Genome-wide identification, phylogenetic analysis, and expression profiling of glycine-rich RNA-binding protein (GRPs) genes in seeded and seedless grapes (Vitis vinifera)

Tang, Yanqiong; Huang, Congbo; Li, Yán; Wang, Yuejin; Zhang, Chaohong

doi:10.1007/s12298-021-01082-3

Cited by 8 publications

(8 citation statements)

References 61 publications

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“…Extensive research has been conducted on numerous GR-RBP genes across various species, including wheat, tobacco, rice, maize, Arabidopsis, apple, sweet potato, and grapes. This is attributed to their pivotal roles in regulating gene expression at post-transcriptional levels [7][8][9][34][35][36][37][38]. GR-RBPs have been recognized for their involvement in crop plants' biotic and abiotic stresses [39].…”

Section: Discussionmentioning

confidence: 99%

“…Glycine-rich proteins (GRPs)/glycine-rich RNA-binding proteins (GR-RBPs) form a superfamily characterized by (Gly)n-X repeats organized in a glycine-rich domain, comprising a conserved glycine-rich domain and an RNA-recognition motif (RRM). Numerous GR-RBPs have been identified across different plant species in the past two decades, with Arabidopsis thaliana having eight, Oryza sativa-six, Zea mays-twenty-three, Vitis vinifera-nineteen, Ipomoea trifida-nine, Gossypium arboretum-thirty-seven, Gossypium raimondii-thirty-two, and Brassica oleracea-nineteen [6][7][8][9][10][11]. Expression of GR-RBPs in various plants is regulated by both biotic and abiotic stresses when their function is investigated [12].…”

Section: Introductionmentioning

confidence: 99%

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Genome-Wide Identification of the Glycine-Rich RNA-Binding Protein Genes and Their Expression Analysis upon Aspergillus flavus Infection in Groundnut (Arachis hypogaea)

Jose,

Tejaswi,

Kokiladevi

et al. 2024

Agronomy

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Aflatoxins, carcinogenic secondary metabolites produced by the Aspergillus fungi, pose a significant threat to groundnut, making them susceptible to infection and compromising their quality. Despite extensive breeding programs, the need for more durable resistance in groundnut germplasm remains a major challenge. Targeting susceptible genes favoring Aspergillus infection in groundnut could offer a promising strategy for achieving durable resistance. The glycine-rich RNA-binding protein (GR-RBP)-coding genes, known for their involvement in plant hypersensitivity and susceptibility to A. flavus, have been studied in model plants. However, there needs to be more understanding of the GR-RBP gene family in groundnut. In this study, twenty-three Arachis hypogaea GR-RBP (Ah.GR-RBP) genes were identified, and the chromosomal location, sub-cellular localization, and regulatory elements in the putative promoter region were analyzed. Expression analysis revealed that Ah.GR-RBP.1, Ah.GR-RBP.12, Ah.GR-RBP.3, and Ah.GR-RBP.15 showed higher expression in the susceptible genotype. This paper would help to provide knowledge on potential candidate target genes for precise breeding interventions for aflatoxin mitigation in groundnut.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification of the Glycine-Rich RNA-Binding Protein Genes and Their Expression Analysis upon Aspergillus flavus Infection in Groundnut (Arachis hypogaea)

Jose,

Tejaswi,

Kokiladevi

et al. 2024

Agronomy

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show abstract

“…Except for lipid accumulation ( Fig. 5d ), the processes of sugar and amino acid synthesis also contribute to seed development, such as BGLU15 , VviGAPDH 71 , glycine-rich protein ( Vitvi021557 , Vitvi036421 ), and 36.4 kDa proline-rich protein ( Vitvi002605 ). Overall, these findings not only emphasize the polygenic nature of seedlessness but also provide novel candidate genes for functional genetics, highlighting the complexity of seed abortion regulation.…”

