Dataset Information

Bioinformatic approach for the discovery of cis-eQTL signals during fruit ripening of a woody species as grape (Vitis vinifera L.).

ABSTRACT: Expression quantitative trait loci (eQTLs) are associations between genetic variants, such as Single Nucleotide Polymorphisms (SNPs), and gene expression. eQTLs are an important tool to understand the genetic variance of gene expression of complex phenotypes. eQTLs analyses are common in biomedical models but are scarce in woody crop species such as fruit trees or grapes. In this study, a comprehensive bioinformatic analysis was conducted leveraging with expression data from two different growth stages, around ripening onset, of 10 genotypes of grape (Vitis vinifera L.). A total of 2170 cis-eQTL were identified in 212 gene modulated at ripening onset. The 48% of these DEGs have a known function. Among the annotated protein-coding genes, terpene synthase, auxin-regulatory factors, GRFS, ANK_REP_REGION domain-containing protein, Kinesin motor domain-containing protein and flavonol synthase were noted. This new inventory of cis-eQTLs influencing gene expression during fruit ripening will be an important resource to examine variation for this trait and will help to elucidate the complex genetic architecture underlying this process in grape.

SUBMITTER: Martinez-Garcia PJ

PROVIDER: S-EPMC9076688 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature

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Bioinformatic approach for the discovery of cis-eQTL signals during fruit ripening of a woody species as grape (Vitis vinifera L.).

Martínez-García Pedro José PJ Mas-Gómez Jorge J Wegrzyn Jill J Botía Juan A JA

Scientific reports 20220506 1

Expression quantitative trait loci (eQTLs) are associations between genetic variants, such as Single Nucleotide Polymorphisms (SNPs), and gene expression. eQTLs are an important tool to understand the genetic variance of gene expression of complex phenotypes. eQTLs analyses are common in biomedical models but are scarce in woody crop species such as fruit trees or grapes. In this study, a comprehensive bioinformatic analysis was conducted leveraging with expression data from two different growth ...[more]

PMID: 35523985

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Project description:BackgroundFruit development is controlled by plant hormones, but the role of hormone interactions during fruit ripening is poorly understood. Interactions between ethylene and the auxin indole-3-acetic acid (IAA) are likely to be crucial during the ripening process, since both hormones have been shown to be implicated in the control of ripening in a range of different fruit species.ResultsGrapevine (Vitis vinifera L.) homologues of the TRYPTOPHAN AMINOTRANSFERASE RELATED (TAR) and YUCCA families, functioning in the only characterized pathway of auxin biosynthesis, were identified and the expression of several TAR genes was shown to be induced by the pre-ripening application of the ethylene-releasing compound Ethrel. The induction of TAR expression was accompanied by increased IAA and IAA-Asp concentrations, indicative of an upregulation of auxin biosynthesis and conjugation. Exposure of ex planta, pre-ripening berries to the ethylene biosynthesis inhibitor aminoethoxyvinylglycine resulted in decreased IAA and IAA-Asp concentrations. The delayed initiation of ripening observed in Ethrel-treated berries might therefore represent an indirect ethylene effect mediated by increased auxin concentrations. During berry development, the expression of three TAR genes and one YUCCA gene was upregulated at the time of ripening initiation and/or during ripening. This increase in auxin biosynthesis gene expression was preceded by high expression levels of the ethylene biosynthesis genes 1-aminocyclopropane-1-carboxylate synthase and 1-aminocyclopropane-1-carboxylate oxidase.ConclusionsIn grape berries, members of both gene families involved in the two-step pathway of auxin biosynthesis are expressed, suggesting that IAA is produced through the combined action of TAR and YUCCA proteins in developing berries. The induction of TAR expression by Ethrel applications and the developmental expression patterns of auxin and ethylene biosynthesis genes indicate that elevated concentrations of ethylene prior to the initiation of ripening might lead to an increased production of IAA, suggesting a complex involvement of this auxin and its conjugates in grape berry ripening.

Project description:BACKGROUND: Global climate change will noticeably affect plant vegetative and reproductive development. The recent increase in temperatures has already impacted yields and composition of berries in many grapevine-growing regions. Physiological processes underlying temperature response and tolerance of the grapevine fruit have not been extensively investigated. To date, all studies investigating the molecular regulation of fleshly fruit response to abiotic stress were only conducted during the day, overlooking possible critical night-specific variations. The present study explores the night and day transcriptomic response of grapevine fruit to heat stress at several developmental stages. Short heat stresses (2 h) were applied at day and night to vines bearing clusters sequentially ordered according to the developmental stages along their vertical axes. The recently proposed microvine model (DRCF-Dwarf Rapid Cycling and Continuous Flowering) was grown in climatic chambers in order to circumvent common constraints and biases inevitable in field experiments with perennial macrovines. Post-véraison berry heterogeneity within clusters was avoided by constituting homogenous batches following organic acids and sugars measurements of individual berries. A whole genome transcriptomic approach was subsequently conducted using NimbleGen 090818 Vitis 12X (30 K) microarrays. RESULTS: Present work reveals significant differences in heat stress responsive pathways according to day or night treatment, in particular regarding genes associated with acidity and phenylpropanoid metabolism. Precise distinction of ripening stages led to stage-specific detection of malic acid and anthocyanin-related transcripts modulated by heat stress. Important changes in cell wall modification related processes as well as indications for heat-induced delay of ripening and sugar accumulation were observed at véraison, an effect that was reversed at later stages. CONCLUSIONS: This first day - night study on heat stress adaption of the grapevine berry shows that the transcriptome of fleshy fruits is differentially affected by abiotic stress at night. The present results emphasize the necessity of including different developmental stages and especially several daytime points in transcriptomic studies.

Project description:Using barcoded pyrosequencing fungal and bacterial communities associated with grape berry clusters (Vitis vinifera L.) obtained from conventional, organic and biodynamic vineyard plots were investigated in two subsequent years at different stages during berry ripening. The four most abundant operational taxonomic units (OTUs) based on fungal ITS data were Botrytis cinerea, Cladosporium spp., Aureobasidium pullulans and Alternaria alternata which represented 57% and 47% of the total reads in 2010 and 2011, respectively. Members of the genera Sphingomonas, Gluconobacter, Pseudomonas, Erwinia, and Massilia constituted 67% of the total number of bacterial 16S DNA reads in 2010 samples and 78% in 2011 samples. Viticultural management system had no significant effect on abundance of fungi or bacteria in both years and at all three sampling dates. Exceptions were A. alternata and Pseudomonas spp. which were more abundant in the carposphere of conventional compared to biodynamic berries, as well as Sphingomonas spp. which was significantly less abundant on conventional compared to organic berries at an early ripening stage in 2011. In general, there were no significant differences in fungal and bacterial diversity indices or richness evident between management systems. No distinct fungal or bacterial communities were associated with the different maturation stages or management systems, respectively. An exception was the last stage of berry maturation in 2011, where the Simpson diversity index was significantly higher for fungal communities on biodynamic compared to conventional grapes. Our study highlights the existence of complex and dynamic microbial communities in the grape cluster carposphere including both phytopathogenic and potentially antagonistic microorganisms that can have a significant impact on grape production. Such knowledge is particularly relevant for development, selection and application of effective control measures against economically important pathogens present in the grape carposphere.

Dataset Information

Bioinformatic approach for the discovery of cis-eQTL signals during fruit ripening of a woody species as grape (Vitis vinifera L.).

Publications

Bioinformatic approach for the discovery of cis-eQTL signals during fruit ripening of a woody species as grape (Vitis vinifera L.).

Similar Datasets

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