The Experts below are selected from a list of 258 Experts worldwide ranked by ideXlab platform
Carlos H Crisosto - One of the best experts on this subject based on the ideXlab platform.
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Genomic Sequencing of Japanese Plum (Prunus salicina Lindl.) Mutants Provides a New Model for Rosaceae Fruit Ripening Studies
Frontiers in Plant Science, 2018Co-Authors: Angel V. Fernández I Martí, Christopher A. Saski, George A. Manganaris, Ksenija Gasic, Carlos H CrisostoAbstract:It has recently been described that the Japanese plum ‘Santa Rosa’ Bud Sport series contains variations in ripening pattern: climacteric, suppressed-climacteric and non-climacteric types. This provides an interesting model to study the role of ethylene and other key mechanisms governing fruit ripening, softening and senescence. The aim of the current study was to investigate such differences at the genomic level, using this series of plum Bud Sports, with special reference to genes involved in ethylene biosynthesis, signal transduction, and sugar metabolism. Genomic DNA, isolated from leaf samples of six Japanese plum cultivars (‘Santa Rosa’, ‘July Santa Rosa’, ‘Late Santa Rosa’, ‘Sweet Miriam’, ‘Roysum’, and ‘Casselman’), was used to construct paired-end standard Illumina libraries. Sequences were aligned to the Prunus persica genome, and genomic variations (SNPs, INDELS, and CNV’s) were investigated. Results determined twelve potential candidate genes with significant copy number variation, being associated with ethylene perception and signal transduction components. Additionally, the Maximum Likelihood (ML) phylogenetic tree showed two sorbitol dehydrogenase genes grouping into a distinct clade, indicating that this natural group is well-defined and presents high sequence identity among its members. In contrast, the ethylene group, which includes ACO1, ACS1, ACS4, ACS5, CTR1, ERF1, ERF3 and ethylene-receptor genes, was widely distributed and clustered into ten different groups. Thus, ACS, ERF and sorbitol dehydrogenase proteins potentially share a common ancestor for different plant genomes, while the expansion rate may be related to ancestral expansion rather than species-specific events. Based on the distribution of the clades, we suggest that gene function diversification for the ripening pathway occurred prior to family extension. We herein report all the frameshift mutations in genes involved in sugar tranSport and ethylene biosynthesis detected as well as the gene copy number variation implicated in ripening differences.
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discovery of non climacteric and suppressed climacteric Bud Sport mutations originating from a climacteric japanese plum cultivar prunus salicina lindl
Frontiers in Plant Science, 2015Co-Authors: Ioannis S Minas, Carolina Font I Forcada, Gerald S Dangl, Thomas M Gradziel, Abhaya M Dandekar, Carlos H CrisostoAbstract:Japanese plums are classified as climacteric; however, some economically important cultivars selected in California produce very little ethylene and require long ripening both ‘on’ and ‘off’ the tree to reach eating-ripe firmness. To unravel the ripening behavior of different Japanese plum cultivars, ripening was examined in the absence (air) or in the presence of ethylene or propylene (an ethylene analogue) following a treatment or not with 1-methylcyclopropene (1-MCP, an ethylene action inhibitor). Detailed physiological studies revealed for the first time three distinct ripening types in plum fruit: climacteric, suppressed-climacteric and non-climacteric. Responding to exogenous ethylene or propylene, the slow-softening supressed-climacteric cultivars produced detectable amounts of ethylene, in contrast to the novel non-climacteric cultivar that produced no ethylene and softened extremely slowly. Genetic analysis using microsatellite markers produced identical DNA profiles for the climacteric cultivars ‘Santa Rosa’ and ‘July Santa Rosa’, the suppressed-climacteric cultivars ‘Late Santa Rosa’, ‘Casselman’ and ‘Roysum’ and the novel non-climacteric ‘Sweet Miriam’, as expected since historic records present most of these cultivars as Bud-Sport mutations derived initially from ‘Santa Rosa’. This present study provides a novel fruit system to address the molecular basis of ripening and to develop markers that assist breeders in providing high-quality stone fruit cultivars that can remain ‘on-tree’, increasing fruit flavor, saving harvesting costs, and potentially reducing the need for low-temperature storage during postharvest handling.
