Identification and functional analysis of light-responsive unique genes and gene family members in rice.
Identification and functional analysis of light-responsive unique genes and gene family members in rice.
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DOI：
10.1371/journal.pgen.1000164
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发表时间：
2008-08-22
期刊：
影响因子：
4.5
通讯作者：
Ronald PC
中科院分区：
文献类型：
--
作者：
Jung KH;Lee J;Dardick C;Seo YS;Cao P;Canlas P;Phetsom J;Xu X;Ouyang S;An K;Cho YJ;Lee GC;Lee Y;An G;Ronald PC
功能冗余限制了许多生物体中基因的详细分析。在这里，我们报告了一种方法，以有效地克服这一障碍相结合的基因表达数据与基因索引突变体的分析。使用水稻NSF 45 K寡核苷酸微阵列比较2周龄的光和黑暗生长的水稻叶片组织，我们确定了365个基因，显示出显着的8倍或更高的诱导，在光相对于黑暗条件。然后，我们筛选水稻T-DNA插入突变体的集合，以确定在强光诱导的基因突变的水稻品系。从这个分析中，我们确定了74个不同的线，包括两个独立的突变株系的37个光诱导基因。通过挖掘基因表达数据来进一步细化该列表，以排除由于共表达的家族成员而具有潜在功能冗余的基因（12个基因）和在其他公开可用的微阵列数据集中具有不一致的光响应的基因（5个基因）。接下来，我们描述了在剩下的10个候选基因中携带突变的水稻品系的表型，然后进行了与这些基因相关的共表达分析。该分析有效地提供了两个先前未知功能的基因和一个与测试的生化途径不直接相关的基因的候选功能。这些数据表明，即使在多基因家族的成员中，基于基因家族的表达谱与插入突变体的分析相结合以鉴定新基因及其功能的效率。水稻是单子叶植物的典范，也是第一个完成全基因组测序的作物。虽然全基因组转录组分析工具和全基因组，基因索引的突变体收集已产生的水稻，只有少数水稻基因的功能已被揭示迄今。研究水稻等作物的功能基因组学方法在维护植物方面比研究拟南芥（一种模式双子叶植物）更加劳动密集和困难。在这里，我们描述了一种有效的方法来解剖基因功能的水稻和其他作物。我们确定了10个基因的光响应相关的表型，其功能是以前未知的水稻。我们还进行了72个基因的共表达分析，这些基因参与了这10个基因中携带突变的特定生化途径。这一分析导致了一组新的基因可能参与这些途径的鉴定。农作物功能基因组学的快速进展将为在不久的将来克服粮食危机做出重大贡献。
Functional redundancy limits detailed analysis of genes in many organisms. Here, we report a method to efficiently overcome this obstacle by combining gene expression data with analysis of gene-indexed mutants. Using a rice NSF45K oligo-microarray to compare 2-week-old light- and dark-grown rice leaf tissue, we identified 365 genes that showed significant 8-fold or greater induction in the light relative to dark conditions. We then screened collections of rice T-DNA insertional mutants to identify rice lines with mutations in the strongly light-induced genes. From this analysis, we identified 74 different lines comprising two independent mutant lines for each of 37 light-induced genes. This list was further refined by mining gene expression data to exclude genes that had potential functional redundancy due to co-expressed family members (12 genes) and genes that had inconsistent light responses across other publicly available microarray datasets (five genes). We next characterized the phenotypes of rice lines carrying mutations in ten of the remaining candidate genes and then carried out co-expression analysis associated with these genes. This analysis effectively provided candidate functions for two genes of previously unknown function and for one gene not directly linked to the tested biochemical pathways. These data demonstrate the efficiency of combining gene family-based expression profiles with analyses of insertional mutants to identify novel genes and their functions, even among members of multi-gene families. Rice, a model monocot, is the first crop plant to have its entire genome sequenced. Although genome-wide transcriptome analysis tools and genome-wide, gene-indexed mutant collections have been generated for rice, the functions of only a handful of rice genes have been revealed thus far. Functional genomics approaches to studying crop plants like rice are much more labor-intensive and difficult in terms of maintaining the plants than when studying Arabidopsis, a model dicot. Here, we describe an efficient method for dissecting gene function in rice and other crop plants. We identified light response-related phenotypes for ten genes, the functions for which were previously unknown in rice. We also carried out co-expression analysis of 72 genes involved in specific biochemical pathways connected in lines carrying mutations in these ten genes. This analysis led to the identification of a novel set of genes likely involved in these pathways. The rapid progress of functional genomics in crops will significantly contribute to overcoming a food crisis in the near future.
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影响因子：
7.4
作者：
Agrawal, GK;Yamazaki, M;Hirochika, H
通讯作者：
Hirochika, H
影响因子：
11.6
作者：
Guevara-García, A;San Román, C;León, P
通讯作者：
León, P
影响因子：
7.2
作者：
Burlat, V;Oudin, A;St-Pierre, B
通讯作者：
St-Pierre, B
影响因子：
3.1
作者：
Fujino, K;Sekiguchi, H;Kiguchi, T
通讯作者：
Kiguchi, T
影响因子：
11.6
作者：
Coschigano, KT;Melo-Oliveira, R;Coruzzi, GM
通讯作者：
Coruzzi, GM