Arora Rita, Agarwal Pinky, Ray Swatismita, Singh Ashok Kumar, Singh Vijay Pal, Tyagi Akhilesh K, Kapoor Sanjay
Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India.
BMC Genomics. 2007 Jul 18;8:242. doi: 10.1186/1471-2164-8-242.
MADS-box transcription factors, besides being involved in floral organ specification, have also been implicated in several aspects of plant growth and development. In recent years, there have been reports on genomic localization, protein motif structure, phylogenetic relationships, gene structure and expression of the entire MADS-box family in the model plant system, Arabidopsis. Though there have been some studies in rice as well, an analysis of the complete MADS-box family along with a comprehensive expression profiling was still awaited after the completion of rice genome sequencing. Furthermore, owing to the role of MADS-box family in flower development, an analysis involving structure, expression and functional aspects of MADS-box genes in rice and Arabidopsis was required to understand the role of this gene family in reproductive development.
A genome-wide molecular characterization and microarray-based expression profiling of the genes encoding MADS-box transcription factor family in rice is presented. Using a thorough annotation exercise, 75 MADS-box genes have been identified in rice and categorized into MIKCc, MIKC*, Malpha, Mbeta and Mgamma groups based on phylogeny. Chromosomal localization of these genes reveals that 16 MADS-box genes, mostly MIKCc-type, are located within the duplicated segments of the rice genome, whereas most of the M-type genes, 20 in all, seem to have resulted from tandem duplications. Nine members belonging to the Mbeta group, which was considered absent in monocots, have also been identified. The expression profiles of all the MADS-box genes have been analyzed under 11 temporal stages of panicle and seed development, three abiotic stress conditions, along with three stages of vegetative development. Transcripts for 31 genes accumulate preferentially in the reproductive phase, of which, 12 genes are specifically expressed in seeds, and six genes show expression specific to panicle development. Differential expression of seven genes under stress conditions is also evident. An attempt has been made to gain insight into plausible functions of rice MADS-box genes by collating the expression data of functionally validated genes in rice and Arabidopsis.
Only a limited number of MADS genes have been functionally validated in rice. A comprehensive annotation and transcriptome profiling undertaken in this investigation adds to our understanding of the involvement of MADS-box family genes during reproductive development and stress in rice and also provides the basis for selection of candidate genes for functional validation studies.
MADS-box转录因子除参与花器官的特化外，还与植物生长发育的多个方面有关。近年来，在模式植物拟南芥中已有关于整个MADS-box家族的基因组定位、蛋白质基序结构、系统发育关系、基因结构和表达的报道。尽管在水稻中也有一些研究，但在水稻基因组测序完成后，仍有待对完整的MADS-box家族进行分析并进行全面的表达谱分析。此外，由于MADS-box家族在花发育中的作用，需要对水稻和拟南芥中MADS-box基因的结构、表达和功能方面进行分析，以了解该基因家族在生殖发育中的作用。
本文展示了水稻中编码MADS-box转录因子家族基因的全基因组分子特征分析和基于微阵列的表达谱分析。通过全面的注释工作，在水稻中鉴定出75个MADS-box基因，并根据系统发育将其分为MIKCc、MIKC*、Mα、Mβ和Mγ组。这些基因的染色体定位表明，16个MADS-box基因（大多为MIKCc型）位于水稻基因组的重复片段内，而大多数M型基因（共20个）似乎是串联重复产生的。还鉴定出了9个属于Mβ组的成员，单子叶植物中原本认为不存在该组。分析了所有MADS-box基因在穗和种子发育的11个时间阶段、三种非生物胁迫条件以及营养发育的三个阶段下的表达谱。31个基因的转录本在生殖阶段优先积累，其中12个基因在种子中特异性表达，6个基因在穗发育过程中特异性表达。7个基因在胁迫条件下的差异表达也很明显。通过整理水稻和拟南芥中功能已验证基因的表达数据，试图深入了解水稻MADS-box基因可能的功能。
在水稻中只有少数MADS基因的功能得到了验证。本研究中进行的全面注释和转录组分析有助于我们了解MADS-box家族基因在水稻生殖发育和胁迫过程中的作用，也为功能验证研究中候选基因的选择提供了依据。
