Genome-wide analysis of the SCPL gene family in grape (Vitis vinifera L.)

Wang, Xicheng; Wu, Wei‐Min; Zhou, Beibei; Wang, Zhuangwei; Qian, Yaming; Wang, Bo; Yan, Lichun

doi:10.1016/s2095-3119(20)63587-0

Cited by 6 publications

(4 citation statements)

References 41 publications

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“…Random genes were assigned a chromosome number but without any certain placement within the chromosome [57]. Likewise, two members of the SCPL gene family were mapped on random positions of chromosome 7 and 10 [58]. In the present study, VvBTB8, VvBTB42 and VvBTB44 were found to be located at random positions on chromosome 3, 11 and 12, respectively.…”

Section: Discussionmentioning

confidence: 53%

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Genome-Wide Identification of BTB Domain-Containing Gene Family in Grapevine (Vitis vinifera L.)

et al. 2023

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BTB (broad-complex, tram track and bric-a-brac) proteins have broad functions in different growth processes and biotic and abiotic stresses. However, the biological role of these proteins has not yet been explored in grapevine, which draws our attention towards the BTB gene family. Herein, we identified 69 BTB genes (VvBTB) in the Vitis vinifera genome and performed comprehensive in silico analysis. Phylogenetic analysis classified VvBTB proteins into five groups, and further domain analysis revealed the presence of other additional functional domains. The majority of BTB proteins were localized in the nucleus. We also performed differential expression analysis by harnessing RNA- seq data of 10 developmental stages and different biotic and abiotic stresses. Our findings revealed the plausible roles of the BTB gene family in developmental stages; Fifty VvBTB were differentially expressed at different developmental stages. In addition, 47 and 16 VvBTB were responsive towards abiotic and biotic stresses, respectively. Interestingly, 13 VvBTB genes exhibited differential expression in at least one of the developmental stages and biotic and abiotic stresses. Further, miRNA target prediction of 13 VvBTB genes revealed that vvi-miR482 targets VvBTB56, and multiple miRNAs, such as vvi-miR172, vvi-miR169 and vvi-miR399, target VvBTB24, which provides an insight into the essential role of the BTB family in the grapevine. Our study provides the first comprehensive analysis and essential information that can potentially be used for further functional investigation of BTB genes in this economically important fruit crop.

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Section: Discussionmentioning

confidence: 53%

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification of BTB Domain-Containing Gene Family in Grapevine (Vitis vinifera L.)

et al. 2023

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“…The SCPL proteins contain a conserved catalytic triplet composed of three amino acid residues—a serine, an aspartate and a histidine (Ser‐Asp‐His) (Mugford and Milkowski, 2012)—that participates in transacylation reactions in plant secondary metabolism pathways (Weier et al ., 2008). Members of the SCPL class have been identified and characterized in wheat ( Triticum aestivum ) (Xu et al ., 2021), rapeseed ( Brassica napus ) (Liu et al ., 2022), grape ( Vitis vinifera ) (Wang et al ., 2021), cotton ( Gossypium hirsutum ) (Wang et al ., 2022) and tea ( Camellia sinensis ) (Ahmad et al ., 2020). Previous studies have ascertained that SCPLs play essential functions in determining seed weight and size (Dong et al ., 2023; Li et al ., 2011), signal transduction (Xu et al ., 2015), development and senescence of organs (Cercós et al ., 2003; Domínguez et al ., 2002), plant abiotic stress responses (Xu et al ., 2021) and plant disease resistance (Mugford et al ., 2009; Wang et al ., 2022).…”

Section: Discussionmentioning

confidence: 99%

A 5.2‐kb insertion in the coding sequence of PavSCPL, a serine carboxypeptidase‐like enhances fruit firmness in Prunus avium

