scholarly journals LncRNA regulates tomato fruit cracking by coordinating gene expression via a  hormone-redox-cell wall network

2020 ◽  
Author(s):  
Lingzi Xue ◽  
Mintao Sun ◽  
Zhen Wu ◽  
Lu Yu ◽  
Qinghui Yu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
Abiotic Stress ◽  
Regulatory Networks ◽  
Tomato Fruit ◽  
Fruit Production ◽  
Differentially Expressed ◽  
Oxidoreductase Activity ◽  
Fruit Cracking ◽  
Stress Signals

Abstract Background Fruit cracking occurs easily under unsuitable environmental conditions and is one of the main types of damage that occurs in fruit production. It is widely accepted that plants have developed defence mechanisms and regulatory networks that respond to abiotic stress, which involves perceiving, integrating and responding to stress signals by modulating the expression of related genes. Fruit cracking is also a physiological disease caused by abiotic stress. It has been reported that a single or several genes may regulate fruit cracking. However, almost none of these reports have involved cracking regulatory networks. Results Here, RNA expression in 0 h, 8 h and 30 h saturated irrigation-treated fruits from two contrasting tomato genotypes, ‘LA1698’ (cracking-resistant, CR) and ‘LA2683’ (cracking-susceptible, CS), was analysed by mRNA and lncRNA sequencing. The GO pathways of the differentially expressed mRNAs were mainly enriched in the ‘hormone metabolic process’, ‘cell wall organization’, ‘oxidoreductase activity’ and ‘catalytic activity’ categories. According to the gene expression analysis, significantly differentially expressed genes included Solyc02g080530.3 ( Peroxide, POD ), Solyc01g008710.3 ( Mannan endo-1,4-beta-mannosidase, MAN ), Solyc08g077910.3 ( Expanded, EXP ), Solyc09g075330.3 ( Pectinesterase , PE ), Solyc07g055990.3 ( Xyloglucan endotransglucosylase-hydrolase 7, XTH7 ), Solyc12g011030.2 ( X yloglucan endotransglucosylase-hydrolase 9 , XTH9 ), Solyc10g080210.2 ( Polygalacturonase-2, PG2 ), Solyc08g081010.2 ( Gamma-glutamylcysteine synthetase, gamma-GCS ), Solyc09g008720.2 ( Ethylene receptor , ER ), Solyc11g042560.2 ( Ethylene-responsive transcription factor 4, ERF4 ) etc. In addition, the lncRNAs (XLOC_134491 and XLOC_036966) regulated the expression of their neighbouring genes, and genes related to tomato cracking were selected to construct a lncRNA-mRNA network influencing tomato cracking. Conclusions This study provides insight into the responsive network for water-induced cracking in tomato fruit. Specifically, lncRNAs regulate the hormone-redox-cell wall network, including plant hormone (auxin, ethylene) and ROS (H 2 O 2 ) signal transduction and many cell wall-related mRNAs (EXP, PG, XTH), as well as some lncRNAs ( XLOC_134491 and XLOC_104931, etc.). Keywords Tomato, LncRNA, mRNA, Transcriptome, Network, Fruit cracking

scholarly journals LncRNA regulates tomato fruit cracking by coordinating gene expression via a  hormone-redox-cell wall network

2020 ◽  
Author(s):  
Lingzi Xue ◽  
Mintao Sun ◽  
Zhen Wu ◽  
Lu Yu ◽  
Qinghui Yu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
Abiotic Stress ◽  
Regulatory Networks ◽  
Tomato Fruit ◽  
Fruit Production ◽  
Differentially Expressed ◽  
Oxidoreductase Activity ◽  
Fruit Cracking ◽  
Stress Signals

