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      Evolution and expression analysis reveal the potential role of the HD-Zip gene family in regulation of embryo abortion in grapes ( Vitis vinifera L.)

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          Abstract

          Background

          The HD-Zip family has a diversity of functions during plant development. In this study, we identify 33 HD-Zip transcription factors in grape and detect their expressions in ovules and somatic embryos, as well as in various vegetative organs.

          Results

          A genome-wide survey for HD-Zip transcription factors in Vitis was conducted based on the 12 X grape genome ( V. vinifera L.). A total of 33 members were identified and classified into four subfamilies (I-IV) based on phylogeny analysis with Arabidopsis, rice and maize. VvHDZs in the same subfamily have similar protein motifs and intron/exon structures. An evaluation of duplication events suggests several HD-Zip genes arose before the divergence of the grape and Arabidopsis lineages. The 33 members of HD-Zip were differentially expressed in ovules of the stenospermic grape, Thompson Seedless and of the seeded grape, Pinot noir. Most have higher expressions during ovule abortion in Thompson Seedless. In addition, transcripts of the HD-Zip family were also detected in somatic embryogenesis of Thompson Seedless and in different vegetative organs of Thompson Seedless at varying levels. Additionally, VvHDZ28 is located in the nucleus and had transcriptional activity consistent with the typical features of the HD-Zip family. Our results provide a foundation for future grape HD-Zip gene function research.

          Conclusions

          The identification and expression profiles of the HD-Zip transcription factors in grape, reveal their diverse roles during ovule abortion and organ development. Our results lay a foundation for functional analysis of grape HDZ genes.

          Electronic supplementary material

          The online version of this article (10.1186/s12864-017-4110-y) contains supplementary material, which is available to authorized users.

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          Gene duplication and evolutionary novelty in plants.

          Lex E. Flagel, Jonathan Wendel (2009)
          Duplication is a prominent feature of plant genomic architecture. This has led many researchers to speculate that gene duplication may have played an important role in the evolution of phenotypic novelty within plants. Until recently, however, it was difficult to make this connection. We are now beginning to understand how duplication has contributed to adaptive evolution in plants. In this review we introduce the sources of gene duplication and predictions of the various fates of duplicates. We also highlight several recent and pertinent examples from the literature. These examples demonstrate the importance of the functional characteristics of genes and the source of duplication in influencing evolutionary outcome.
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            Radial patterning of Arabidopsis shoots by class III HD-ZIP and KANADI genes.

            John Emery, Sandra K. Floyd, John Alvarez … (2003)
            Shoots of all land plants have a radial pattern that can be considered to have an adaxial (central)-abaxial (peripheral) polarity. In Arabidopsis, gain-of-function alleles of PHAVOLUTA and PHABULOSA, members of the class III HD-ZIP gene family, result in adaxialization of lateral organs. Conversely, loss-of-function alleles of the KANADI genes cause an adaxialization of lateral organs. Thus, the class III HD-ZIP and KANADI genes comprise a genetic system that patterns abaxial-adaxial polarity in lateral organs produced from the apical meristem. We show that gain-of-function alleles of REVOLUTA, another member of the class III HD-ZIP gene family, are characterized by adaxialized lateral organs and alterations in the radial patterning of vascular bundles in the stem. The gain-of-function phenotype can be obtained by changing only the REVOLUTA mRNA sequence and without changing the protein sequence; this finding indicates that this phenotype is likely mediated through an interference with microRNA binding. Loss of KANADI activity results in similar alterations in vascular patterning as compared to REVOLUTA gain-of-function alleles. Simultaneous loss-of-function of PHABULOSA, PHAVOLUTA, and REVOLUTA abaxializes cotyledons, abolishes the formation of the primary apical meristem, and in severe cases, eliminates bilateral symmetry; these phenotypes implicate these three genes in radial patterning of both embryonic and postembryonic growth. Based on complementary vascular and leaf phenotypes of class III HD-ZIP and KANADI mutants, we propose that a common genetic program dependent upon miRNAs governs adaxial-abaxial patterning of leaves and radial patterning of stems in the angiosperm shoot. This finding implies that a common patterning mechanism is shared between apical and vascular meristems.
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              Class III homeodomain-leucine zipper gene family members have overlapping, antagonistic, and distinct roles in Arabidopsis development.