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Non-climacteric ripening and sorbitol homeostasis in plum fruits
Plant Science, 2014Co-Authors: Macarena Farcuh, Carlos H Crisosto, Yuval Cohen, Avi Sadka, Eduardo BlumwaldAbstract:a b s t r a c t During ripening fruits undergo several physiological and biochemical modifications that influence quality-related properties, such as texture, color, aroma and taste. We studied the differences in eth- ylene and sugar metabolism between two genetically related Japanese plum cultivars with contrasting ripening behaviors. 'Santa Rosa' (SR) behaved as a typical climacteric fruit, while the Bud Sport mutant 'Sweet Miriam' (SM) displayed a non-climacteric ripening pattern. SM fruit displayed a delayed ripening that lasted 120 days longer than that of the climacteric fruit. At the full-ripe stage, both cultivars reached similar final size and weight but the non-climacteric fruits were firmer than the climacteric fruits. Fully ripe non-climacteric plum fruits, showed an accumulation of sorbitol that was 2.5 times higher than that of climacteric fruits, and the increase in sorbitol were also par- alleled to an increase in sucrose catabolism. These changes were highly correlated with decreased activity and expression of NAD + -dependent sorbitol dehydrogenase and sorbitol oxidase and increased sorbitol- 6-phosphate dehydrogenase activity, suggesting an enhanced sorbitol synthesis in non-climacteric fruits.
Baihong Chen - One of the best experts on this subject based on the ideXlab platform.
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Whole-genome DNA methylation patterns and complex associations with gene expression associated with anthocyanin biosynthesis in apple fruit skin.
Planta, 2019Co-Authors: Wenfang Li, Gai-xing Ning, Qi Zhou, Baihong ChenAbstract:MAIN CONCLUSION: DNA methylation of anthocyanin biosynthesis-related genes and MYB/bHLH transcription factors was associated with apple fruit skin color revealed by whole-genome bisulfite sequencing. DNA methylation is a common feature of epigenetic regulation and is associated with various biological processes. Anthocyanins are among the secondary metabolites that contribute to fruit colour, which is a key appearance and nutrition quality attribute of apple fruit. Although few studies reported that DNA methylation in the promoter of MYB transcription factor was associated with fruit skin color, there is a general lack of understanding of the dynamics of global and genic DNA methylation in apple fruit. Here, whole-genome bisulfite sequencing was carried out in fruit skin of apple (Malus domestica Borkh.) cv. 'Red Delicious' (G0) and its four-generation Bud Sport mutants, including 'Starking Red' (G1), 'Starkrimson' (G2), 'Campbell Redchief' (G3) and 'Vallee spur' (G4) at color break stage. Correlation and linear-regression analysis between DNA methylation level and anthocyanin content, as well as the transcription levels of genes related to anthocyanin biosynthesis were carried out. The results showed that the number of differentially methylated regions (DMRs) and differentially methylated genes (DMGs) was considerably increased from G1 to G4 versus the number observed in G0. The (m)CHH context was dominant in apple, but the levels of (m)CG and (m)CHG of DMGs were significantly higher than that of the (m)CHH. Genetic variation of Bud Sport mutants from 'Red Delicious' was associated with differential DNA methylation. Additionally, hypomethylation of (m)CG and (m)CHG contexts in flavonoid biosynthesis pathway genes (PAL, 4CL, CYP98A, PER, CCoAOMT, CHS, and F3'H), (m)CHG context in MYB10 at upstream, led to transcriptional activation and was conductive to anthocyanin accumulation. However, hypermethylation of (m)CG context in bHLH74 at upstream led to transcriptional inhibition, inhibiting anthocyanin accumulation.
