Comparative transcriptome reveals molecular mechanism in apple genotypes differing in CO2 tolerance in CA storage

2022 ◽  
Vol 185 ◽  
pp. 111807
Author(s):  
Yongxin Li ◽  
Ce Zheng ◽  
Chao Wang ◽  
John B. Golding ◽  
Lei Ru
Keyword(s):  
Molecular Mechanism ◽  
Comparative Transcriptome ◽  
Co2 Tolerance

scholarly journals Comparative Transcriptome Combined with Proteome Analyses Revealed Key Factors Involved in Alfalfa (Medicago sativa) Response to Waterlogging Stress

2019 ◽  
Vol 20 (6) ◽  
pp. 1359 ◽  
Author(s):  
Ningbo Zeng ◽  
Zhijian Yang ◽  
Zhifei Zhang ◽  
Longxing Hu ◽  
Liang Chen
Keyword(s):  
Medicago Sativa ◽  
Molecular Mechanism ◽  
Crop Production ◽  
Expression Profiles ◽  
Resistance Breeding ◽  
Ethylene Response Factor ◽  
Proline Metabolism ◽  
Comparative Transcriptome ◽  
Waterlogging Stress ◽  
Protein Levels

Alfalfa (Medicago sativa) is the most widely grown and most important forage crop in the world. However, alfalfa is susceptible to waterlogging stress, which is the major constraint for its cultivation area and crop production. So far, the molecular mechanism of alfalfa response to the waterlogging is largely unknown. Here, comparative transcriptome combined with proteomic analyses of two cultivars (M12, tolerant; M25, sensitive) of alfalfa showing contrasting tolerance to waterlogging were performed to understand the mechanism of alfalfa in response to waterlogging stress. Totally, 748 (581 up- and 167 down-regulated) genes were differentially expressed in leaves of waterlogging-stressed alfalfa compared with the control (M12_W vs. M12_CK), whereas 1193 (740 up- and 453 down-regulated) differentially abundant transcripts (DATs) were detected in the leaves of waterlogging-stressed plants in comparison with the control plants (M25_W vs. M25_CK). Furthermore, a total of 187 (122 up- and 65 down-regulated) and 190 (105 up- and 85 down-regulated) differentially abundant proteins (DAPs) were identified via isobaric tags for relative and absolute quantification (iTRAQ) method in M12_W vs. M12_CK and M25_W vs. M25_CK comparison, respectively. Compared dataset analysis of proteomics and transcriptomics revealed that 27 and eight genes displayed jointly up-regulated or down-regulated expression profiles at both mRNA and protein levels in M12_W vs. M12_CK comparison, whereas 30 and 27 genes were found to be co-up-regulated or co-down-regulated in M25_W vs. M25_CK comparison, respectively. The strongly enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways for co-up-regulated genes at mRNA and protein levels in M12_W vs. M12_CK comparison were ‘Amino sugar and nucleotide sugar metabolism’, ‘Arginine and proline metabolism’ and ‘Starch and sucrose metabolism’, whereas co-up-regulated protein-related pathways including ‘Arginine and proline metabolism’ and ‘Valine, leucine and isoleucine degradation’ were largely enriched in M25_W vs. M25_CK comparison. Importantly, the identified genes related to beta-amylase, Ethylene response Factor (ERF), Calcineurin B-like (CBL) interacting protein kinases (CIPKs), Glutathione peroxidase (GPX), and Glutathione-S-transferase (GST) may play key roles in conferring alfalfa tolerance to waterlogging stress. The present study may contribute to our understanding the molecular mechanism underlying the responses of alfalfa to waterlogging stress, and also provide important clues for further study and in-depth characterization of waterlogging-resistance breeding candidate genes in alfalfa.

scholarly journals Comparative transcriptome profiling reveals cold stress responsiveness in two contrasting Chinese jujube cultivars

2020 ◽  
Author(s):  
Heying Zhou ◽  
Ying He ◽  
Yongsheng Zhu ◽  
Meiyu Li ◽  
Shuang Song ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Freezing Tolerance ◽  
Molecular Mechanisms ◽  
Enrichment Analysis ◽  
Transcriptome Profiling ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Freezing Stress ◽  
Comparative Transcriptome ◽  
Chinese Jujube

