Genome-Wide Characterization and Expression Profiling of GASA Genes during Different Stages of Seed Development in Grapevine (Vitis vinifera L.) Predict Their Involvement in Seed Development

Ahmad, Bilal; Yao, Jin; Zhang, Songlin; Li, Xingmei; Zhang, Xiuming; Yadav, Vivek; Wang, Xiping

doi:10.3390/ijms21031088

Cited by 40 publications

(89 citation statements)

References 48 publications

(68 reference statements)

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“…Previously, some transcription factors and gene families have been reported for their roles in grapevine seed development, such as MADS-box, B3, and GASA gene family [33,34,41]. In Arabidopsis HMs genes, especially SDG family has been well studied for their potential roles in vegetative and reproductive growth of plant.…”

Section: Discussionmentioning

confidence: 99%

“…The HMs protein sequences of Arabidopsis and grapes were used for phylogenetic analysis. MEGA 6.0 software was used to construct phylogenetic trees with the following parameters: 'W' approach for sequence alignments, the neighbor-joining (NJ) method, p-distance, complete deletion and 1000 bootstrap values [34]. Different phylogenetic trees were generated for different subfamilies.…”

Section: Phylogenetic and Exon-intron Distribution Analysis Of Hms Genesmentioning

confidence: 99%

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Bioinformatics and expression analysis of histone modification genes in grapevine predict their involvement in seed development, powdery mildew resistance, and hormonal signaling

et al. 2020

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Background: Histone modification genes (HMs) play potential roles in plant growth and development via influencing gene expression and chromatin structure. However, limited information is available about HMs genes in grapes (Vitis vinifera L.). Results: Here, we described detailed genome-wide identification of HMs gene families in grapevine. We identified 117 HMs genes in grapevine and classified these genes into 11 subfamilies based on conserved domains and phylogenetic relationships with Arabidopsis. We described the genes in terms of their chromosomal locations and exon-intron distribution. Further, we investigated the evolutionary history, gene ontology (GO) analysis, and syntenic relationships between grapes and Arabidopsis. According to results 21% HMs genes are the result of duplication (tandem and segmental) events and all the duplicated genes have negative mode of selection. GO analysis predicted the presence of HMs proteins in cytoplasm, nucleus, and intracellular organelles. According to seed development expression profiling, many HMs grapevine genes were differentially expressed in seeded and seedless cultivars, suggesting their roles in seed development. Moreover, we checked the response of HMs genes against powdery mildew infection at different time points. Results have suggested the involvement of some genes in disease resistance regulation mechanism. Furthermore, the expression profiles of HMs genes were analyzed in response to different plant hormones (Abscisic acid, Jasmonic acid, Salicylic acid, and Ethylene) at different time points. All of the genes showed differential expression against one or more hormones. Conclusion: VvHMs genes might have potential roles in grapevine including seed development, disease resistance, and hormonal signaling pathways. Our study provides first detailed genome-wide identification and expression profiling of HMs genes in grapevine.

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Section: Discussionmentioning

confidence: 99%

Section: Phylogenetic and Exon-intron Distribution Analysis Of Hms Genesmentioning

confidence: 99%

Bioinformatics and expression analysis of histone modification genes in grapevine predict their involvement in seed development, powdery mildew resistance, and hormonal signaling

et al. 2020

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“…Previously, some transcription factors and gene families have been reported for their roles in grapevine seed development, such as MADS-box, B3, and GASA gene family [34,35,42]. In Arabidopsis HMs genes, especially SDG family has been well studied for their potential roles in vegetative and reproductive growth of plant.…”

Section: Discussionmentioning

confidence: 99%

Bioinformatics and Expression Analysis of Histone Modification Genes in Grapevine Predict Their Involvement in Seed Development, Powdery Mildew Resistance, and Hormonal Signaling