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anthocyanin accumulation correlates with hormones in the fruit skin of red delicious and its four generation Bud Sport mutants
BMC Plant Biology, 2018Co-Authors: Wenfang Li, Shijin Yang, Mohammed Mujitaba Dawuda, Baihong ChenAbstract:Bud Sport mutants of apple (Malus domestica Borkh.) trees with a highly blushed colouring pattern are mainly caused by the accumulation of anthocyanins in the fruit skin. Hormones are important factors modulating anthocyanin accumulation. However, a good understanding of the interplay between hormones and anthocyanin synthesis in apples, especially in mutants at the molecular level, remains elusive. Here, physiological and comparative transcriptome approaches were used to reveal the molecular basis of color pigmentation in the skin of ‘Red Delicious’ (G0) and its mutants, including ‘Starking Red’ (G1), ‘Starkrimson’ (G2), ‘Campbell Redchief’ (G3) and ‘Vallee spur’ (G4). Pigmentation in the skin gradually proliferated from G0 to G4. The anthocyanin content was higher in the mutants than in ‘Red Delicious’. The activation of early phenylpropanoid biosynthesis genes, including ASP3, PAL, 4CL, PER, CHS, CYP98A and F3’H, was more responsible for anthocyanin accumulation in mutants at the color break stage. In addition, IAA and ABA had a positive regulatory effect on the synthesis of anthocyanins, while GA had the reverse effect. The down-regulation of AACT1, HMGS, HMGR, MVK, MVD2, IDI1 and FPPS2 involved in terpenoid biosynthesis influences anthocyanin accumulation by positively regulating transcripts of AUX1 and SAUR that contribute to the synthesis of IAA, GID2 to GA, PP2C and SnRK2 to ABA. Furthermore, MYB and bHLH members, which are highly correlated (r=0.882–0.980) with anthocyanin content, modulated anthocyanin accumulation by regulating the transcription of structural genes, including CHS and F3’H, involved in the flavonoid biosynthesis pathway. The present comprehensive transcriptome analyses contribute to the understanding of the the relationship between hormones and anthocyanin synthesis as well as the molecular mechanism involved in apple skin pigmentation.
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Anthocyanin accumulation correlates with hormones in the fruit skin of ‘Red Delicious’ and its four generation Bud Sport mutants
BMC Plant Biology, 2018Co-Authors: Wenfang Li, Shijin Yang, Mohammed Mujitaba Dawuda, Zonghuan Ma, Baihong ChenAbstract:Bud Sport mutants of apple (Malus domestica Borkh.) trees with a highly blushed colouring pattern are mainly caused by the accumulation of anthocyanins in the fruit skin. Hormones are important factors modulating anthocyanin accumulation. However, a good understanding of the interplay between hormones and anthocyanin synthesis in apples, especially in mutants at the molecular level, remains elusive. Here, physiological and comparative transcriptome approaches were used to reveal the molecular basis of color pigmentation in the skin of ‘Red Delicious’ (G0) and its mutants, including ‘Starking Red’ (G1), ‘Starkrimson’ (G2), ‘Campbell Redchief’ (G3) and ‘Vallee spur’ (G4). Pigmentation in the skin gradually proliferated from G0 to G4. The anthocyanin content was higher in the mutants than in ‘Red Delicious’. The activation of early phenylpropanoid biosynthesis genes, including ASP3, PAL, 4CL, PER, CHS, CYP98A and F3’H, was more responsible for anthocyanin accumulation in mutants at the color break stage. In addition, IAA and ABA had a positive regulatory effect on the synthesis of anthocyanins, while GA had the reverse effect. The down-regulation of AACT1, HMGS, HMGR, MVK, MVD2, IDI1 and FPPS2 involved in terpenoid biosynthesis influences anthocyanin accumulation by positively regulating transcripts of AUX1 and SAUR that contribute to the synthesis of IAA, GID2 to GA, PP2C and SnRK2 to ABA. Furthermore, MYB and bHLH members, which are highly correlated (r=0.882–0.980) with anthocyanin content, modulated anthocyanin accumulation by regulating the transcription of structural genes, including CHS and F3’H, involved in the flavonoid biosynthesis pathway. The present comprehensive transcriptome analyses contribute to the understanding of the the relationship between hormones and anthocyanin synthesis as well as the molecular mechanism involved in apple skin pigmentation.
Eduardo Blumwald - One of the best experts on this subject based on the ideXlab platform.