Abstract Background: Low temperature is a major factor influencing the growth and development of Chinese jujube ( Ziziphus jujuba Mill.) in cold winter and spring. Little is known about the molecular mechanisms enabling jujube to cope with different freezing stress conditions. To elucidate the freezing-related molecular mechanism, we conducted comparative transcriptome analysis between ‘Dongzao’ (low freezing tolerance cultivar) and ‘Jinsixiaozao’ (high freezing tolerance cultivar) using RNA-Seq. Results: More than 20,000 genes were detected at chilling (4°C) and freezing (-10°C, -20°C, -30°C and -40°C) stress between the two cultivars. The numbers of differentially expressed genes (DEGs) between the two cultivars were 1831, 2030, 1993, 1845 and 2137 under the five treatments. Functional enrichment analysis suggested that the metabolic pathway, response to stimulus and catalytic activity were significantly enriched under stronger freezing stress. Among the DEGs, nine participated in the Ca 2+ signal pathway, thirty-two were identified to participate in sucrose metabolism, and others were identified to participate in the regulation of ROS, plant hormones and antifreeze proteins. In addition, important transcription factors ( WRKY , AP2 / ERF , NAC and bZIP ) participating in freezing stress were activated under different degrees of freezing stress. Conclusions: Our research first provides a more comprehensive understanding of DEGs involved in freezing stress at the transcriptome level in two Z. jujuba cultivars with different freezing tolerances. These results may help to elucidate the molecular mechanism of freezing tolerance in jujube and also provides new insights and candidate genes for genetically enhancing freezing stress tolerance.

scholarly journals Comparative transcriptome analysis between inbred and hybrids reveals molecular insights into yield heterosis of upland cotton

2020 ◽  
Author(s):  
Kashif Shahzad ◽  
Xuexian Zhang ◽  
Liping Guo ◽  
Tingxiang Qi ◽  
Lisheng Bao ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Transcriptome Analysis ◽  
Upland Cotton ◽  
Tissue Expression ◽  
Cotton Yield ◽  
Comparative Transcriptome ◽  
Seed Cotton ◽  
Comparative Transcriptome Analysis ◽  
Seed Cotton Yield ◽  
Efficient Breeding

Abstract Background Utilization of heterosis has greatly improved the productivity of many crops worldwide. Understanding the potential molecular mechanism about how hybridization produces superior yield in upland cotton is critical for efficient breeding programs. Results In this study, high, medium, and low hybrids varying in the level of yield heterosis were screened based on field experimentation of different years and locations. Phenotypically, high hybrid produced a mean of 14% more seed cotton yield than its better parent. Whole-genome RNA sequencing of these hybrids and their four inbred parents was performed using different tissues of the squaring stage. Comparative transcriptomic differences in each hybrid parent triad revealed a higher percentage of differentially expressed genes (DEGs) in each tissue. Expression level dominance analysis identified majority of hybrids DEGs were biased towards parent like expressions. An array of DEGs involved in ATP and protein binding, membrane, cell wall, mitochondrion, and protein phosphorylation had more functional annotations in hybrids. Sugar metabolic and plant hormone signal transduction pathways were most enriched in each hybrid. Further, these two pathways had most mapped DEGs on known seed cotton yield QTLs. Integration of transcriptome, QTLs, and gene co-expression network analysis discovered genes Gh_A03G1024, Gh_D08G1440, Gh_A08G2210, Gh_A12G2183, Gh_D07G1312, Gh_D08G1467, Gh_A03G0889, Gh_A08G2199, and Gh_D05G0202 displayed a complex regulatory network of many interconnected genes. qRT-PCR of these DEGs was performed to ensure the accuracy of RNA-Seq data. Conclusions Through genome-wide comparative transcriptome analysis, the current study identified nine key genes and pathways associated with biological process of yield heterosis in upland cotton. Our results and data resources provide novel insights and will be useful for dissecting the molecular mechanism of yield heterosis in cotton

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