Systematic Analysis of Sequences and Expression Patterns of Drought-Responsive Members of the HD-Zip Gene Family in Maize

Abstract

BackgroundMembers of the homeodomain-leucine zipper (HD-Zip) gene family encode transcription factors that are unique to plants and have diverse functions in plant growth and development such as various stress responses, organ formation and vascular development. Although systematic characterization of this family has been carried out in Arabidopsis and rice, little is known about HD-Zip genes in maize (Zea mays L.).Methods and FindingsIn this study, we described the identification and structural characterization of HD-Zip genes in the maize genome. A complete set of 55 HD-Zip genes (Zmhdz1-55) were identified in the maize genome using Blast search tools and categorized into four classes (HD-Zip I-IV) based on phylogeny. Chromosomal location of these genes revealed that they are distributed unevenly across all 10 chromosomes. Segmental duplication contributed largely to the expansion of the maize HD-ZIP gene family, while tandem duplication was only responsible for the amplification of the HD-Zip II genes. Furthermore, most of the maize HD-Zip I genes were found to contain an overabundance of stress-related cis-elements in their promoter sequences. The expression levels of the 17 HD-Zip I genes under drought stress were also investigated by quantitative real-time PCR (qRT-PCR). All of the 17 maize HD-ZIP I genes were found to be regulated by drought stress, and the duplicated genes within a sister pair exhibited the similar expression patterns, suggesting their conserved functions during the process of evolution.ConclusionsOur results reveal a comprehensive overview of the maize HD-Zip gene family and provide the first step towards the selection of Zmhdz genes for cloning and functional research to uncover their roles in maize growth and development.

Genome-wide identification of pear HD-Zip gene family and expression patterns under stress induced by drought, salinity, and pathogen

“…The HD-Zip family members were widely investigated in A. thaliana (Schena and Davis 1992), Z. mays (Zhao et al 2011), O. sativa (Agalou et al 2008), P. trichocarpa (Hu et al 2012), and other species (Liu et al 2013;Chen et al 2014;Zhang et al 2014). Until now, no genome-wide research, including gene identification, genome organization, and phylogenetic analysis, has been reported in pear.…”

A genome-wide survey of homeodomain-leucine zipper genes and analysis of cold-responsive HD-Zip I members’ expression in tomato

“…The original β clade was also divided into β1 and β2 clades as reported in maize and rice. 42,43) β2, φ1, ε clades were grouped by tomato and Arabidopsis genes. SlHZ12 in β1 clade, SlHZ08, -13 and -28,-01 in α clade, SlHZ16, -17, -18, -19 in δ clade, SlHZ20, -32, -41, -05 in γ clade were clustered with Arabidopsis and rice in their clades.…”

“…Expression patterns of SlHZ I genes under cold stress HD-Zip I genes have been reported to play an important role in abiotic and biotic stress. 11,42,43) Expression patterns of SlHZ I genes were checked in leaves of three-week-old tomato cv. Micro-Tom under cold stress using semi-quantitative RT-PCR.…”

“…68) In this study, most of SlHZ genes in tomato occurred in segmental duplication (55%), and segmental duplications were also identified in Arabidopsis (75%), 41,44,69,70) rice (54%) 71) , and maize (62%). 43) Therefore, the segmental duplication was regarded as the major mechanism for expansion of HD-Zip family, although segmental and tandem duplication both occurred in the expansion of the four species. The results suggested they might experience similar evolutionary mechanisms.…”

“…11,42,43) However, there is few investigation about HD-Zip gene under cold stress, especially in tomato. So we investigated the expression patterns of tomato HD-Zip I genes under cold stress.…”