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Genome-wide analysis of the MADS-box gene family in Brassica rapa (Chinese cabbage)

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Abstract

The MADS-box gene family is an ancient and well-studied transcription factor family that functions in almost every developmental process in plants. There are a number of reports about the MADS-box family in different plant species, but systematic analysis of the MADS-box transcription factor family in Brassica rapa (Chinese cabbage) is still lacking. In this study, 160 MADS-box transcription factors were identified from the entire Chinese cabbage genome and compared with the MADS-box factors from 21 other representative plant species. A detailed list of MADS proteins from these 22 species was sorted. Phylogenetic analysis of the BrMADS genes, together with their Arabidopsis and rice counterparts, showed that the BrMADS genes were categorised into type I (Mα, Mβ, Mγ) and type II (MIKCC, MIKC*) groups, and the MIKCC proteins were further divided into 13 subfamilies. The Chinese cabbage type II group has 95 members, which is twice as much as the Arabidopsis type II group, indicating that the Chinese cabbage type II genes have been retained more frequently than the type I genes. Finally, RNA-seq transcriptome data and quantitative real-time PCR analysis revealed that BrMADS genes are expressed in a tissue-specific manner similar to Arabidopsis. Interestingly, a number of BrMIKC genes showed responses to different abiotic stress treatments, suggesting a function for some of the genes in these processes as well. Taken together, the characterization of the B. rapa MADS-box family presented here, will certainly help in the selection of appropriate candidate genes and further facilitate functional studies in Chinese cabbage.

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Acknowledgments

This work is supported by the National Basic Research Program of China (973 Program, 2012CB113903), the Fundamental Research Funds for the Central Universities of China (KYZ201111), the National Natural Science Foundation of China (31272173, 1301782) and the Jiangsu Province Natural Science Foundation (BK20130673).

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  1. State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, People’s Republic of China

    Weike Duan, Xiaoming Song, Tongkun Liu, Zhinan Huang, Jun Ren, Xilin Hou & Ying Li

  2. Key laboratory of Biology and Germplasm Enhancement of Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, People’s Republic of China

    Weike Duan, Xiaoming Song, Tongkun Liu, Zhinan Huang, Jun Ren, Xilin Hou & Ying Li

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  1. Weike Duan
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  2. Xiaoming Song
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  3. Tongkun Liu
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  4. Zhinan Huang
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Correspondence to Ying Li.

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Communicated by S. Hohmann.

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Duan, W., Song, X., Liu, T. et al. Genome-wide analysis of the MADS-box gene family in Brassica rapa (Chinese cabbage). Mol Genet Genomics 290, 239–255 (2015). https://doi.org/10.1007/s00438-014-0912-7

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