scholarly journals Advances in Mechanisms and Omics Pertaining to Fruit Cracking in Horticultural Plants

Agronomy ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1045
Author(s):  
Yuying Wang ◽  
Linhui Guo ◽  
Xueqing Zhao ◽  
Yujie Zhao ◽  
Zhaoxiang Hao ◽  
...  
Keyword(s):  
Cell Wall ◽  
Gene Family ◽  
High Throughput Sequencing ◽  
Gene Families ◽  
Economic Losses ◽  
Fruit Cracking ◽  
Horticultural Plants ◽  
Genetic And Environmental Factors ◽  
Xth Gene Family ◽  
Integrative Omics

Fruit cracking is a physiological disease that occurs during fruit development, which limits the quality and marketability of the fruit and causes great economic losses. Fruit cracking is affected by physiological, genetic and environmental factors. In this paper, the mechanism of fruit cracking was elaborated from cutin and cell wall, especially the gene families related to cell wall metabolism, including the polygalacturonase (PG) gene family, xylologlucan endotransglucosylase/hydrolase (XTH) gene family and expansin gene family. In addition, due to the advancement of high-throughput sequencing technology, an increasing number of horticultural plants have completed genome sequencing. This paper expounds the application of omics, including transcriptome, proteome, metabolomics and integrative omics in fruit cracking. The measures to reduce fruit cracking include using plastic rain covers and bagging, and spraying mineral and plant growth regulators. In this paper, the mechanisms of fruit cracking are reviewed at the molecular level, and the problems needing to be solved in fruit cracking research are put forward.

scholarly journals Genome-wide identification, and phylogenetic and expression profiling analyses, of XTH gene families in Brassica rapa L. and Brassica oleracea L.

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Di Wu ◽  
Anqi Liu ◽  
Xiaoyu Qu ◽  
Jiayi Liang ◽  
Min Song
Keyword(s):  
Cell Wall ◽  
Gene Family ◽  
Brassica Oleracea ◽  
Brassica Rapa ◽  
Multigene Family ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Families ◽  
Specific Expression ◽  
Group I

Abstract Background Xyloglucan endotransglucosylase/hydrolase genes (XTHs) are a multigene family and play key roles in regulating cell wall extensibility in plant growth and development. Brassica rapa and Brassica oleracea contain XTHs, but detailed identification and characterization of the XTH family in these species, and analysis of their tissue expression profiles, have not previously been carried out. Results In this study, 53 and 38 XTH genes were identified in B. rapa and B. oleracea respectively, which contained some novel members not observed in previous studies. All XTHs of B. rapa, B. oleracea and Arabidopsis thaliana could be classified into three groups, Group I/II, III and the Early diverging group, based on phylogenetic relationships. Gene structures and motif patterns were similar within each group. All XTHs in this study contained two characteristic conserved domains (Glyco_hydro and XET_C). XTHs are located mainly in the cell wall but some are also located in the cytoplasm. Analyses of the mechanisms of gene family expansion revealed that whole-genome triplication (WGT) events and tandem duplication (TD) may have been the major mechanisms accounting for the expansion of the XTH gene family. Interestingly, TD genes all belonged to Group I/II, suggesting that TD was the main reason for the largest number of genes being in these groups. B. oleracea had lost more of the XTH genes, the conserved domain XET_C and the conserved active-site motif EXDXE compared with B. rapa, consistent with asymmetrical evolution between the two Brassica genomes. A majority of XTH genes exhibited different tissue-specific expression patterns based on RNA-seq data analyses. Moreover, there was differential expression of duplicated XTH genes in the two species, indicating that their functional differentiation occurred after B. rapa and B. oleracea diverged from a common ancestor. Conclusions We carried out the first systematic analysis of XTH gene families in B. rapa and B. oleracea. The results of this investigation can be used for reference in further studies on the functions of XTH genes and the evolution of this multigene family.

scholarly journals Effect of calcium on relieving berry cracking in grape (Vitis vinifera L.) ‘Xiangfei’

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9896 ◽  
Author(s):  
Jun Yu ◽  
Mingtao Zhu ◽  
Miao Bai ◽  
Yanshuai Xu ◽  
Shaogang Fan ◽  
...  
Keyword(s):  
Cell Wall ◽  
Grape Berry ◽  
Water Soluble ◽  
Economic Losses ◽  
Vitis Vinifera L ◽  
Cell Wall Metabolism ◽  
Physiological Disorder ◽  
Fruit Cracking ◽  
Underlying Mechanisms ◽  
Cell Wall Disassembly

