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KMID : 0381120140360040509
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Genes and Genomics
2014 Volume.36 No. 4 p.509 ~ p.525
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Genome-wide identification, characterization, and comparative phylogeny analysis of MADS-box transcription factors in Brassica rapa
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Rameneni Jana Jeevan
Dhandapani Vignesh
Paul Parameswari
Im Su-Bin
Oh Man-Ho
Choi Su-Ryun
Lim Yong-Pyo
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Abstract
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The involvement of MADS-box transcription factors in the development of seeds, flowers, and fruit is well known. Large numbers of MADS-box genes have been characterized and reported in major plants such as Arabidopsis thaliana (107), Oryza sativa (75), Zea mays (75), and Cucumis sativus (43). However, there is little information about MADS-box genes in the economically and morphologically important genus Brassica. Thus, we performed a series of computational analyses on the recently published Brassica rapa genome and identified 167 potential MADS-box genes. Chromosomal localization of these genes revealed many duplicate genes and 10 tandem repeats from B. rapa chromosomes, though none on A04, A08, and A10. Neighbor-joining phylogenetic analysis was performed between B. rapa, A. thaliana, O. sativa, Z. mays, and C. sativus genes, and type-I and type-II groups were differentiated by their gene clades. Based on their phylogeny and functional characters, type-I group was divided into three clades and type-II group into 14 clades. Prediction and comparison of intron and exon patterns of MADS-box genes authenticates the major difference between the groups. Semi-quantitative RT-PCR analysis was carried out for 25 functionally categorized BrMADS-box genes and comparatively studied among buds, sepals, petals, stamens, carpels, and siliques of the parental line RcBr. The structural and functional annotation, as well as expressional profiling of BrMADS in floral organs in this study will be the basis of further functional validation and molecular breeding of B. rapa crops.
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KEYWORD
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MADS-box gene family, Chinese cabbage, Brassica rapa, Molecular characterization, Evolution
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