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

Li, Zhiqian; Zhang, Chen; Guo, Yurui; Niu, Weili; Wang, Yuejin; Xu, Yan

doi:10.1186/s12864-017-4110-y

Cited by 58 publications

(58 citation statements)

References 65 publications

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“…Its target gene was DlHD-Zip 8 (ATHB8), it was significantly more highly expressed in GE than that in NEC and EC. Zhiqian Li investigated the HD-zip family from the whole-genome analysis of ovules and somatic embryos in grape, and found that HD-zip genes family might regulate seed abortion 60 . However, ATHB8 of the HD-Zip family was induced by auxin in Arabidopsis thaliana, and it was strongly expressed in vascular tissue when embryos developed to the heart embryonic stage 43 .…”

Section: Many Mirnas Are Involved In Early Se In Longanmentioning

confidence: 99%

Genome-wide identification of miRNAs and their targets during early somatic embryogenesis in Dimocarpus longan Lour.

Chen

et al. 2020

Sci Rep

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miRNAs are endogenous regulatory factors that play pivotal roles in post-transcriptional regulation. However, their specific roles in early somatic embryogenesis (SE) remain unclear. Study of the SE system is fundamental for clarifying the molecular mechanisms in Dimocarpus longan. We identified 289 known miRNAs from 106 different miRNA families and 1087 novel miRNAs during early longan SE, including embryogenic callus (EC), incomplete pro-embryogenic culture (ICpEC), globular embryo (GE), and non-embryogenic callus (NEC). The abundances of known miRNAs were concentrated in GE. The differentially expression (DE) miRNAs showed five expression patterns during early SE. Largely miRNAs were expressed highly and specially in EC, ICpEC, and GE, respectively. Some miRNAs and putative target genes were enriched in lignin metabolism. Most potential targets were related to the pathways of plant hormone signal transduction, alternative splicing, tyrosine metabolism and sulfur metabolism in early longan SE. The regulatory relationships between dlo-miR166a-3p and DlHD-zip8, dlo-miR397a and DlLAC7, dlo-miR408-3p and DlLAC12 were confirmed by RNA ligase-mediated rapid amplification of cDNA ends. The expression patterns of eight DE miRNAs detected by qRT-PCR were consistent with RNA-seq. Finally, the miRNA regulatory network in early SE was constructed, which provided new insight into molecular mechanism of early SE in longan.Plant somatic embryogenesis (SE) is physiologically and morphologically similar to that of zygotic embryos. Therefore, SE is usually used as a model system for studying embryonic development in higher plants. Previously study demonstrated that transcription factors (TFs) regulated embryogenic transformation in SE 1 ; this TFs included BABY BOOM (BBM), AGAMOUS-LIKE15 (AGL15), LEC2 and SERK, which functioned in the process of cell division and differentiation in embryonic development 2 . miRNAs are a kind of small endogenous RNAs of 18-24nt in length, which mainly recognize the complementary binding sites of their target mRNAs. miRNAs were transcribed by RNA polymerase II (Pol II). miRNAs could mediate mRNA cleavage and inhibiting translation at transcriptional or post-transcriptional level in eukaryotes 3,4 . Over the past decade, miRNAs have been reported to be involved in a broad range of metabolic and physiological processes in plants, such as plant growth, development and responses to stresses. However, the regulation of miRNA of plant SE was still unclear.The miRNA regulatory pathway is particularly important in plant growth and development, hormone regulation, organ differentiation, alternative splicing and secondary metabolite accumulation 5-7 . The SE could be influenced by epigenetics in some plant 8 . For instance, expression levels of miR171, 159, 169 and 172 affected in the embryogenic potency of Larix gmelini 9 , these particular miRNAs targeted to multifunctional TFs and participated in ABA signal transduction, growth and development, and stress response. In Citrus sinensis (L.), miR156, 168 an...

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Section: Many Mirnas Are Involved In Early Se In Longanmentioning

confidence: 99%

Genome-wide identification of miRNAs and their targets during early somatic embryogenesis in Dimocarpus longan Lour.

Chen

et al. 2020

Sci Rep

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“…By previous research on ZHD family members of other species in plant, we can have a fundmental understanging of ZHD. HD-Zip gene family expression were investigated in regulation of embryo abortion in grapes [31]. However, in order to let us have a further understanding of ZHD TFs.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide analysis and expression characterization of zinc finger homeodomain (ZHD) family genes responsed to different abiotic stresses and hormonal treatments in grape (Vitis vinifera L.)