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Ethylene Response of Plum ACC Synthase 1 (ACS1) Promoter is Mediated through the Binding Site of Abscisic Acid Insensitive 5 (ABI5)
Plants (Basel Switzerland), 2019Co-Authors: Avi Sadka, Macarena Farcuh, David Toubiana, Lyudmila Shlizerman, Jianrong Feng, Yunting Zhang, Eduardo BlumwaldAbstract:The enzyme 1-amino-cyclopropane-1-carboxylic acid synthase (ACS) participates in the ethylene biosynthesis pathways and it is tightly regulated transcriptionally and post-translationally. Notwithstanding its major role in climacteric fruit ripening, the transcriptional regulation of ACS during ripening is not fully understood. We studied fruit ripening in two Japanese plum cultivars, the climacteric Santa Rosa (SR) and its non-climacteric Bud Sport mutant, Sweet Miriam (SM). As the two cultivars show considerable difference in ACS expression, they provide a good system for the study of the transcriptional regulation of the gene. To investigate the differential transcriptional regulation of ACS1 genes in the SR and SM, their promoter regions, which showed only minor sequence differences, were isolated and used to identify the binding of transcription factors interacting with specific ACS1 cis-acting elements. Three transcription factors (TFs), abscisic acid-insensitive 5 (ABI5), GLABRA 2 (GL2), and TCP2, showed specific binding to the ACS1 promoter. Synthetic DNA fragments containing multiple cis-acting elements of these TFs fused to β-glucuronidase (GUS), showed the ABI5 binding site mediated ethylene and abscisic acid (ABA) responses of the promoter. While TCP2 and GL2 showed constant and similar expression levels in SM and SR fruit during ripening, ABI5 expression in SM fruits was lower than in SR fruits during advanced fruit ripening states. Overall, the work demonstrates the complex transcriptional regulation of ACS1.
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Hormone balance in a climacteric plum fruit and its non-climacteric Bud mutant during ripening
Plant Science, 2018Co-Authors: Macarena Farcuh, Avi Sadka, David Toubiana, Nir Sade, Rosa M. Rivero, Adi Doron-faigenboim, Eiji Nambara, Eduardo BlumwaldAbstract:Abstract Hormone balance plays a crucial role in the control of fruit ripening. We characterized and compared hormone balance in two Japanese plum cultivars (Prunus salicina Lindl.), namely Santa Rosa, a climacteric type, and Sweet Miriam, its non-climacteric Bud-Sport mutant. We assessed hormonal changes in gene expression associated with hormone biosynthesis, perception and signaling during ripening on-the tree and throughout postharvest storage and in response to ethylene treatments. Non-climacteric fruit displayed lower ethylene levels than climacteric fruit at all stages and lower auxin levels during the initiation of ripening on-the-tree and during most of post-harvest storage. Moreover, 1-MCP-induced ethylene decrease also resulted in low auxin contents in Santa Rosa, supporting the role of auxin in climacteric fruit ripening. The differences in auxin contents between Santa Rosa and Sweet Miriam fruit could be the consequence of different routed auxin biosynthesis pathways as indicated by the significant negative correlations between clusters of auxin metabolism-associated genes. Ethylene induced increased ABA levels throughout postharvest storage in both ripening types. Overall, ripening of Santa Rosa and Sweet Miriam fruit are characterized by distinct hormone accumulation pathways and interactions.
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Sugar metabolism reprogramming in a non-climacteric Bud mutant of a climacteric plum fruit during development on the tree
Journal of Experimental Botany, 2017Co-Authors: Macarena Farcuh, Avi Sadka, Rosa M. Rivero, Bosheng Li, Lyudmila Shlizerman, Eduardo BlumwaldAbstract:We investigated sugar metabolism in leaves and fruits of two Japanese plum (Prunus salicina Lindl.) cultivars, the climacteric Santa Rosa and its Bud Sport mutant the non-climacteric Sweet Miriam, during development on the tree. We previously characterized differences between the two cultivars. Here, we identified key sugar metabolic pathways. Pearson coefficient correlations of metabolomics and transcriptomic data and weighted gene co-expression network analysis (WGCNA) of RNA sequencing (RNA-Seq) data allowed the identification of 11 key sugar metabolism-associated genes: sucrose synthase, sucrose phosphate synthase, cytosolic invertase, vacuolar invertase, invertase inhibitor, α-galactosidase, β-galactosidase, galactokinase, trehalase, galactinol synthase, and raffinose synthase. These pathways were further assessed and validated through the biochemical characterization of the gene products and with metabolite analysis. Our results demonstrated the reprogramming of sugar metabolism in both leaves and fruits in the non-climacteric plum, which displayed a shift towards increased sorbitol synthesis. Climacteric and non-climacteric fruits showed differences in their UDP-galactose metabolism towards the production of galactose and raffinose, respectively. The higher content of galactinol, myo-inositol, raffinose, and trehalose in the non-climacteric fruits could improve the ability of the fruits to cope with the oxidative processes associated with fruit ripening. Overall, our results support a relationship between sugar metabolism, ethylene, and ripening behavior.