Fruit cracking is a physiological disorder in many plant species that leads to severe economic losses. The aim of this study was to investigate the effect of calcium on fruit cracking and explore the underlying mechanisms. We studied the effect of exogenous calcium on grape berry cracking, calcium absorbance and distribution, and cell wall metabolism in the cracking-susceptible cultivar ‘Xiangfei’. Calcium significantly reduced the frequency of fruit cracking, increased the break force of the berry skin, and stimulated storage of calcium. In addition, calcium increased the content of protopectin and inhibited the increase in content of water-soluble pectin, by regulating the transcription and activities of enzymes associated with cell wall metabolism. Taken together, the results indicated that dipping grape berries in calcium solution is effective in preventing fruit cracking by stimulating calcium uptake, inhibiting cell wall disassembly, and promoting cell wall strengthening.

scholarly journals GenFam: A web application and database for gene family-based classification and functional enrichment analysis

2018 ◽  
Author(s):  
Renesh Bedre ◽  
Kranthi Mandadi
Keyword(s):  
Gene Family ◽  
Web Application ◽  
High Throughput Sequencing ◽  
Source Code ◽  
Enrichment Analysis ◽  
Gene Families ◽  
Functional Enrichment ◽  
Multiple Testing Correction ◽  
Web Based ◽  
Link Type

ABSTRACTGenome-scale studies using high-throughput sequencing (HTS) technologies generate substantial lists of differentially expressed genes under different experimental conditions. These gene lists need to be further mined to narrow down biologically relevant genes and associated functions in order to guide downstream functional genetic analyses. A popular approach is to determine statistically overrepresented genes in a user-defined list through enrichment analysis tools, which rely on functional annotations of genes based on Gene Ontology (GO) terms. Here, we propose a new approach, GenFam, which allows classification and enrichment of genes based on their gene family, thus simplifying identification of candidate gene families and associated genes that may be relevant to the query. GenFam and its integrated database comprises of three-hundred and eighty-four unique gene families and supports gene family classification and enrichment analyses for sixty plant genomes. Four comparative case studies with plant species belonging to different clades and families were performed using GenFam which demonstrated its robustness and comprehensiveness over preexisting functional enrichment tools. To make it readily accessible for plant biologists, GenFam is available as a web-based application where users can input gene IDs and export enrichment results in both tabular and graphical formats. Users can also customize analysis parameters by choosing from the various statistical enrichment tests and multiple testing correction methods. Additionally, the web-based application, source code and database are freely available to use and download. Website: http://mandadilab.webfactional.com/home/. Source code and database: http://mandadilab.webfactional.com/home/dload/.

scholarly journals Genome-wide identification, and phylogenetic and expression profiling analyses of XTH gene families in Brassica rapa L. and Brassica oleracea L.

2020 ◽  
Author(s):  
Min Song ◽  
Di Wu ◽  
Anqi Liu ◽  
Xiaoyu Qu ◽  
Jiayi Liang
Keyword(s):  
Cell Wall ◽  
Gene Family ◽  
Brassica Rapa ◽  
Expression Patterns ◽  
Gene Families ◽  
Functional Differentiation ◽  
Specific Expression ◽  
Major Mechanism ◽  
Group I ◽  
Gene Structures

Abstract Background Xyloglucan endotransglucosylase/hydrolase genes (XTHs) are a multigene family and play key roles in regulating cell wall extensibility in plant growth and development. XTH genes of Brassica have not been reported. Results In this study, 53 and 38 XTH genes were identified in Brassica rapa and Brassica olerecea, respectively. All XTHs of B. rapa, B. oleracea and Arabidopsis thaliana can be classified into three groups including Group I/II, III and Ancestral Group based on phylogenetic relationships. Gene structures and motif patterns were similar in the same group. All XTHs in this study contained two characteristic conserved domains (Glyco_hydro and XET_C). XTHs mainly located in the cell wall and some also located in cytoplasm. Expansion mechanism analyses uncovered that whole-genome triplication (WGT) events and tandem duplication (TD) may be the major mechanism accounting for the expansion of XTH gene family. Interestingly, TD genes were all belong to Group I/II, which suggested TD was the main reason for the largest number of genes in the groups. B. oleracea had a higher loss rate of XTH genes, conserved domain XET_C and conserved motif EXDXE compared with B. rapa, consistent with the asymmetrical evolution between the two Brassica genomes. A majority of XTH genes exhibited different tissue-specific expression patterns based on RNA-seq data analyses. Moreover, the differential expressions of duplicated XTH genes in the two species were found and indicated their functional differentiation occurred after B. rapa and B. olerecea diverged from a common ancestor. Conclusions We first systematic analyzed XTH gene families in B. rapa and B. oleracea. The results of this paper can be used for reference to further study the function of XTH gene and the evolution pattern of multi gene family.

scholarly journals Genome-wide identification, and phylogenetic and expression profiling analyses, of XTH gene families in Brassica rapa L. and Brassica oleracea L.