Abstract Background Fruit cracking occurs easily under unsuitable environmental conditions and is one of the main types of damage that occurs in fruit production. It is widely accepted that plants have developed defence mechanisms and regulatory networks that respond to abiotic stress, which involves perceiving, integrating and responding to stress signals by modulating the expression of related genes. Fruit cracking is also a physiological disease caused by abiotic stress. It has been reported that a single or several genes may regulate fruit cracking. However, almost none of these reports have involved cracking regulatory networks. Results Here, RNA expression in 0 h, 8 h and 30 h saturated irrigation-treated fruits from two contrasting tomato genotypes, ‘LA1698’ (cracking-resistant, CR) and ‘LA2683’ (cracking-susceptible, CS), was analysed by mRNA and lncRNA sequencing. The GO pathways of the differentially expressed mRNAs were mainly enriched in the ‘hormone metabolic process’, ‘cell wall organization’, ‘oxidoreductase activity’ and ‘catalytic activity’ categories. According to the gene expression analysis, significantly differentially expressed genes included Solyc02g080530.3 ( Peroxide, POD ), Solyc01g008710.3 ( Mannan endo-1,4-beta-mannosidase, MAN ), Solyc08g077910.3 ( Expanded, EXP ), Solyc09g075330.3 ( Pectinesterase , PE ), Solyc07g055990.3 ( Xyloglucan endotransglucosylase-hydrolase 7, XTH7 ), Solyc12g011030.2 ( X yloglucan endotransglucosylase-hydrolase 9 , XTH9 ), Solyc10g080210.2 ( Polygalacturonase-2, PG2 ), Solyc08g081010.2 ( Gamma-glutamylcysteine synthetase, gamma-GCS ), Solyc09g008720.2 ( Ethylene receptor , ER ), Solyc11g042560.2 ( Ethylene-responsive transcription factor 4, ERF4 ) etc. In addition, the lncRNAs (XLOC_16662 and XLOC_033910, etc) regulated the expression of their neighbouring genes, and genes related to tomato cracking were selected to construct a lncRNA-mRNA network influencing tomato cracking. Conclusions This study provides insight into the responsive network for water-induced cracking in tomato fruit. Specifically, lncRNAs regulate the hormone-redox-cell wall network, including plant hormone (auxin, ethylene) and ROS (H 2 O 2 ) signal transduction and many cell wall-related mRNAs ( EXP, PG, XTH ), as well as some lncRNAs ( XLOC_16662 and XLOC_033910, etc.).

scholarly journals LncRNA regulates tomato fruit cracking by coordinating gene expression via a  hormone-redox-cell wall network

2020 ◽  
Author(s):  
Lingzi Xue ◽  
Mintao Sun ◽  
Zhen Wu ◽  
Lu Yu ◽  
Qinghui Yu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
Abiotic Stress ◽  
Regulatory Networks ◽  
Tomato Fruit ◽  
Fruit Production ◽  
Differentially Expressed ◽  
Oxidoreductase Activity ◽  
Fruit Cracking ◽  
Stress Signals

Abstract Background Fruit cracking occurs easily under unsuitable environmental conditions and is one of the main types of damage that occurs in fruit production. It is widely accepted that plants have developed defence mechanisms and regulatory networks that respond to abiotic stress, which involves perceiving, integrating and responding to stress signals by modulating the expression of related genes. Fruit cracking is also a physiological disease caused by abiotic stress. It has been reported that a single or several genes may regulate fruit cracking. However, almost none of these reports have involved cracking regulatory networks. Results Here, RNA expression in 0 h, 8 h and 30 h saturated irrigation-treated fruits from two contrasting tomato genotypes, ‘LA1698’ (cracking-resistant, CR) and ‘LA2683’ (cracking-susceptible, CS), was analysed by mRNA and lncRNA sequencing. The GO pathways of the differentially expressed mRNAs were mainly enriched in the ‘hormone metabolic process’, ‘cell wall organization’, ‘oxidoreductase activity’ and ‘catalytic activity’ categories. According to the gene expression analysis, significantly differentially expressed genes included Solyc02g080530.3 ( Peroxide, POD ), Solyc01g008710.3 ( Mannan endo-1,4-beta-mannosidase, MAN ), Solyc08g077910.3 ( Expanded, EXP ), Solyc09g075330.3 ( Pectinesterase , PE ), Solyc07g055990.3 ( Xyloglucan endotransglucosylase-hydrolase 7, XTH7 ), Solyc12g011030.2 ( X yloglucan endotransglucosylase-hydrolase 9 , XTH9 ), Solyc10g080210.2 ( Polygalacturonase-2, PG2 ), Solyc08g081010.2 ( Gamma-glutamylcysteine synthetase, gamma-GCS ), Solyc09g008720.2 ( Ethylene receptor , ER ), Solyc11g042560.2 ( Ethylene-responsive transcription factor 4, ERF4 ) etc. In addition, the lncRNAs (XLOC_16662 and XLOC_033910, etc) regulated the expression of their neighbouring genes, and genes related to tomato cracking were selected to construct a lncRNA-mRNA network influencing tomato cracking. Conclusions This study provides insight into the responsive network for water-induced cracking in tomato fruit. Specifically, lncRNAs regulate the hormone-redox-cell wall network, including plant hormone (auxin, ethylene) and ROS (H 2 O 2 ) signal transduction and many cell wall-related mRNAs ( EXP, PG, XTH ), as well as some lncRNAs ( XLOC_16662 and XLOC_033910, etc.).