Nai

Mao

et al. 2020

Preprint

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Background Zinc finger homeodomain (ZHD) proteins transcription factors (TFs) family occupy a crucial role in regulating plant growth and development. The ZHD TFs family had been studied in diverse organisms such as humans, Drosophila, nematode worms and plants. Especially in plants there is an extensive exploration involved in photosynthesis, defense mechanisms and responses to stress. In this further research, we will provide a better understanding of the ZHD gene family in grape. Results In this study, a total of 12 VvZHD genes were identified from the Grape Genome. The exploration of detailed bioinformatics found that the full length of VvZHD genes ranges from 150 bp (base pair) to 26706 bp, isoelectric points (pIs) were 6.25–9.68, molecular weights (MWs) ranged from 10.28 kilodaltons (KDa) to 97.93 kDa. Also, analysis of phylogenetic evolution showed there existed a common ancestor between Arabidopsis and grape. Ka (Nonsynonymous) / Ks (Synonymous) was lower than 1 and strong collinearity showed there were tandem duplications of genes between Arabidopsis and grape. Codon bias levels of ZHD gene family were relatively higher overall. Gene chip data analysis of cabernet sauvignon seedlings showed VvZHD genes had different expression under different time of different treatments, and with the prolongation of treatment time, most of VvZHD genes were slightly downregulated. The qRT-PCR was carried out under different hormones and stresses to verify expression profiles in grape roots and leaves. Results revealed that most VvZHD genes had higher expressions in roots but lower expressions in leaves. Also, most of the VvZHD gene members were responsed with high expressions after the treatment of ABA, IAA and MeJA in roots. However, VvZHD9, VvZHD11 and VvZHD12 were highly expressed by inducing of PEG in leaves. Conclusions Through genome-wide analysis and expression characterization of ZHD family genes, results showed 12 members had the diversity of function, structure and unique expression characterization under various abiotic stress and hormone treatments. This study will provide us with a newer insight on ZHD gene family of grape and promote to explore the biological functions of ZHD genes in other plants.

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“…6a). Common among these were the GCN4 motif and Skn-1 motif related to endosperm expression, TGACG motif and CGTCA motif involved in methyl jasmonate responses, TCA element involved in salicylic acid responses, ABRE element associated with abscisic acid, HSE element involved in heat stress, MBS element related to drought inducibility, TC-rich repeats associated with defense and stress responses, LAMP element and AE-box involved in light response, and 5' UTR Py-rich stretch conferring high transcription levels [27].…”

Section: Deletion Analysis Of the Vvhb58 Promotermentioning

confidence: 99%

The grapevine homeobox gene VvHB58 influences seed and fruit development through multiple hormonal signaling pathways

Zhang

Dong

et al. 2019

Preprint

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Background: Seedlessness is one of the most valuable traits in grapevine ( Vitis vinifera ), especially for the raisin and table grape industries. Previous transcriptome analyses of seed development in grape hybrids suggested that specific homeodomain transcription factors are involved in seed development in seedless cultivars. However, the molecular mechanism of homeobox gene regulating seed development in grape is rarely reported. Results: Here, we report that the grapevine VvHB58 gene, encoding a homeodomain-leucine zipper (HD-Zip I) transcription factor, participates in regulating fruit size and seed number. The VvHB58 gene was differentially expressed during seed development between seedless and seeded cultivars . Subcellular localization assays revealed that the VvHB58 protein was located in the nucleus. Transgenic expression of VvHB58 in tomato led to loss of apical dominance, a reduction in fruit pericarp expansion, reduced fruit size and seed number , and larger endosperm cells. Analysis of the sequence and cytosine methylation within the VvHB58 promoter indicated that the differential expression during seed development between seedless and seeded grapes may be caused by different transcriptional regulatory mechanisms rather than promoter DNA methylation. Measurements of five classic endogenous hormones and expression analysis of hormone-related genes between VvHB58 transgenic and nontransgenic control plants showed that expression of VvHB58 resulted in significant changes in auxin, gibberellin and ethylene signaling pathways. Additio nally, several DNA methylation-related gene s were expressed differentially during seed development stages in seedless and seeded grapes , suggesting changes in methylation levels during seed development may be associated with seed abortion . Conclusion: VvHB58 has a potential function in regulating fruit and seed development by impacting multiple hormonal pathways. These results expand understanding of homeodomain transcription factors and potential regulatory mechanism of seed development in grapevine, and provided insights into molecular breeding for grapes.

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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.)

Cited by 58 publications

References 65 publications

Genome-wide identification of miRNAs and their targets during early somatic embryogenesis in Dimocarpus longan Lour.

Genome-wide identification of miRNAs and their targets during early somatic embryogenesis in Dimocarpus longan Lour.

Genome-wide analysis and expression characterization of zinc finger homeodomain (ZHD) family genes responsed to different abiotic stresses and hormonal treatments in grape (Vitis vinifera L.)

The grapevine homeobox gene VvHB58 influences seed and fruit development through multiple hormonal signaling pathways

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