regions of genes uniformly expressed in all other tissues. Many of the RT and/or RI specifically or differentially expressed genes were located in the QTL regions associated with rhizome expression, rhizome abundance and rhizome growth-related traits in O. longistaminata and thus are good candidate genes for these QTLs. The initiation and development of the rhizomatous trait in O. longistaminata are controlled by very complex gene networks involving several plant hormones and regulatory genes, different members of gene families showing tissue specificity and their regulated pathways. Auxin/IAA appears to act as a negative regulator in rhizome development, while GA acts as the activator in rhizome development. Co-localization of the genes specifically expressed in rhizome tips and rhizome internodes with the QTLs for rhizome traits identified a large set of candidate genes for rhizome initiation and development in rice for further confirmation.
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影响因子：
7.4
作者：
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