              Michael J Prigge, Denichiro Otsuga, José M. Alonso … (2005)
              The Arabidopsis thaliana genome contains five class III homeodomain-leucine zipper genes. We have isolated loss-of-function alleles for each family member for use in genetic analysis. This gene family regulates apical embryo patterning, embryonic shoot meristem formation, organ polarity, vascular development, and meristem function. Genetic analyses revealed a complex pattern of overlapping functions, some of which are not readily inferred by phylogenetic relationships or by gene expression patterns. The PHABULOSA and PHAVOLUTA genes perform overlapping functions with REVOLUTA, whereas the PHABULOSA, PHAVOLUTA, and CORONA/ATHB15 genes perform overlapping functions distinct from REVOLUTA. Furthermore, ATHB8 and CORONA encode functions that are both antagonistic to those of REVOLUTA within certain tissues and overlapping with REVOLUTA in other tissues. Differences in expression patterns explain some of these genetic interactions, whereas other interactions are likely attributable to differences in protein function as indicated by cross-complementation studies.
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                Author and article information

                Contributors
                Zhiqian Li: lizhiqian@nwsuaf.edu.cn
                Chen Zhang: zhangchen5859@126.com
                Yurui Guo: 18792728401@163.com
                Weili Niu: niuweili@nwsuaf.edu.cn
                Yuejin Wang: wangyj@nwsuaf.edu.cn
                Yan Xu: yan.xu@nwsuaf.edu.cn
                Journal
                Journal ID (nlm-ta): BMC Genomics
                Journal ID (iso-abbrev): BMC Genomics
                Title: BMC Genomics
                Publisher: BioMed Central (London )
                ISSN (Electronic): 1471-2164
                Publication date (Electronic): 21 September 2017
                Publication date PMC-release: 21 September 2017
                Publication date Collection: 2017
                Volume: 18
                Electronic Location Identifier: 744
                Affiliations
                [1 ]ISNI 0000 0004 1760 4150, GRID grid.144022.1, College of Horticulture, Northwest A&F University, ; Yangling, Shaanxi People’s Republic of China
                [2 ]ISNI 0000 0004 1760 4150, GRID grid.144022.1, State Key Laboratory of Crop Stress Biology in Arid Areas, , Northwest A&F University, ; Yangling, Shaanxi People’s Republic of China
                [3 ]ISNI 0000 0004 0369 6250, GRID grid.418524.e, Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, ; Yangling, Shaanxi People’s Republic of China
                Article
                Publisher ID: 4110
                DOI: 10.1186/s12864-017-4110-y
                PMC ID: 5609062
                PubMed ID: 28934927
                SO-VID: 5f6e8bd2-8200-4788-a8e7-0aa1a29eff85
                Copyright © © The Author(s). 2017
                License:

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                Date received : 23 May 2017
                Date accepted : 1 September 2017
                Funding
                Funded by: ‘948’ Program, Ministry of Agriculture, China
                Award ID: 2016-X11
                Award Recipient :
                Funded by: Overall innovation project of Shaanxi Province Plant Science and Technology
                Award ID: 2013KTCL02-01
                Award Recipient :
                Categories
                Subject: Research Article
                Custom metadata
                issue-copyright-statement © The Author(s) 2017

                ScienceOpen disciplines: Genetics
                Keywords: homeobox,hd-zip,vitis vinifera,seedless grape,embryo abortion
                Data availability:
                ScienceOpen disciplines: Genetics
                Keywords: homeobox, hd-zip, vitis vinifera, seedless grape, embryo abortion

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