Wang

Ahmad

Chen

et al. 2020

Preprint

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Background: Histone modification genes (HMs) play potential roles in plant growth and development via influencing gene expression and chromatin structure. However, limited information is available about HMs genes in grapes (Vitis vinifera L.).Results: Here, we described detailed genome-wide identification of HMs gene families in grapevine. We identified 117 HMs genes in grapevine and classified these genes into 11 subfamilies based on conserved domains and phylogenetic relationships with Arabidopsis. We described the genes in terms of their chromosomal locations and exon-intron distribution. Further, we investigated the evolutionary history, gene ontology (GO) analysis, and syntenic relationships between grapes and Arabidopsis. According to results 21% HMs genes are the result of duplication (tandem and segmental) events and all the duplicated genes have negative mode of selection. GO analysis predicted the presence of HMs proteins in cytoplasm, nucleus, and intracellular organelles. According to seed development expression profiling, many HMs grapevine genes were differentially expressed in seeded and seedless cultivars, suggesting their roles in seed development. Moreover, we checked the response of HMs genes against powdery mildew infection at different time points. Results have suggested the involvement of some genes in disease resistance regulation mechanism. Furthermore, the expression profiles of HMs genes were analyzed in response to different plant hormones (Abscisic acid, Jasmonic acid, Salicylic acid, and Ethylene) at different time points. All of the genes showed differential expression against one or more hormones.Conclusion: VvHMs genes might have potential roles in grapevine including seed development, disease resistance, and hormonal signaling pathways. Our study provides first detailed genome-wide identification and expression profiling of HMs genes in grapevine.

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“…In the last two decades, a number of other genes have been proposed to play a role in stenospermocarpic ovule/seed abortion or in normal seed development [42][43][44][45][46][47][48][49][50][51][52][53][54][55]. Nonetheless, the differential expression detected for these genes in the comparison of seeded and seedless whole fruits might be a consequence (instead of a cause) of the seedless syndrome (with the concurrent lower proportion of seed-related tissues) if these transcripts accumulate specifically in seeds [41].…”

Section: The Genetic Determinism Of Seedlessness In Grapevinementioning

confidence: 99%

Mechanisms and Candidate Genes for Seed and Fruit Set in Grapevine

Costantini¹,

Nwafor²,

Lorenzi³

et al. 2020

Preprint

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Background: Grapevine reproductive development has direct implications on yield. It also impacts on berry and wine quality by affecting traits like cluster compactness, bunch and berry size, berry skin to pulp ratio or seedlessness. Seasonal fluctuations in yield, fruit composition and wine attributes, which are largely driven by climatic factors, are major challenges for worldwide table grape and wine industry. Accordingly, a better understanding of reproductive processes such as gamete development, fertilization, seed and fruit set is of paramount relevance for managing yield and quality. With the aim of providing new insights into this field, we searched for clones with contrasting seed content in two germplasm collections. Results: We identified eight variant pairs that seemingly differ only in seed-related characteristics while showing identical genotype when tested with the GrapeReSeq_Illumina_20K_SNP_chip and several microsatellites. We performed multi-year observations on fruit and seed set deriving from different pollination treatments, with special emphasis on the pair composed by Sangiovese and its seedless variant locally named Corinto Nero. The pollen of Corinto Nero failed to germinate in vitro and gave poor berry set when used to pollinate other varieties. Most berries from both open- and cross-pollinated Corinto Nero inflorescences did not contain seeds. The genetic analysis of seedlings derived from occasional Corinto Nero normal seeds revealed that the few Corinto Nero functional gametes are mostly unreduced. A number of genes potentially involved in sporogenesis and gametogenesis showed contrasting expression between Corinto Nero and Sangiovese and five missense single nucleotide polymorphisms were identified from transcriptomic data. The above findings suggest that the seedless phenotype of Corinto Nero is driven by pollen and/or embryo sac defects, and both events likely arise from meiotic anomalies. Finally, three genotypes, including Sangiovese and Corinto Nero, were unexpectedly found to develop fruits without pollen contribution and occasionally showed normal-like seeds. Conclusions: Our collective results suggest that parthenocarpy and stenospermocarpy are not restricted to Black Corinth (alias Korinthiaki) and Sultanina-derived cultivars. The single nucleotide polymorphisms identified between Sangiovese and its parthenocarpic variant Corinto Nero are suitable for testing as traceability markers for propagated material and as functional candidates for the seedless phenotype.

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Genome-Wide Characterization and Expression Profiling of GASA Genes during Different Stages of Seed Development in Grapevine (Vitis vinifera L.) Predict Their Involvement in Seed Development

Cited by 40 publications

References 48 publications

Bioinformatics and expression analysis of histone modification genes in grapevine predict their involvement in seed development, powdery mildew resistance, and hormonal signaling

Bioinformatics and expression analysis of histone modification genes in grapevine predict their involvement in seed development, powdery mildew resistance, and hormonal signaling

Bioinformatics and Expression Analysis of Histone Modification Genes in Grapevine Predict Their Involvement in Seed Development, Powdery Mildew Resistance, and Hormonal Signaling

Mechanisms and Candidate Genes for Seed and Fruit Set in Grapevine

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