Genome-wide identification and expression analysis of the GRAS family proteins in <Emphasis Type="Italic">Medicago truncatula</Emphasis>

The GRAS gene family performs a variety of functions in plant growth and development processes, and they also play essential roles in plant response to environmental stresses. Medicago truncatula is a diploid plant with a small genome used as a model organism. Despite the vital role of GRAS genes in plant growth regulation, few studies on these genes in M. truncatula have been conducted to date. Using the M. truncatula reference genome data, we identified 68 MtGRAS genes, which were classified into 16 groups by phylogenetic analysis, located on eight chromosomes. The structure analysis indicated that MtGRAS genes retained a relatively constant exon–intron composition during the evolution of the M. truncatula genome. Most of the closely related members in the phylogenetic tree had similar motif compositions. Different motifs distributed in different groups of the MtGRAS genes were the sources of their functional divergence. Twenty-eight MtGRAS genes were expressed in six tissues, namely root, bud, blade, seedpod, nodule, and flower tissues, suggesting their putative function in many aspects of plant growth and development. Nine MtGRAS genes were upregulated under cold, freezing, drought, ABA, and salt stress treatments, indicating that they play vital roles in the response to abiotic stress in M. truncatula. Our study provides valuable information that can be utilized to improve the quality and agronomic benefits of M. truncatula and other plants.     

Genome-wide identification,systematic analysis and characterization of <Emphasis Type="Italic">SRO</Emphasis> family genes in maize (<Emphasis Type="Italic">Zea mays</Emphasis> L.)

SIMILAR TO RCD ONE (SRO) is a small plant-specific gene family, which play essential roles in plant growth and development as well as in abiotic stresses. However, the function of SROs in maize is still unknown. In our study, six putative SRO genes were isolated from the maize genome. A systematic analysis was performed to characterize the ZmSRO gene family. The ZmSRO gene family was divided into two groups according to the motif and intron/exon analysis. Phylogenetic analysis of them with other plants showed that the clades of SROs along with the divergence of monocot and dicot and ZmSROs were more closely with OsSROs. Many abiotic stress response and hormone-induced cis-regulatory elements were identified from the promoter region of ZmSROs. Furthermore, RNA-seq analysis indicated that SRO genes were widely expressed in different tissues and development stages in maize, and the expression divergence was also obviously observed. Analyses of expression in response to PEG6000 and NaCl treatment, in addition to exogenous application of ABA and GA hormones showed that the majority of the members display stress-induced expression patterns. Taken together, our results provide valuable reference for further functional analysis of the SRO gene family in maize, especially in abiotic stress responses.     

Vernalization and Photoperiods Mediated IAA and ABA Synthesis Genes Expression in <Emphasis Type="Italic">Beta vulgaris</Emphasis>

Biennial plants perceived seasonal stimuli through the photoperiods and vernalization pathways respectively to optimize developmental time. Photoperiods combining with vernalization modulate hormone homeostasis to promote plant normally growth. IAA and ABA play important roles in plant development. Although a series of IAA and ABA genes and their regulation mechanisms have been investigated and characterized extensively in model plants, these underlined mechanisms in Beta vulgaris L. especially under abiotic stress were not entirely clear. This study aimed at exploring IAA and ABA biosynthetic pathway genes and investigating their expression patterns and quantitating analysis hormone by UPLC-MS/MS (ultra performance liquid chromatography-tandem mass spectrometry) in order to demonstrate the molecular mechanism of phytohormone in B. vulgaris. As the results showed BvNIT4 and BvIAA8 contributed to IAA accumulation under nonvernalization condition. Endogenous ABA accumulation in leaves was contributed coordinately by the expression of BvABA2 and BvNCED1 genes both in the vernalized and nonvernalized samples under long day conditions. Vernalization and photoperiods indeed disturb phytohormone genes expression patterns, which data were consistent with the previous studies. New insight was provided to further clarify the molecular mechanism of endogenous hormone in B. vulgaris.     