scholarly journals LncRNA regulates tomato fruit cracking by coordinating gene expression via a  hormone-redox-cell wall network

2020 ◽  
Author(s):  
Lingzi Xue ◽  
Mintao Sun ◽  
Zhen Wu ◽  
Lu Yu ◽  
Qinghui Yu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
Abiotic Stress ◽  
Regulatory Networks ◽  
Tomato Fruit ◽  
Fruit Production ◽  
Differentially Expressed ◽  
Oxidoreductase Activity ◽  
Fruit Cracking ◽  
Stress Signals

Abstract Background Fruit cracking occurs easily under unsuitable environmental conditions and is one of the main types of damage that occurs in fruit production. It is widely accepted that plants have developed defence mechanisms and regulatory networks that respond to abiotic stress, which involves perceiving, integrating and responding to stress signals by modulating the expression of related genes. Fruit cracking is also a physiological disease caused by abiotic stress. It has been reported that a single or several genes may regulate fruit cracking. However, almost none of these reports have involved cracking regulatory networks. Results Here, RNA expression in 0 h, 8 h and 30 h saturated irrigation-treated fruits from two contrasting tomato genotypes, ‘LA1698’ (cracking-resistant, CR) and ‘LA2683’ (cracking-susceptible, CS), was analysed by mRNA and lncRNA sequencing. The GO pathways of the differentially expressed mRNAs were mainly enriched in the ‘hormone metabolic process’, ‘cell wall organization’, ‘oxidoreductase activity’ and ‘catalytic activity’ categories. According to the gene expression analysis, significantly differentially expressed genes included Solyc02g080530.3 ( Peroxide, POD ), Solyc01g008710.3 ( Mannan endo-1,4-beta-mannosidase, MAN ), Solyc08g077910.3 ( Expanded, EXP ), Solyc09g075330.3 ( Pectinesterase , PE ), Solyc07g055990.3 ( Xyloglucan endotransglucosylase-hydrolase 7, XTH7 ), Solyc12g011030.2 ( X yloglucan endotransglucosylase-hydrolase 9 , XTH9 ), Solyc10g080210.2 ( Polygalacturonase-2, PG2 ), Solyc08g081010.2 ( Gamma-glutamylcysteine synthetase, gamma-GCS ), Solyc09g008720.2 ( Ethylene receptor , ER ), Solyc11g042560.2 ( Ethylene-responsive transcription factor 4, ERF4 ) etc. In addition, the lncRNAs (XLOC_134491 and XLOC_036966) regulated the expression of their neighbouring genes, and genes related to tomato cracking were selected to construct a lncRNA-mRNA network influencing tomato cracking. Conclusions This study provides insight into the responsive network for water-induced cracking in tomato fruit. Specifically, lncRNAs regulate the hormone-redox-cell wall network, including plant hormone (auxin, ethylene) and ROS (H 2 O 2 ) signal transduction and many cell wall-related mRNAs (EXP, PG, XTH), as well as some lncRNAs ( XLOC_134491 and XLOC_104931, etc.). Keywords Tomato, LncRNA, mRNA, Transcriptome, Network, Fruit cracking

scholarly journals LncRNA regulates tomato fruit cracking by coordinating gene expression in hormone-redox-cell wall network

2019 ◽  
Author(s):  
Lingzi Xue ◽  
Fangling Jiang ◽  
Mintao Sun ◽  
Zhen Wu ◽  
Lu Yu ◽  
...  
Keyword(s):  
Cell Wall ◽  
Abiotic Stress ◽  
Defense Mechanisms ◽  
Regulatory Networks ◽  
Tomato Fruit ◽  
Fruit Production ◽  
Oxidoreductase Activity ◽  
Fruit Cracking ◽  
Stress Signals ◽  
Insight Into

