Transcriptome Analysis Reveals Genes Associated with Flooding Tolerance in Mulberry Plants

Hu, Jingtao; Duan, Yufeng; Jiao, Yang; Gan, Liping; Chen, Wenjing; Yang, Jin; Xiao, Guosheng; Guan, Lingliang; Chen, Jingsheng

doi:10.3390/life13051087

Cited by 5 publications

(3 citation statements)

References 77 publications

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“…This was corroborated by a transcriptome analysis that revealed the up-regulation of genes associated with ethylene biosynthesis in submerged roots [16,49]. Hu et al [50] reported forty differentially expressed genes involved in ethylene signaling in mulberry plants under waterlogging. This finding emphasizes the important role of phytohormones in modulating the signaling networks that respond to waterlogging in plants.…”

Section: Wt Line Maintained Cellular Membrane Integrity and Exhibited...mentioning

confidence: 79%

Comparative Morpho-Physiological, Biochemical, and Gene Expressional Analyses Uncover Mechanisms of Waterlogging Tolerance in Two Soybean Introgression Lines

Sharmin,

Karikari,

Bhuiyan

et al. 2024

Plants

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Waterlogging is one of the key abiotic factors that severely impedes the growth and productivity of soybeans on a global scale. To develop soybean cultivars that are tolerant to waterlogging, it is a prerequisite to unravel the mechanisms governing soybean responses to waterlogging. Hence, we explored the morphological, physiological, biochemical, and transcriptional changes in two contrasting soybean introgression lines, A192 (waterlogging tolerant, WT) and A186 (waterlogging sensitive, WS), under waterlogging. In comparison to the WT line, waterlogging drastically decreased the root length (RL), shoot length (ShL), root fresh weight (RFW), shoot fresh weight (ShFW), root dry weight (RDW), and shoot dry weight (ShDW) of the WS line. Similarly, waterlogging inhibited soybean plant growth by suppressing the plant’s photosynthetic capacity, enhancing oxidative damage from reactive oxygen species, and decreasing the chlorophyll content in the WS line but not in the WT line. To counteract the oxidative damage and lipid peroxidation, the WT line exhibited increased activity of antioxidant enzymes such as peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT), as well as higher levels of proline content than the WS line. In addition, the expression of antioxidant enzyme genes (POD1, POD2, FeSOD, Cu/ZnSOD, CAT1, and CAT2) and ethylene-related genes (such as ACO1, ACO2, ACS1, and ACS2) were found to be up-regulated in WT line under waterlogging stress conditions. In contrast, these genes showed a down-regulation in their expression levels in the stressed WS line. The integration of morpho-physiological, biochemical, and gene expression analyses provide a comprehensive understanding of the responses of WT and WS lines to waterlogging conditions. These findings would be beneficial for the future development of soybean cultivars that can withstand waterlogging.

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Section: Wt Line Maintained Cellular Membrane Integrity and Exhibited...mentioning

confidence: 79%

Comparative Morpho-Physiological, Biochemical, and Gene Expressional Analyses Uncover Mechanisms of Waterlogging Tolerance in Two Soybean Introgression Lines

Sharmin,

Karikari,

Bhuiyan

et al. 2024

Plants

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“…The localized QTLs were mainly concentrated in linkage groups 4, 6, 8, 10, and 11, which is consistent with some previous studies [ 33 , 53 , 54 ]. Transcriptome analysis has been used to study the response of many plant species to various environmental stresses [ 55 , 56 , 57 , 58 , 59 ]. With the development of high-throughput sequencing technology and the continuous improvement of transcriptome databases, the combination of transcriptome data with traditional QTL mapping or GWAS has been widely used in the prediction of candidate genes.…”

Section: Discussionmentioning

confidence: 99%

Mapping of Candidate Genes for Nitrogen Uptake and Utilization in Japonica Rice at Seedling Stage