2020 ◽  
Author(s):  
Di Wu ◽  
Anqi Liu ◽  
Xiaoyu Qu ◽  
Jiayi Liang ◽  
Min Song
Keyword(s):  
Cell Wall ◽  
Gene Family ◽  
Brassica Oleracea ◽  
Brassica Rapa ◽  
Multigene Family ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Families ◽  
Specific Expression ◽  
Group I

Abstract Background: Xyloglucan endotransglucosylase/hydrolase genes ( XTHs ) are a multigene family and play key roles in regulating cell wall extensibility in plant growth and development. Brassica rapa and Brassica oleracea contain XTHs, but detailed identification and characterization of the XTH family in these species, and analysis of their tissue expression profiles, have not previously been carried out. Results: In this study, 53 and 38 XTH genes were identified in B. rapa and B. oleracea respectively, which contained some novel members not observed in previous studies. All XTHs of B. rapa , B. oleracea and Arabidopsis thaliana could be classified into three groups, Group I/II, III and the Early diverging group, based on phylogenetic relationships. Gene structures and motif patterns were similar within each group. All XTHs in this study contained two characteristic conserved domains (Glyco_hydro and XET_C). XTHs are located mainly in the cell wall but some are also located in the cytoplasm. Analyses of the mechanisms of gene family expansion revealed that whole-genome triplication (WGT) events and tandem duplication (TD) may have been the major mechanisms accounting for the expansion of the XTH gene family. Interestingly, TD genes all belonged to Group I/II, suggesting that TD was the main reason for the largest number of genes being in these groups. B. oleracea had lost more of the XTH genes, the conserved domain XET_C and the conserved active-site motif EXDXE compared with B. rapa , consistent with asymmetrical evolution between the two Brassica genomes. A majority of XTH genes exhibited different tissue-specific expression patterns based on RNA-seq data analyses. Moreover, there was differential expression of duplicated XTH genes in the two species, indicating that their functional differentiation occurred after B. rapa and B. oleracea diverged from a common ancestor. Conclusions: We carried out the first systematic analysis of XTH gene families in B. rapa and B. oleracea . The results of this investigation can be used for reference in further studies on the functions of XTH genes and the evolution of this multigene family.

scholarly journals Isolation and Characterization Of Rice R Genes: Evidence for Distinct Evolutionary Paths in Rice and Maize

Genetics ◽  
1996 ◽  
Vol 142 (3) ◽  
pp. 1021-1031 ◽  
Author(s):  
Jianping Hu ◽  
Beth Anderson ◽  
Susan R Wessler
Keyword(s):  
Gene Family ◽  
Gene Families ◽  
Chromosome 1 ◽  
R Gene ◽  
R Genes ◽  
Helix Loop Helix ◽  
Isolation And Characterization ◽  
Undetermined Function ◽  
Evolutionary Paths

Abstract R and B genes and their homologues encode basic helix-loop-helix (bHLH) transcriptional activators that regulate the anthocyanin biosynthetic pathway in flowering plants. In maize, R/B genes comprise a very small gene family whose organization reflects the unique evolutionary history and genome architecture of maize. To know whether the organization of the R gene family could provide information about the origins of the distantly related grass rice, we characterized members of the R gene family from rice Oryza sativa. Despite being a true diploid, O. sativa has at least two R genes. An active homologue (Ra) with extensive homology with other R genes is located at a position on chromosome 4 previously shown to be in synteny with regions of maize chromosomes 2 and 10 that contain the B and R loci, respectively. A second rice R gene (Rb) of undetermined function was identified on chromosome 1 and found to be present only in rice species with AA genomes. All non-AA species have but one R gene that is Ra-like. These data suggest that the common ancestor shared by maize and rice had a single R gene and that the small R gene families of grasses have arisen recently and independently.

scholarly journals Expression of a gene duplication encoding conserved sperm tail proteins is translationally regulated in Drosophila melanogaster.

1993 ◽  
Vol 13 (3) ◽  
pp. 1708-1718 ◽  
Author(s):  
M Schäfer ◽  
D Börsch ◽  
A Hülster ◽  
U Schäfer
Keyword(s):  
Drosophila Melanogaster ◽  
Gene Family ◽  
Translational Control ◽  
Germ Line ◽  
Gene Families ◽  
Homologous Gene ◽  
Male Sterile ◽  
Sperm Tail ◽  
Repetitive Motif ◽  
Carboxy Terminal