Abstract Background Fruit cracking, occurs easily under unsuitable environmental conditions, is one of the main disorders in fruit production. It is widely accepted that plant have developed a defense mechanisms or regulatory networks in response to abiotic stress. This involves perceiving, integrating and responding to stress signals by modulating the expression of related genes. Fruit cracking is also a kind of physiological disease caused by abiotic stress. Previously reported a single or sevel genes may regulate fruit cracking. However, almost none of these efforts have involved cracking regulatory network. Results Here, 0, 8 and 30 h irrigation treatments resulted in differential expression of 1028 mRNAs and 87 lncRNAs in ‘LA1698’ (cracking resistant, CR) at 8 h_vs_0 h, 468 mRNAs and 15 lncRNAs at CR_30 h_vs_CR_0 h, 321 mRNAs and 19 lncRNAs at CR_30 h_vs_CR_8 h; 531 mRNAs and 75 lncRNAs in ‘LA2683’ (cracking susceptible, CS) at 8 h_vs_0 h, 420 mRNAs and 24 lncRNAs at CS_30 h_vs_CS_0 h, 270 mRNAs and 20 lncRNAs at CS_30 h_vs_CS_8 h; 339 mRNAs and 64 lncRNAs in the two contrasting tomato genotypes at 0 h, 338 mRNAs and 94 lncRNAs at 8 h, and 369 mRNAs and 77 lncRNAs at 30 h. The GO pathway of the differentially expressed mRNAs are mainly enriched in ‘hormone metabolic process’, ‘cell wall organization’, ‘oxidoreductase activity’ and ‘catalytic activity’. In addition, lncRNAs regulated the expression of their neighboring genes and genes related to tomato cracking were selected to construct a lncRNA-mRNA network that influence tomato cracking. Conclutions This study provides insight into the responsive network for water-induced cracking in tomato fruit. specifically lncRNAs regulated hormone-redox-cell wall network, including plant hormone (including auxin, ethylene) and ROS (H 2 O 2 ) signal transduction and many cell wall related mRNAs ( EXP, PG, XTH ), as well as some lncRNAs (XLOC_010878 and XLOC_016662, ect) .

scholarly journals LncRNA regulates tomato fruit cracking by coordinating gene expression via a  hormone-redox-cell wall network

2019 ◽  
Author(s):  
Lingzi Xue ◽  
Mintao Sun ◽  
Zhen Wu ◽  
Lu Yu ◽  
Qinghui Yu ◽  
...  
Keyword(s):  
Cell Wall ◽  
Abiotic Stress ◽  
Regulatory Networks ◽  
Tomato Fruit ◽  
Fruit Production ◽  
Oxidoreductase Activity ◽  
Fruit Cracking ◽  
Cell Wall Organization ◽  
Stress Signals ◽  
Insight Into

Abstract Background Fruit cracking occurs easily under unsuitable environmental conditions and is one of the main types of damage that occurs in fruit production. It is widely accepted that plants have developed defence mechanisms and regulatory networks that respond to abiotic stress, which involves perceiving, integrating and responding to stress signals by modulating the expression of related genes. Fruit cracking is also a physiological disease caused by abiotic stress. It has been reported that a single or several genes may regulate fruit cracking. However, almost none of these reports have involved cracking regulatory networks. Results Here, 0, 8 and 30 h irrigation treatments resulted in the differential expression of 1028 mRNAs and 87 lncRNAs in ‘LA1698’ (cracking resistant, CR) at 8 h_vs_0 h, 468 mRNAs and 15 lncRNAs in CR_30 h_vs_CR_0 h, 321 mRNAs and 19 lncRNAs in CR_30 h_vs_CR_8 h; 531 mRNAs and 75 lncRNAs in ‘LA2683’ (cracking susceptible, CS) at 8 h_vs_0 h, 420 mRNAs and 24 lncRNAs in CS_30 h_vs_CS_0 h, 270 mRNAs and 20 lncRNAs in CS_30 h_vs_CS_8 h; and 339 mRNAs and 64 lncRNAs in the two contrasting tomato genotypes at 0 h, 338 mRNAs and 94 lncRNAs at 8 h, and 369 mRNAs and 77 lncRNAs at 30 h. The GO pathways of the differentially expressed mRNAs were mainly enriched in the ‘hormone metabolic process’, ‘cell wall organization’, ‘oxidoreductase activity’ and ‘catalytic activity’ categories. In addition, the lncRNAs regulated the expression of their neighbouring genes, and genes related to tomato cracking were selected to construct a lncRNA-mRNA network influencing tomato cracking. Conclusions This study provides insight into the responsive network for water-induced cracking in tomato fruit. Specifically, lncRNAs regulate the hormone-redox-cell wall network, including plant hormone (auxin, ethylene) and ROS (H 2 O 2 ) signal transduction and many cell wall-related mRNAs ( EXP, PG, XTH ), as well as some lncRNAs (XLOC_010878 and XLOC_016662, etc.).

