Abstract
The MADS-box gene family is an important transcription factor (TF) family that is involved in various aspects of plant growth and development, especially flowering time and floral organogenesis. Although it has been reported in many plant species, the systematic identification and characterization of MADS-box TF family is still limited in radish (Raphanus sativus L.). In the present study, a comprehensive analysis of MADS-box genes was performed, and a total of 144 MADS-box family members were identified from the whole radish genome. Meanwhile, a detailed list of MADS-box genes from other 28 plant species was also investigated. Through the phylogenetic analysis between radish and Arabidopsis thaliana, all the RsMADS genes were classified into two groups including 68 type I (31 Mα, 12 Mβ and 25Mγ) and 76 type II (70 MIKCC and 6 MIKC∗). Among them, 41 (28.47%) RsMADS genes were located in nine linkage groups of radish from R1 to R9. Moreover, the homologous MADS-box gene pairs were identified among radish, A. thaliana, Chinese cabbage and rice. Additionally, the expression profiles of RsMADS genes were systematically investigated in different tissues and growth stages. Furthermore, quantitative real-time PCR analysis was employed to validate expression patterns of some crucial RsMADS genes. These results could provide a valuable resource to explore the potential functions of RsMADS genes in radish, and facilitate dissecting MADS-box gene-mediated molecular mechanisms underlying flowering and floral organogenesis in root vegetable crops.
Highlights
MADS-box genes, which were primarily identified as floral homeotic genes, encode a family of transcription factors (TFs) containing a highly conserved MADS domain of approximately 60-amino-acid sequences in the N-terminal region (Norman et al, 1988), which bind to (CC[A/T]6GG) that is known as CArG boxes (Pellegrini et al, 1995; Shore and Sharrocks, 1995; Sasaki et al, 2010)
To define the candidate MADS-box proteins in radish, a profile hidden Markov model (HMM) search against NODAI radish genome protein sequences was carried out using the SRF-TF domain (PF00319), and totally 157 putative MADSbox protein genes were obtained
To study the comparative evolution among various plant species, MADS-box genes from 28 other plant species were collected by searching for SRF-TF domain (PF00319) in their genomes (Figure 1A; Supplementary Tables S3 and S4)
Summary
MADS-box genes, which were primarily identified as floral homeotic genes, encode a family of transcription factors (TFs) containing a highly conserved MADS domain of approximately 60-amino-acid sequences in the N-terminal region (Norman et al, 1988), which bind to (CC[A/T]6GG) that is known as CArG boxes (Pellegrini et al, 1995; Shore and Sharrocks, 1995; Sasaki et al, 2010). Type I proteins are further divided into three subgroups including Mα, Mβ and Mγ, while type II can be classified into the subgroups MIKCC and MIKC∗ according to the sequence divergence at I domain (De Bodt et al, 2003; Wells et al, 2015). The most well-known MADS-box proteins belong to MIKC-type proteins which contains four common domains including MADS (M), Intervening (I), Keratin (K) and the C-terminal (C) domain (Kaufmann et al, 2005). Among the 46 Type II genes, 39 MIKCC type genes were further classified into 12 groups based on their phylogenetic relationships, there were only seven genes belonging to the MIKC∗ type (Duan et al, 2015)
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