We have analyzed a locus of Drosophila melanogaster located at 98C on chromosome 3, which contains two tandemly arranged genes, named Mst98Ca and Mst98Cb. They are two additional members of the Mst(3)CGP gene family by three criteria. (i) Both genes are exclusively transcribed in the male germ line. (ii) Both transcripts encode a protein with a high proportion of the repetitive motif Cys-Gly-Pro. (iii) Their expression is translationally controlled; while transcripts can be detected in diploid stages of spermatogenesis, association with polysomes can be shown only in haploid stages of sperm development. The genes differ markedly from the other members of the gene family in structure; they do not contain introns, they are of much larger size, and they have the Cys-Gly-Pro motifs clustered at the carboxy-terminal end of the encoded proteins. An antibody generated against the Mst98Ca protein recognizes both Mst98C proteins in D. melanogaster. In a male-sterile mutation in which spermiogenesis is blocked before individualization of sperm, both of these proteins are no longer synthesized. This finding provides proof of late translation for the Mst98C proteins and thereby independent proof of translational control of expression. Northern (RNA) and Western immunoblot analyses indicate the presence of homologous gene families in many other Drosophila species. The Mst98C proteins share sequence homology with proteins of the outer dense fibers in mammalian spermatozoa and can be localized to the sperm tail by immunofluorescence with an anti-Mst98Ca antibody.

scholarly journals Genome-wide search and structural and functional analyses for late embryogenesis-abundant (LEA) gene family in poplar

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zihan Cheng ◽  
Xuemei Zhang ◽  
Wenjing Yao ◽  
Kai Zhao ◽  
Lin Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Higher Plants ◽  
Abiotic Stress Tolerance ◽  
Gene Families ◽  
Regulatory Elements ◽  
Late Embryogenesis Abundant ◽  
Genome Wide ◽  
Lea Gene ◽  
Late Embryogenesis ◽  
Genome Wide Search

Abstract Background The Late Embryogenesis-Abundant (LEA) gene families, which play significant roles in regulation of tolerance to abiotic stresses, widely exist in higher plants. Poplar is a tree species that has important ecological and economic values. But systematic studies on the gene family have not been reported yet in poplar. Results On the basis of genome-wide search, we identified 88 LEA genes from Populus trichocarpa and renamed them as PtrLEA. The PtrLEA genes have fewer introns, and their promoters contain more cis-regulatory elements related to abiotic stress tolerance. Our results from comparative genomics indicated that the PtrLEA genes are conserved and homologous to related genes in other species, such as Eucalyptus robusta, Solanum lycopersicum and Arabidopsis. Using RNA-Seq data collected from poplar under two conditions (with and without salt treatment), we detected 24, 22 and 19 differentially expressed genes (DEGs) in roots, stems and leaves, respectively. Then we performed spatiotemporal expression analysis of the four up-regulated DEGs shared by the tissues, constructed gene co-expression-based networks, and investigated gene function annotations. Conclusion Lines of evidence indicated that the PtrLEA genes play significant roles in poplar growth and development, as well as in responses to salt stress.

scholarly journals Shoot Regeneration Is Not a Single Cell Event

Plants ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 58
Author(s):  
Patharajan Subban ◽  
Yaarit Kutsher ◽  
Dalia Evenor ◽  
Eduard Belausov ◽  
Hanita Zemach ◽  
...  
Keyword(s):  
Gene Family ◽  
Single Cell ◽  
Shoot Regeneration ◽  
Major Gene ◽  
Molecular Genetic ◽  
Plant Biotechnology ◽  
Gene Families ◽  
Regeneration Medium ◽  
Developmental Processes ◽  
Leaf Segments

Shoot regeneration is a key tool of modern plant biotechnology. While many researchers use this process empirically, very little is known about the early molecular genetic factors and signaling events that lead to shoot regeneration. Using tobacco as a model system, we found that the inductive events required for shoot regeneration occur in the first 4–5 days following incubation on regeneration medium. Leaf segments placed on regeneration medium did not produce shoots if removed from the medium before four days indicating this time frame is crucial for the induction of shoot regeneration. Leaf segments placed on regeneration medium for longer than five days maintain the capacity to produce shoots when removed from the regeneration medium. Analysis of gene expression during the early days of incubation on regeneration medium revealed many changes occurring with no single expression pattern evident among major gene families previously implicated in developmental processes. For example, expression of Knotted gene family members increased during the induction period, whereas transcription factors from the Wuschel gene family were unaltered during shoot induction. Expression levels of genes involved in cell cycle regulation increased steadily on regeneration medium while expression of NAC genes varied. No obvious possible candidate genes or developmental processes could be identified as a target for the early events (first few days) in the induction of shoot regeneration. On the other hand, observations during the early stages of regeneration pointed out that regeneration does not occur from a single cell but a group of cells. We observed that while cell division starts just as leaf segments are placed on regeneration medium, only a group of cells could become shoot primordia. Still, these primordia are not identifiable during the first days.

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