scholarly journals LncRNA regulates tomato fruit cracking by coordinating gene expression via a hormone-redox-cell wall network

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Lingzi Xue ◽  
Mintao Sun ◽  
Zhen Wu ◽  
Lu Yu ◽  
Qinghui Yu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
Tomato Fruit ◽  
Fruit Cracking

scholarly journals Microtubule Dynamics Plays a Vital Role in Plant Adaptation and Tolerance to Salt Stress

2021 ◽  
Vol 22 (11) ◽  
pp. 5957
Author(s):  
Hyun Jin Chun ◽  
Dongwon Baek ◽  
Byung Jun Jin ◽  
Hyun Min Cho ◽  
Mi Suk Park ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
Salt Stress ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Related Gene ◽  
Plant Adaptation ◽  
Salt Stress Response ◽  
Network Analyses ◽  
Cell Wall Biogenesis

Although recent studies suggest that the plant cytoskeleton is associated with plant stress responses, such as salt, cold, and drought, the molecular mechanism underlying microtubule function in plant salt stress response remains unclear. We performed a comparative proteomic analysis between control suspension-cultured cells (A0) and salt-adapted cells (A120) established from Arabidopsis root callus to investigate plant adaptation mechanisms to long-term salt stress. We identified 50 differentially expressed proteins (45 up- and 5 down-regulated proteins) in A120 cells compared with A0 cells. Gene ontology enrichment and protein network analyses indicated that differentially expressed proteins in A120 cells were strongly associated with cell structure-associated clusters, including cytoskeleton and cell wall biogenesis. Gene expression analysis revealed that expressions of cytoskeleton-related genes, such as FBA8, TUB3, TUB4, TUB7, TUB9, and ACT7, and a cell wall biogenesis-related gene, CCoAOMT1, were induced in salt-adapted A120 cells. Moreover, the loss-of-function mutant of Arabidopsis TUB9 gene, tub9, showed a hypersensitive phenotype to salt stress. Consistent overexpression of Arabidopsis TUB9 gene in rice transgenic plants enhanced tolerance to salt stress. Our results suggest that microtubules play crucial roles in plant adaptation and tolerance to salt stress. The modulation of microtubule-related gene expression can be an effective strategy for developing salt-tolerant crops.

scholarly journals De-novo transcriptome analysis unveils differentially expressed genes regulating drought and salt stress response in Panicum sumatrense

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Rasmita Rani Das ◽  
Seema Pradhan ◽  
Ajay Parida
Keyword(s):  
Gene Expression ◽  
Salt Stress ◽  
Abiotic Stress ◽  
Stress Tolerance ◽  
Differentially Expressed Genes ◽  
Salinity Stress ◽  
Abiotic Stress Tolerance ◽  
Differentially Expressed ◽  
Little Millet ◽  
Drought And Salt Stress

AbstractScreening the transcriptome of drought tolerant variety of little millet (Panicum sumatrense), a marginally cultivated, nutritionally rich, susbsistent crop, can identify genes responsible for its hardiness and enable identification of new sources of genetic variation which can be used for crop improvement. RNA-Seq generated ~ 230 million reads from control and treated tissues, which were assembled into 86,614 unigenes. In silico differential gene expression analysis created an overview of patterns of gene expression during exposure to drought and salt stress. Separate gene expression profiles for leaf and root tissue revealed the differences in regulatory mechanisms operating in these tissues during exposure to abiotic stress. Several transcription factors were identified and studied for differential expression. 61 differentially expressed genes were found to be common to both tissues under drought and salinity stress and were further validated using qRT-PCR. Transcriptome of P. sumatrense was also used to mine for genic SSR markers relevant to abiotic stress tolerance. This study is first report on a detailed analysis of molecular mechanisms of drought and salinity stress tolerance in a little millet variety. Resources generated in this study can be used as potential candidates for further characterization and to improve abiotic stress tolerance in food crops.