Chen,

Ma,

Xia

et al. 2024

Genes

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Nitrogen (N) is one of the essential nutrients for the growth and development of crops. The adequate application of N not only increases the yield of crops but also improves the quality of agricultural products, but the excessive application of N can cause many adverse effects on ecology and the environment. In this study, genome-wide association analysis (GWAS) was performed under low- and high-N conditions based on 788,396 SNPs and phenotypic traits relevant to N uptake and utilization (N content and N accumulation). A total of 75 QTLs were obtained using GWAS, which contained 811 genes. Of 811 genes, 281 genes showed different haplotypes, and 40 genes had significant phenotypic differences among different haplotypes. Of these 40 genes, 5 differentially expressed genes (Os01g0159250, Os02g0618200, Os02g0618400, Os02g0630300, and Os06g0619000) were finally identified as the more valuable candidate genes based on the transcriptome data sequenced from Longjing31 (low-N-tolerant variety) and Songjing 10 (low-N-sensitive variety) under low- and high-N treatments. These new findings enrich the genetic resources for N uptake and utilization in rice, as well as lay a theoretical foundation for improving the efficiency of N uptake and utilization in rice.

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“…Furthermore, additional studies have partially revealed the mechanism of hypoxia-induced transcriptional and translational regulation in plants [18]. A study of Morus alba showed that genes associated with cytokinin, ethylene, and MAPK signaling were significantly upregulated under flooding treatment [19]. Another study focused on Salix matsudana, which overexpressed SmTTF30 and enhanced its tolerance to flooding stress by increasing peroxidase activity and reducing malondialdehyde content [20].…”

Section: Introductionmentioning

confidence: 99%

Comparative Transcriptome Analysis Reveals the Molecular Mechanism of Salt Combined with Flooding Tolerance in Hybrid Willow (Salix matsudana × alba)

Chen,

Gao,

et al. 2023

Forests

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Plants in coastal areas often face the combined stress of salt and flooding, which can cause severe damage. The impact of multiple stresses on plant growth and survival is greater than that of individual stresses. However, the molecular responses of hybrid willow (Salix matsudana × alba) to the combination of salt and flooding have not been well understood. In this study, we conducted a comparative transcriptome analysis to investigate the molecular mechanism underlying the tolerance of hybrid willow to salt-flooding. Seedings were, respectively, treated with 200 mM NaCl and flooded with water or 200 mM NaCl solution for 3 d, 10 d, and 17 d. We identified 1842, 3350, and 2259 differentially expressed genes (DEGs) regulated by hybrid willow under single salt stress, single flooding stress, and combined salt and flooding stress, respectively. Many DEGs detected in single salt- and flooding-treated plants were expressed differentially after the combined salt and flooding. Most of the shared transcripts exhibited similar fold changes in common molecular responses such as detoxification of reactive oxygen species (ROS) and signaling pathways related to calcium, phytohormones, and protein kinases, which were also observed in plants exposed to each stress individually. Additionally, a large number of specific DEGs were identified under salt-flooding stress, primarily associated with cell wall remodeling, osmotic adjustments, stress signaling, primary metabolism, and ROS scavenging. KEGG (Kyoto Encyclopedia of Genes and Genomes) annotation indicated that hybrid willow leaves responded to salt-flooding stress mainly through phytohormone signaling and MAPK signaling pathways. Overall, this study provides new insights into the molecular mechanisms underlying the response of Salix species to multiple stresses and identifies potential candidate genes for enhancing the performance of hybrid willows.

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Transcriptome Analysis Reveals Genes Associated with Flooding Tolerance in Mulberry Plants

Cited by 5 publications

References 77 publications

Comparative Morpho-Physiological, Biochemical, and Gene Expressional Analyses Uncover Mechanisms of Waterlogging Tolerance in Two Soybean Introgression Lines

Comparative Morpho-Physiological, Biochemical, and Gene Expressional Analyses Uncover Mechanisms of Waterlogging Tolerance in Two Soybean Introgression Lines

Mapping of Candidate Genes for Nitrogen Uptake and Utilization in Japonica Rice at Seedling Stage

Comparative Transcriptome Analysis Reveals the Molecular Mechanism of Salt Combined with Flooding Tolerance in Hybrid Willow (Salix matsudana × alba)

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