Genome-wide evolutionary characterization and expression analysis of SIAMESE-RELATED family genes in maize

Abstract

Background: The SIAMESE (SIM) locus is a cell-cycle kinase inhibitor (CKI) gene that has to date been identified only in plants; it encodes a protein that promotes transformation from mitosis to endoreplication. Members of the SIAMESE-RELATED (SMR) family have similar functions, and some are related to cell-cycle responses and abiotic stresses. However, the functions of SMRs are poorly understood in maize (Zea mays L.).

Results: In the present study, 12 putative SMRs were identified throughout the entire genome of maize, and these were clustered into six groups together with the SMRs from seven other plant species. Members of the ZmSMR family were divided into four groups according to their protein sequences. Various cis-acting elements in the upstream sequences of ZmSMRs responded to abiotic stresses. Expression analyses revealed that all ZmSMRs were upregulated at 5, 20, 25, and 35 days after pollination. In addition, we found that ZmSMR9/11/12 may have regulated the initiation of endoreplication in endosperm central cells. Additionally, ZmSMR2/10 may have been primarily responsible for the endoreplication regulation of outer endosperm or aleurone cells. The relatively high expression levels of almost all ZmSMRs in the ears and tassels also implied that these genes may function in seed development. The effects of treatments with ABA, heat, cold, salt, and drought on maize seedlings and expression of ZmSMR genes suggested that ZmSMRs were strongly associated with response to abiotic stresses.

Conclusion: The present study is the first to conduct a genome-wide analysis of members of the ZmSMR family by investigating their locations in chromosomes, identifying regulatory elements in their promoter regions, and examining motifs in their protein sequences. Expression analysis of different endosperm developmental periods, tissues, abiotic stresses, and hormonal treatments suggests that ZmSMR genes may function in endoreplication and regulate the development of reproductive organs. These results may provide valuable information for future studies of the functions of the SMR family in maize.

Keywords: Endoreduplication; Endosperm; Gene expression; Genome-wide analysis; Maize; Stress tolerance; ZmSMR gene family.

Fig. 1

Chromosomal distribution of 12 ZmSMR genes. The chromosome number is indicated on the top of each chromosome. The value of the position of each gene and centromere on the chromosome is labeled on the right side of the chromosome bar. The scale of the chromosome length is 50 px = 50 Mb

Fig. 2

Distribution of genome syntenic and intergenomic synteny SMR gene pairs in multiple species. Analyzed species are Zea mays (Zmchr), Brachypodium distachyon (Bdchr), Oryza sativa (Oschr), Sorghum bicolor (Sbchr), Setaria italic (Sichr), Populus trichocarpa (Ptchr) and Glycine max (Gmchr). The scale line of the chromosome size is also identified in the figure

Fig. 3

Phylogenetic analysis and motif composition of ZmSMR proteins. The phylogenetic tree was constructed using MEGA6 software by the Neighbor-joining method with 1000 bootstrap iterations based on the 12 full-length amino acids of ZmSMR, and the proteins were clustered into four subgroups (A, B, C, D) marked with different background to facilitate subfamily identification. Schematic representation of the conserved motifs in the ZmSMR proteins was analyzed by MEME. Each motif is represented by a colored box numbered at the bottom, and the consensus sequences of each motif are also shown. The details of sequence logo of the motifs are given in Additional file 6

Fig. 4

Phylogenetic tree of SMR proteins from Z. mays, Arabidopsis, O. sativa and other species. The complete amino acid sequences of 12 Z. mays, 28 Arabidopsis, 17 O. sativa and 71 SMR proteins from other species were aligned by ClustalW, and the phylogenetic tree was constructed using Molecular Evolutionary Genetics Analysis 6 (MEGA6.06) by the Neighbor-joining method with 1000 bootstrap replicates. Each species’ gene is labeled with a different symbol. ZmSMR represents Z. mays SMR; AtSMR represents A. thaliana SMR; OsSMR represents O. sativa SMR; BdSMR represents B. distachyod SMR; SiSMR represents S. italica SMR; SbSMR represents Sorghum bicolor SMR; GmSMR represents Glycine max SMR; PtSMR represents Populus trichocarpa SMR; PpSMR represent Physcomitrella patens SMR. The phylogenetic tree was divided into six phylogenetic groups as Group I-VII using different colors

Fig. 5

Grain-filling rate and expression profile of the ZmSMR family genes in maize endosperm. a The grain-filling rate was measured from 5 to 35 DAP every 5 days. The trendline was drawn through the weight increase of hundred-grain weight every 5 days. b The maize endosperm samples were taken every 5 days from 5 to 35 DAP. Relative expression ratios in these sample were calculated with reference to the sample in which the respective transcript exhibited the lowest expression. The relative expression values were log2 transformed. The qRT-PCR data were normalized against the expression of Actin as an internal control. Error bars indicate standard deviations. The names of the genes are written in the upper right corner of each bar diagram

Fig. 6

Expression analysis of 12 ZmSMR genes in different tissues. Relative quantities of 12 ZmSMR members in Root, Leaf, Internode (IN), Node, Ear and Tassel (TL) tissues of maize determined using qRT-PCR. Relative quantities in different tissue samples were calculated with reference to tissue samples in which the respective transcript exhibited the lowest expression. The relative expression values were log2 transformed. The qRT-PCR data were normalized against the expression of Actin as an internal control. Error bars indicate standard deviations. Gene-specific primers were used for qRT-PCR analysis of ZmSMR genes

Fig. 7

Expression profiles of ZmSMR genes under various abiotic conditions. The x-axes represent treatment time, and y-axes indicate scales of relative expression levels. Three-leaf maize seedlings were treated with 4 °C (low temperature), 42 °C (high temperature), or 100 μM of ABA for 24 h, or with 20% PEG and 200 mM of NaCl for 72 h. Mixed leaves of three seedlings as well as the untreated leaves were collected after treatment for 2, 6, 12, 24, 48, 72 h, where the untreated leaves were regarded as the control check (CK). The relative expression values were log2 transformed. The qRT-PCR data were normalized against the expression of Actin as an internal control. Error bars indicate standard deviations