scholarly journals Identification of Key Genes and miRNA-mRNA Regulatory Pathways in Bronchopulmonary Dysplasia in Preterm Infants by Bioinformatics Methods

2020 ◽  
Author(s):  
Tong Sun ◽  
Haiyang Yu ◽  
Jianhua Fu
Keyword(s):  
Gene Expression ◽  
Preterm Infants ◽  
Bronchopulmonary Dysplasia ◽  
Regulatory Networks ◽  
Enrichment Analysis ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Regulatory Pathways ◽  
Ppi Networks ◽  
Key Genes

Abstract Background: Bronchopulmonary dysplasia (BPD) remains a severe respiratory complication of preterm infants in neonatal intensive care units (NICUs). However, its pathogenesis has been unclear. Bioinformatics analysis, which can help us explore genetic alternations and recognize latent diagnostic biomarkers, has recently promoted the comprehension of the molecular mechanisms underlying disease occurrence and development. Methods: In this study, we identified key genes and miRNA-mRNA regulatory networks in BPD in preterm infants to elucidate the pathogenesis of BPD. We downloaded and analyzed miRNA and gene expression microarray datasets from the Gene Expression Omnibus database (GEO). Differentially expressed miRNA (DEMs) and differentially expressed genes (DEGs) were obtained through NetworkAnalyst. We performed pathway enrichment analysis using the Database for Annotation, Visualization and Integrated Discovery program (DAVID), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG). Then we used the STRING to establish protein–protein interactions and the Cytoscape tool to establish miRNA–mRNA regulatory networks. Results: We identified 19 significant DEMs and 140 and 33 significantly upregulated and downregulated DEGs, respectively. Functional enrichment analysis indicated that significant DEGs were associated with the antigen processing and presentation, and B-cell receptor signaling pathways in BPD. Key DEGs, such as CD19, CD79B, MS4A1, and FCGR2B were selected as hub genes in PPI networks. Conclusions: In this study, we screened out 19 DEMs that might play important roles in the regulatory networks of BPD. Higher expression of miRNAs such as miR-15b-5p, hsa-miR-32-5p, miR-3613-3p, and miR-33a-5p and lower expression of miRNAs such as miR-3960, miR-425-5p, and miR-3202 might be correlated with the process of BPD.

scholarly journals Integrative transcriptome and proteome analyses provide new insights into different stages of Akebia trifoliata fruit cracking during ripening

2020 ◽  
Author(s):  
Juan Niu ◽  
Yaliang Shi ◽  
Kunyong Huang ◽  
Yicheng Zhong ◽  
Jing Chen ◽  
...  
Keyword(s):  
Cell Wall ◽  
Fruit Ripening ◽  
Differentially Expressed ◽  
Wall Structure ◽  
Mrna Levels ◽  
Galactose Metabolism ◽  
Pests And Diseases ◽  
Fruit Cracking ◽  
Resistant Varieties ◽  
Fruit Decay

Abstract Background: Akebia trifoliata (Thunb.) Koid may have applications as a new source of biofuels owing to its high seed count, seed oil content, and in-field yields. However, the pericarp of A. trifoliata cracks longitudinally during fruit ripening, which increases the incidence of pests and diseases and can lead to fruit decay and deterioration, resulting in significant losses in yield. Few studies have evaluated the mechanisms underlying A. trifoliata fruit cracking. Results: In this study, by observing the cell wall structure of the pericarp, we found that the cell wall became thinner and looser and showed substantial breakdown in the pericarp of cracking fruit compared with that in non-cracking fruit. Moreover, integrative analyses of transcriptome and proteome profiles at different stages of fruit ripening demonstrated changes in the expression of various genes and proteins after cracking. Furthermore, the mRNA levels of 20 differentially expressed genes were analyzed, and parallel reaction monitoring analysis of 20 differentially expressed proteins involved in cell wall metabolism was conducted. Among the molecular targets, pectate lyases and pectinesterase, which are involved in pentose and glucuronate interconversion, and β-galactosidase 2, which is involved in galactose metabolism, were significantly upregulated in cracking fruits than in non-cracking fruits. This suggested that they might play crucial roles in A. trifoliata fruit cracking. Conclusions: Our findings provided new insights into potential genes influencing the fruit cracking trait in A. trifoliata and established a basis for further research on the breeding of cracking-resistant varieties to increase seed yields for biorefineries.

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