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Gene. 2006 Aug 15;378:84-94. Epub 2006 Jul 10.

Genome-wide analysis of the MADS-box gene family in Populus trichocarpa.

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Department of Biological Sciences, Northern Illinois University, DeKalb, IL 60115, USA.


Populus trichocarpa (poplar) is distinguished from its herbaceous counterparts Arabidopsis and rice by its woody structure, perennial life cycle, and dioecious, two-whorled flowers. MADS-box genes are known to be involved in many important processes during plant development. Investigation of the poplar genome revealed 105 putative functional MADS-box genes and 12 pseudogenes. These numbers are comparable to those in Arabidopsis. However, poplar has 64 type II MADS-box genes, implying a higher birth rate when compared with Arabidopsis (64 vs.47). In addition to duplications for floral organ identity genes, TM3-like, StMADS11, ANR1 and Bs clades were significantly increased. As indicated by the phylogenetic analysis, there exist at least two MIKC* MADS-box genes in the poplar genome. In contrast, only 41 putative functional type I genes and 9 pseudogenes were found, suggesting that the poplar type I MADS-box genes have experienced a lower rate in both birth and death. Poplar MADS-box genes were distributed on all linkage groups (LGs), except LG XIX. Like other gene families, poplar MADS-box gene family has expanded through tandem gene duplication and segmental duplication events as demonstrated by two genomic regions where clustered MADS-box genes exhibited high similarities in the MADS-box domains. A survey of poplar EST sequences showed that MADS-box genes were expressed in wood and cambium tissues, which are specific to woody plants. The expression of common MADS-box gene in tree-specific tissues suggests that the novel function combinations of a set of genes similar to those in herbaceous plants may account for the development of woody characteristics in poplar.

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