Mol Genet Genomics (2015)290:239-255 D0I10.1007/s00438-014-0912.7 ORIGINAL PAPER Genome-wide analysis of the MADS-box gene family in Brassica rapa(Chinese cabbage) Weike Duan·Xiaoming Song·Tongkun Liu· Zhinan Huang·Jun Ren·Xilin Hou·Ying Li Received:29 June 2014/Accepted:28 August 2014 /Published online:13 September 2014 Springer-Verlag Berlin Heidelberg 2014 Abstract The MADS-box gene family is an ancient and the type I genes.Finally,RNA-seq transcriptome data and well-studied transcription factor family that functions in quantitative real-time PCR analysis revealed that BrMADS almost every developmental process in plants.There are a genes are expressed in a tissue-specific manner similar to number of reports about the MADS-box family in differ- Arabidopsis.Interestingly,a number of BrMIKC genes ent plant species,but systematic analysis of the MADS-box showed responses to different abiotic stress treatments,sug- transcription factor family in Brassica rapa (Chinese cab- gesting a function for some of the genes in these processes bage)is still lacking.In this study,160 MADS-box tran- as well.Taken together,the characterization of the B.rapa scription factors were identified from the entire Chinese MADS-box family presented here,will certainly help in the cabbage genome and compared with the MADS-box factors selection of appropriate candidate genes and further facilitate from 21 other representative plant species.A detailed list of functional studies in Chinese cabbage. MADS proteins from these 22 species was sorted.Phylo- genetic analysis of the BrMADS genes,together with their Keywords Abiotic stress.Chinese cabbage.Genome- Arabidopsis and rice counterparts,showed that the BrMADS wide analysis.MADS-box transcription factor.qRT-PCR genes were categorised into type I (Ma,MB,My)and type II (MIKCC,MIKC*)groups,and the MIKCC proteins were further divided into 13 subfamilies.The Chinese cabbage Introduction type II group has 95 members,which is twice as much as the Arabidopsis type II group,indicating that the Chinese cab- MADS-box genes encode transcription factors that are bage type II genes have been retained more frequently than involved in developmental control and signal transduction in eukaryotes (Riechmann and Meyerowitz 1997).These Communicated by S.Hohmann genes are found in fungi (Passmore et al.1988),animals (Norman et al.1988)and plants (Sommer et al.1990; Electronic supplementary material The online version of this Yanofsky et al.1990).They constitute a large gene family. article(doi:10.1007/s00438-014-0912-7)contains supplementary which is named after a few of its earliest members,MCMI material,which is available to authorized users. (from yeast)(Passmore et al.1988),AGAMOUS (from W.Duan.X.Song.T.Liu.Z.Huang J.Ren.X.Hou. A.thaliana)(Yanofsky et al.1990).DEFICIENS (from Y.Li(☒) Antirrhinum majus)(Sommer et al.1990)and SRF(from State Key Laboratory of Crop Genetics and Germplasm Homo sapiens)(Norman et al.1988).Previous studies of Enhancement,Ministry of Agriculture,Nanjing Agricultural University,Nanjing 210095,People's Republic of China the MADS-box genes have included a thorough compari- e-mail:yingli@njau.edu.cn son analysis of their roles in plant growth and development. However,there are relatively few analyses of the response W.Duan.X.Song.T.Liu.Z.Huang.J.Ren.X.Hou.Y.Li of these genes to stress conditions.Brassica rapa ssp.peki- Key laboratory of Biology and Germplasm Enhancement nensis (Chinese cabbage)is one of the subspecies of Bras- of Crops in East China,Ministry of Agriculture,Nanjing Agricultural University,Nanjing 210095,People's Republic sica rapa.This subspecies,which originated in China,is of China one of the most economically significant vegetable crops 鱼Springer1 3 Mol Genet Genomics (2015) 290:239–255 DOI 10.1007/s00438-014-0912-7 ORIGINAL PAPER Genome‑wide analysis of the MADS‑box gene family in Brassica rapa (Chinese cabbage) Weike Duan · Xiaoming Song · Tongkun Liu · Zhinan Huang · Jun Ren · Xilin Hou · Ying Li Received: 29 June 2014 / Accepted: 28 August 2014 / Published online: 13 September 2014 © Springer-Verlag Berlin Heidelberg 2014 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, sug￾gesting 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. Keywords Abiotic stress · Chinese cabbage · Genome￾wide analysis · MADS-box transcription factor · qRT-PCR Introduction MADS-box genes encode transcription factors that are involved in developmental control and signal transduction in eukaryotes (Riechmann and Meyerowitz 1997). These genes are found in fungi (Passmore et al. 1988), animals (Norman et al. 1988) and plants (Sommer et al. 1990; Yanofsky et al. 1990). They constitute a large gene family, which is named after a few of its earliest members, MCM1 (from yeast) (Passmore et al. 1988), AGAMOUS (from A. thaliana) (Yanofsky et al. 1990), DEFICIENS (from Antirrhinum majus) (Sommer et al. 1990) and SRF (from Homo sapiens) (Norman et al. 1988). Previous studies of the MADS-box genes have included a thorough compari￾son analysis of their roles in plant growth and development. However, there are relatively few analyses of the response of these genes to stress conditions. Brassica rapa ssp. peki￾nensis (Chinese cabbage) is one of the subspecies of Bras￾sica rapa. This subspecies, which originated in China, is one of the most economically significant vegetable crops 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 differ￾ent plant species, but systematic analysis of the MADS-box transcription factor family in Brassica rapa (Chinese cab￾bage) is still lacking. In this study, 160 MADS-box tran￾scription 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. Phylo￾genetic 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 cab￾bage type II genes have been retained more frequently than Communicated by S. Hohmann. Electronic supplementary material The online version of this article (doi:10.1007/s00438-014-0912-7) contains supplementary material, which is available to authorized users. W. Duan · X. Song · T. Liu · Z. Huang · J. Ren · X. Hou · Y. Li (*) State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China e-mail: yingli@njau.edu.cn W. Duan · X. Song · T. Liu · Z. Huang · J. Ren · X. Hou · Y. Li 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