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Non-climacteric ripening and sorbitol homeostasis in plum fruits
Plant Science, 2014Co-Authors: Macarena Farcuh, Carlos H Crisosto, Yuval Cohen, Avi Sadka, Eduardo BlumwaldAbstract:a b s t r a c t During ripening fruits undergo several physiological and biochemical modifications that influence quality-related properties, such as texture, color, aroma and taste. We studied the differences in eth- ylene and sugar metabolism between two genetically related Japanese plum cultivars with contrasting ripening behaviors. 'Santa Rosa' (SR) behaved as a typical climacteric fruit, while the Bud Sport mutant 'Sweet Miriam' (SM) displayed a non-climacteric ripening pattern. SM fruit displayed a delayed ripening that lasted 120 days longer than that of the climacteric fruit. At the full-ripe stage, both cultivars reached similar final size and weight but the non-climacteric fruits were firmer than the climacteric fruits. Fully ripe non-climacteric plum fruits, showed an accumulation of sorbitol that was 2.5 times higher than that of climacteric fruits, and the increase in sorbitol were also par- alleled to an increase in sucrose catabolism. These changes were highly correlated with decreased activity and expression of NAD + -dependent sorbitol dehydrogenase and sorbitol oxidase and increased sorbitol- 6-phosphate dehydrogenase activity, suggesting an enhanced sorbitol synthesis in non-climacteric fruits.
Shenchun Qu - One of the best experts on this subject based on the ideXlab platform.
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swath ms facilitated proteomic profiling of fruit skin between fuji apple and a red skin Bud Sport mutant
BMC Plant Biology, 2019Co-Authors: Moxian Chen, Kailu Zhang, Yuchen Song, Yuan Tian, Xi Chen, Nenghui Ye, Jianhua Zhang, Shenchun QuAbstract:Apple is one of the most popular fruit crops world-wide and its skin color is an important quality consideration essential for commercial value. However, the strategy on genetic breeding for red skin apple and the genetic basis of skin color differentiation is very limited and still largely unknown. Here, we reported a Bud Sport mutant of Fuji apple with red skin color and enhanced anthocyanins accumulation. Quantitative SWATH-MS (sequential window acquisition of all theoretical spectra-mass spectrometry) proteomics investigations revealed proteome changes in the apple red skin Bud mutation and a total of 451 differentially expressed proteins were identified in apple skin. The mutant showed significantly increased expression levels of photosynthesis-related proteins, stress-related proteins as well as anthocyanins biosynthesis pathway. On the other hand, substantial downregulation of mitogen-activated protein kinase 4 (MAPK4) and mevalonate kinase (MVK) were detected, indicating a promising role for the red skin color development in the mutant. Furthermore, we also hypothesize that a post-transcriptional regulation of the skin color formation occurs in the mutant through the advanced SWATH-MS analysis. Our work provides important information on the application of proteomic methods for analysing proteomes changes in Fuji apple and highlights a clade of regulatory proteins potentially contributing for the molecular breeding of fruit skin color.