Bioinformatic and expression analyses on carotenoid dioxygenase genes in fruit development and abiotic stress responses in <Emphasis Type="Italic">Fragaria vesca</Emphasis>

Carotenoid dioxygenases, including 9-cis-epoxycarotenoid dioxygenases (NCEDs) and carotenoid cleavage dioxygenases (CCDs), can selectively cleave carotenoids into various apocarotenoid products that play important roles in fleshy fruit development and abiotic stress response. In this study, we identified 12 carotenoid dioxygenase genes in diploid strawberry Fragaria vesca, and explored their evolution with orthologous genes from nine other species. Phylogenetic analyses suggested that the NCED and CCDL groups moderately expanded during their evolution, whereas gene numbers of the CCD1, CCD4, CCD7, and CCD8 groups maintained conserved. We characterized the expression profiles of FveNCED and FveCCD genes during flower and fruit development, and in response to several abiotic stresses. FveNCED1 expression positively responded to osmotic, cold, and heat stresses, whereas FveNCED2 was only induced under cold stress. In contrast, FveNCED2 was the unique gene highly and continuously increasing in receptacle during fruit ripening, which co-occurred with the increase in endogenous abscisic acid (ABA) content previously reported in octoploid strawberry. The differential expression patterns suggested that FveNCED1 and FveNCED2 were key genes for ABA biosynthesis in abiotic stress responses and fruit ripening, respectively. FveCCD1 exhibited the highest expression in most stages of flower and fruit development, while the other FveCCDs were expressed in a subset of stages and tissues. Our study suggests distinct functions of FveNCED and FveCCD genes in fruit development and stress responses and lays a foundation for future study to understand the roles of these genes and their metabolites, including ABA and other apocarotenoid products, in the growth and development of strawberry.     

Characterization and expression analysis of cytokinin biosynthesis genes in <Emphasis Type="Italic">Fragaria vesca</Emphasis>

Strawberry is one of the most economically important fruit crops in the world. Cytokinins (CKs) play a critical role in plant growth and development, as well as the stress response, and the level of CKs in plants is regulated by synthesis and degradation pathways. The key synthetic enzymes of CKs are isopentenyl transferases (IPTs) and LONELY GUYS (LOGs). We surveyed the strawberry genome and identified seven FvIPT genes and nine FvLOG genes. We analyzed gene structures, conserved domains, and their phylogenetic relationships with rice and Arabidopsis. The isoelectric points and glycosylation sites of the proteins were predicted. We also analyzed tissue- or organ-specific expression patterns of the FvIPT and FvLOG genes. The FvIPT and FvLOG genes showed different expression profiles in different organs. Most FvIPT and FvLOG genes were down-regulated in response to osmotic stress, high-temperature treatment, and exogenous abscisic acid (ABA) application, suggesting possible roles of these genes in the plants’ resistance to abiotic stresses. In addition, we found that the results of bioinformatics analyses to identify cis-regulatory elements may not be consistent with experimental expression data; thus, computer-predicted putative cis-elements need to be confirmed by experiments. Our systematic analyses of the FvIPT and FvLOG families provide a foundation for characterizing the function of these genes in the regulation of growth, development, and stress tolerance in Fragaria vesca, as well as a reference for improving stress tolerance by manipulating CK content.     

Identification and expression analysis of cytokinin response regulators in <Emphasis Type="Italic">Fragaria vesca</Emphasis>

Cytokinin response regulators (RRs) are important components of the two component signal systems, which are involved in the regulation of plant growth and development, and in the response to abiotic stress. In this study, 18 cytokinin RR genes were identified in Fragaria vesca through the genome-wide search. They were further classified into three types: type-A (FvRR1–7), type-B (FvRR8–14) and type-C (FvRR15–18) according to the domain architecture and the phylogeny. Phylogenetic analysis demonstrated that most cytokinin response regulators of F. vesca and Arabidopsis formed clear orthologous pairs. Expression patterns of the cytokinin FvRR genes in various tissues and organs at reproductive stages were detected in this study. Additionally, gene expression response patterns to ABA and abiotic stresses including high temperature and osmotic stress were investigated. The results showed that different types of cytokinin FvRRs have different expression patterns, suggesting the functional differentiation of cytokinin FvRRs during the evolution. This systematic study provides insights into possible functions of the cytokinin FvRR genes and a basis for further functional analysis.