Qi,

Dong,

Liu

et al. 2024

Plant Biotechnology Journal

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SummaryFruit firmness is an important trait in sweet cherry breeding because it directly positively influences fruit transportability, storage and shelf life. However, the underlying genes responsible and the molecular mechanisms that control fruit firmness remain unknown. In this study, we identified a candidate gene, PavSCPL, encoding a serine carboxypeptidase‐like protein with natural allelic variation, that controls fruit firmness in sweet cherry using map‐based cloning and functionally characterized PavSCPL during sweet cherry fruit softening. Genetic analysis revealed that fruit firmness in the ‘Rainier’ × ‘Summit’ F1 population was controlled by a single dominant gene. Bulked segregant analysis combined with fine mapping narrowed the candidate gene to a 473‐kb region (7418778–7 891 914 bp) on chromosome 6 which included 72 genes. The candidate gene PavSCPL, and a null allele harbouring a 5244‐bp insertion in the second exon that completely inactivated PavSCPL expression and resulted in the extra‐hard‐flesh phenotype, were identified by RNA‐sequencing analysis and gene cloning. Quantitative RT‐PCR analysis revealed that the PavSCPL expression level was increased with fruit softening. Virus‐induced gene silencing of PavSCPL enhanced fruit firmness and suppressed the activities of certain pectin‐degrading enzymes in the fruit. In addition, we developed functional molecular markers for PavSCPL and the Pavscpl5.2‐k allele that co‐segregated with the fruit firmness trait. Overall, this research identified a crucial functional gene for fruit firmness. The results provide insights into the genetic control and molecular mechanism of the fruit firmness trait and present useful molecular markers for molecular‐assisted breeding for fruit firmness in sweet cherry.

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“…A similar up-regulation of phenylpropanoid metabolism has been highlighted by [61] in Pinot Noir plants grafted onto 1103P in comparison with the one grafted onto 101-14MGt when grown on sandy soils. Fasciclin-like arabinogalactan proteins [62], aspartic proteinases [63], and serine carboxypeptidase-like proteins [64] could be proteins involved in the response to water deficit and up-regulated on leaves of Cabernet Sauvignon grafted onto 1103P. This group of genes can explain the stomata closure that occurred on leaves of Cabernet Sauvignon grafted onto 1103P.…”

Section: Rootstock Influences the Scion Leaf Transcriptome Under Wate...mentioning

confidence: 96%

Physiological and Transcriptomic Evaluation of Drought Effect on Own-Rooted and Grafted Grapevine Rootstock (1103P and 101-14MGt)

Bianchi

Ricciardi

Pozzoli

et al. 2023

Plants

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Grapevines worldwide are grafted onto Vitis spp. rootstocks in order to improve their tolerance to biotic and abiotic stresses. Thus, the response of vines to drought is the result of the interaction between the scion variety and the rootstock genotype. In this work, the responses of genotypes to drought were evaluated on 1103P and 101-14MGt plants, own-rooted and grafted with Cabernet Sauvignon, in three different water deficit conditions (80, 50, and 20% soil water content, SWC). Gas exchange parameters, stem water potential, root and leaf ABA content, and root and leaf transcriptomic response were investigated. Under well-watered conditions, gas exchange and stem water potential were mainly affected by the grafting condition, whereas under sever water deficit they were affected by the rootstock genotype. Under severe stress conditions (20% SWC), 1103P showed an “avoidance” behavior. It reduced stomatal conductance, inhibited photosynthesis, increased ABA content in the roots, and closed the stomata. The 101-14MGt maintained a high photosynthetic rate, limiting the reduction of soil water potential. This behavior results in a “tolerance” strategy. An analysis of the transcriptome showed that most of the differentially expressed genes were detected at 20% SWC, and more significantly in roots than in leaves. A core set of genes has been highlighted on the roots as being related to the root response to drought that are not affected by genotype nor grafting. Genes specifically regulated by grafting and genes specifically regulated by genotype under drought conditions have been identified as well. The 1103P, more than the 101-14MGt, regulated a high number of genes in both own-rooted and grafted conditions. This different regulation revealed that 1103P rootstock readily perceived the water scarcity and rapidly faced the stress, in agreement with its avoidance strategy.

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Genome-wide analysis of the SCPL gene family in grape (Vitis vinifera L.)

Cited by 6 publications

References 41 publications

Genome-Wide Identification of BTB Domain-Containing Gene Family in Grapevine (Vitis vinifera L.)

Genome-Wide Identification of BTB Domain-Containing Gene Family in Grapevine (Vitis vinifera L.)

A 5.2‐kb insertion in the coding sequence of PavSCPL, a serine carboxypeptidase‐like enhances fruit firmness in Prunus avium

Physiological and Transcriptomic Evaluation of Drought Effect on Own-Rooted and Grafted Grapevine Rootstock (1103P and 101-14MGt)

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