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Identification of candidate genes for leaf scorch in Populus deltoids by the whole genome resequencing analysis
Scientific Reports, 2018Co-Authors: Weibing Zhuang, Shenchun Qu, Fengjiao Zhang, Zhong Lin WangAbstract:Leaf scorch exists as a common phenomenon in the development of plant, especially when plants encounter various adversities, which leads to great losses in agricultural production. Both Jinhong poplar (JHP) and Caihong poplar (CHP) (Populus deltoids) are obtained from a Bud Sport on Zhonghong poplar. Compared with CHP, JHP always exhibits leaf scorch, poor growth, premature leaf discoloration, and even death. In this study, the candidate genes associated with leaf scorch between JHP and CHP were identified by the whole genome resequencing using Illumina HiSeqTM. There were 218,880 polymorphic SNPs and 46,933 indels between JHP and CHP, respectively. Among these, the candidate genes carrying non-synonymous SNPs in coding regions were classified into 6 groups. The expression pattern of these candidate genes was also explored in JHP and CHP among different sampling stages. Combined with the qRT-PCR analysis, the results showed that genes associated with tranSport of various nutritional elements, senescence and MYB transcription factor might play important roles during the process of leaf scorch in Populus deltoids. Four genes belonging to these three groups carried more than three SNPs in their coding sequence, which might play important roles in leaf scorch. The above results provided candidate genes involved in leaf scorch in Populus deltoids, and made us better understand the molecular regulation mechanism of leaf scorch in Populus deltoids.
Erwin R. Schmidt - One of the best experts on this subject based on the ideXlab platform.
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The columnar mutation (“Co gene”) of apple (Malus × domestica) is associated with an integration of a Gypsy-like retrotransposon
Molecular Breeding, 2014Co-Authors: Dominik Otto, Romina Petersen, Bastienne Brauksiepe, Peter Braun, Erwin R. SchmidtAbstract:The columnar growth habit of apple trees ( Malus × domestica Borkh.) is a unique plant architecture phenotype that arose as a Bud Sport mutation of a McIntosh tree in the 1960s. The mutation (“ Co gene”) led to trees (McIntosh Wijcik) with thick, upright main stems and short internodes that generate short fruit spurs instead of long lateral branches. Although Co has been localized to chromosome 10, in a region approximately between 18.5 and 19 Mb, its molecular nature is unknown. In a classical positional cloning approach in combination with the analysis of NGS data, we cloned and analyzed the Co region. Our results show that the insertion of a Ty3/Gypsy retrotransposon into a non-coding region at position 18.8 Mb is the only detectable genomic difference between McIntosh and McIntosh Wijcik and is found in all columnar cultivars. The genetic effect of the insertion is unclear; however, Illumina^® RNA-seq data of McIntosh and McIntosh Wijcik suggest that the columnar growth habit is associated with differential expression of the retrotransposon transcript, causing changes in the expression levels of many protein coding genes. The mechanism by which the Gypsy retrotransposon is involved in generating the columnar habit is not yet clear; our findings form the basis for tackling this question.
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The columnar mutation (“Co gene”) of apple (Malus × domestica) is associated with an integration of a Gypsy-like retrotransposon
Molecular Breeding, 2013Co-Authors: Dominik Otto, Romina Petersen, Bastienne Brauksiepe, Peter Braun, Erwin R. SchmidtAbstract:The columnar growth habit of apple trees (Malus × domestica Borkh.) is a unique plant architecture phenotype that arose as a Bud Sport mutation of a McIntosh tree in the 1960s. The mutation (“Co gene”) led to trees (McIntosh Wijcik) with thick, upright main stems and short internodes that generate short fruit spurs instead of long lateral branches. Although Co has been localized to chromosome 10, in a region approximately between 18.5 and 19 Mb, its molecular nature is unknown. In a classical positional cloning approach in combination with the analysis of NGS data, we cloned and analyzed the Co region. Our results show that the insertion of a Ty3/Gypsy retrotransposon into a non-coding region at position 18.8 Mb is the only detectable genomic difference between McIntosh and McIntosh Wijcik and is found in all columnar cultivars. The genetic effect of the insertion is unclear; however, Illumina® RNA-seq data of McIntosh and McIntosh Wijcik suggest that the columnar growth habit is associated with differential expression of the retrotransposon transcript, causing changes in the expression levels of many protein coding genes. The mechanism by which the Gypsy retrotransposon is involved in generating the columnar habit is not yet clear; our findings form the basis for tackling this question.
