Whole-genome survey and characterization of MADS-box gene family in maize and sorghum

Abstract

MADS-box genes comprise a large gene family, which codes for transcription factors, and play important functions in various aspects of flowering plant growth and development. However, little is known about the MADS-box genes in maize (Zea mays) and sorghum (Sorghum bicolor). Here, we performed a comprehensive bioinformatics analysis of the MADS-box gene family in the maize and sorghum genomes and identified 75 maize and 65 sorghum MADS-box genes. We subsequently carried out a comparative analysis of these genes, including the gene structure, phylogenetic relationship, conserved protein motifs, gene duplications, chromosomal locations and expression pattern between the two plants. According to these analyses, the MADS-box genes in both maize and sorghum were categorized into five (MIKC C , MIKC*, Ma, Mb and Mc) groups, and the MIKC C groups were further divided into 11 subfamilies. In addition, gene duplications of MADS-box genes were also investigated in the maize, sorghum, rice and Arabidopsis genomes. We found a higher percentage of MADS-box gene duplications in the maize and sorghum genomes, which contributed to the expansion of the MADS-box gene family. Furthermore, both tandem and segmental duplications played a major role in the MADS-box gene expansion in maize and sorghum. A survey of maize and sorghum EST sequences indicated that MADS-box genes exhibit a various expression pattern, suggesting diverse and novel functions of MADS-box gene families in the two plants. These results provided a useful reference for selection of candidate MADS-box genes for cloning and further functional analysis in both maize and sorghum.

Molecular aspects of flower development in grasses

“…Although different MIKC-type genes have been isolated from several grass species (Bommert et al 2005;Whipple and Schmidt 2006;Dwivedi et al 2008), the most comprehensive cloning and characterization of genes encoding MADS-box transcription factors have been carried out in rice, maize, and sorghum (Munster et al 2002;Lee et al 2003a;Arora et al 2007;Zhao et al 2010), thanks to the completion of their whole-genome sequencing, and in wheat, wherein Paolacci et al (2007) carried out an extensive screening for MIKC-type cDNAs.…”

“…The evolutionary relationships between MIKC-type genes of grasses and Arabidopsis were assessed through phylogenetic reconstruction based on the alignment of 134 amino acid sequences deduced from the nucleotide sequences of 34 genes of Arabidopsis (Parenicova et al 2003), 31 of rice (Lee et al 2003a;Arora et al 2007), 40 of maize (Munster et al 2002;Zhao et al 2010), and 29 of wheat (Paolacci et al 2007) (Fig. 4).…”

“…So far, FLC-and AGL15-like genes have been found only in Arabidopsis and other Brassicaceae species (Becker and Theissen 2003). Co-orthologs of these genes have not been found in any grass species, even in the sequenced genomes of rice, maize, and sorghum (Becker and Theissen 2003;Arora et al 2007;Zhao et al 2010). These results demonstrate that the complexity of the MIKC branch of the MADS-box family of wheat, maize, and rice is similar to that of eudicots and that at least 11 different MIKC-type genes were already present in the last common ancestor of monocots and eudicots about 125-150 mya.…”

Conservation and Diversification of Floral Homeotic MADS-box Genes in Eustoma grandiflorum

“…Recent advances in whole-genome sequencing have enabled genome-wide analyses of the MADS-box gene family in economically important crops, such as in grapevine (Diaz-Riquelme et al, 2009), maize, sorghum (Zhao et al, 2011), cucumber (Hu and Liu, 2012), and soybean (Shu et al, 2013). The Arabidopsis, grapevine, and cucumber genomes contained 39, 38, and 30 MIKCtype MADS-box genes, respectively (Diaz-Riquelme et al, 2009;Hu and Liu, 2012;Par̆enicová et al, 2003).…”

Two FT orthologs from Populus simonii Carrière induce early flowering in Arabidopsis and poplar trees

“…Experiments on a variety of plant species have shown that inductive photoperiods cause leaves to emit a mobile signal termed 'florigen', which is a FT protein that travels from the vasculature to its site of action on the flanks of the shoot apical meristem (SAM). The FT protein acts at the shoot apex of the plant in concert with a transcription factor, FLOWERING LOCUS D (FD), to up-regulate expression of some MADSbox genes, such as AP1, a floral meristem identity gene and SOC1, a flowering-timing gene, and then induce the floral transition and initiation (Corbesier et al 2007;Jaeger and Wigge 2007;Mathieu et al 2007;Yang et al 2007;Zhao et al 2011).…”