Section: Discussionmentioning

confidence: 99%

Integrative genomics reveals the polygenic basis of seedlessness in grapevine

Wang,

Liu,

Zhang

et al. 2023

Preprint

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Seedlessness is a crucial quality trait in table grape (Vitis viniferaL.) breeding. However, the development of seeds involved intricate regulations, while the polygenic basis of seed abortion remains unclear. Here, we combine comparative genomics, population genetics, quantitative genetics, and integrative genomics to unravel the evolution and polygenic basis of seedlessness in grapes. We generated four haplotype-resolved telomere-to-telomere (T2T) genomes for two seedless grape cultivars, ‘Thompson Seedless’ (TS, syn. ‘Sultania’) and ‘Black Monukka’ (BM). Comparative genomics identified a ∼4.25 Mb hemizygous inversion on Chr10 specific in seedless cultivars, with seedless-associated genesVvTT16andVvSUS2located at breakpoints. Population genomic analyses of 548 grapevine accessions revealed two distinct clusters of seedless cultivars, tracing the origin of the seedlessness trait back to ‘Sultania’. Introgression, rather than convergent selection, shaped the evolutionary history of seedlessness in grape improvement. Genome-wide association study (GWAS) analysis identified 110 quantitative trait loci (QTLs) associated with 634 candidate genes, including novel candidate genes, such as three11S GLOBULIN SEED STORAGE PROTEINand twoCYTOCHROME P450genes, and well-known genes likeVviAGL11. Integrative genomic analyses resulted in 339 core candidate genes categorized into 13 groups related to seed development. Machine learning based genomic selection achieved a remarkable 99% precision in predicting grapevine seedlessness. Our findings highlight the polygenic nature of seedless and provide novel candidate genes for molecular genetics and an effective prediction for seedlessness in grape genomic breeding.

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“…Lately, nineteen VviGRPs were identified from the grape genome, and seventeen of them were found to be expressed in ovules [97]. Expression analyses conducted during ovule development revealed distinct expression profiles for most ovule-expressed VviGRPs between seeded and stenospermocarpic grapes.…”

Section: Gr-rbps In Fruitsmentioning

confidence: 99%

The Glycine-Rich RNA-Binding Protein Is a Vital Post-Transcriptional Regulator in Crops

Cheng,

Zhang,

et al. 2023

Plants

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Glycine-rich RNA binding proteins (GR-RBPs), a branch of RNA binding proteins (RBPs), play integral roles in regulating various aspects of RNA metabolism regulation, such as RNA processing, transport, localization, translation, and stability, and ultimately regulate gene expression and cell fate. However, our current understanding of GR-RBPs has predominantly been centered on Arabidopsis thaliana, a model plant for investigating plant growth and development. Nonetheless, an increasing body of literature has emerged in recent years, shedding light on the presence and functions of GRPs in diverse crop species. In this review, we not only delineate the distinctive structural domains of plant GR-RBPs but also elucidate several contemporary mechanisms of GR-RBPs in the post-transcriptional regulation of RNA. These mechanisms encompass intricate processes, including RNA alternative splicing, polyadenylation, miRNA biogenesis, phase separation, and RNA translation. Furthermore, we offer an exhaustive synthesis of the diverse roles that GR-RBPs fulfill within crop plants. Our overarching objective is to provide researchers and practitioners in the field of agricultural genetics with valuable insights that may inform and guide the application of plant genetic engineering for enhanced crop development and sustainable agriculture.

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Genome-wide identification, phylogenetic analysis, and expression profiling of glycine-rich RNA-binding protein (GRPs) genes in seeded and seedless grapes (Vitis vinifera)

Cited by 8 publications

References 61 publications

Genome-Wide Identification of the Glycine-Rich RNA-Binding Protein Genes and Their Expression Analysis upon Aspergillus flavus Infection in Groundnut (Arachis hypogaea)

Genome-Wide Identification of the Glycine-Rich RNA-Binding Protein Genes and Their Expression Analysis upon Aspergillus flavus Infection in Groundnut (Arachis hypogaea)

Integrative genomics reveals the polygenic basis of seedlessness in grapevine

The Glycine-Rich RNA-Binding Protein Is a Vital Post-Transcriptional Regulator in Crops

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