Full-Length Transcriptome and RNA-Seq Analyses Reveal the Mechanisms Underlying Waterlogging Tolerance in Kiwifruit (Actinidia valvata)

Li, Zhi; Bai, Danfeng; Zhong, Yunpeng; Lin, Miaomiao; Sun, Lei; Qi, Xiujuan; Hu, Chun-Gen; Fang, Jinbao

doi:10.3390/ijms23063237

Cited by 24 publications

(15 citation statements)

References 97 publications

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“…Results showed that the obtained sequencing data in the present study was reliable and our waterlogged treatment of kiwifruit roots was effective (Figure 2). Previous studies have provided information on variations in the number of responded transcripts of kiwifruit genotypes with different tolerance levels under oxygen deprivation stress [28][29][30]. In this study, we found that there were more up-regulated DEGs than down-regulated ones (Figure 3), indicating the expression induction and enhancement of gene function were more responsible in response to waterlogging stress of A. deliciosa roots, consistent with previous study in A. valvata [30].…”

Section: Discussionsupporting

confidence: 90%

Transcriptome Analysis Reveals the Molecular Mechanism and Responsive Genes of Waterlogging Stress in Actinidia deliciosa Planch Kiwifruit Plants

Xing,

Huang,

Zhang

et al. 2023

IJMS

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Waterlogging stress is one of the major natural issues resulting in stunted growth and loss of agricultural productivity. Cultivated kiwifruits are popular for their rich vitamin C content and unique flavor among consumers, while commonly sensitive to waterlogging stress. The wild kiwifruit plants are usually obliged to survive in harsh environments. Here, we carried out a transcriptome analysis by high-throughput RNA sequencing using the root tissues of Actinidia deliciosa (a wild resource with stress-tolerant phenotype) after waterlogging for 0 d, 3 d, and 7 d. Based on the RNA sequencing data, a high number of differentially expressed genes (DEGs) were identified in roots under waterlogging treatment, which were significantly enriched into four biological processes, including stress response, metabolic processes, molecular transport, and mitotic organization, by gene ontology (GO) simplify enrichment analysis. Among these DEGs, the hypoxia-related genes AdADH1 and AdADH2 were correlated well with the contents of acetaldehyde and ethanol, and three transcription factors Acc26216, Acc08443, and Acc16908 were highly correlated with both AdADH1/2 genes and contents of acetaldehyde and ethanol. In addition, we found that there might be an evident difference among the promoter sequences of ADH genes from A. deliciosa and A. chinensis. Taken together, our results provide additional information on the waterlogging response in wild kiwifruit plants.

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Section: Discussionsupporting

confidence: 90%

Transcriptome Analysis Reveals the Molecular Mechanism and Responsive Genes of Waterlogging Stress in Actinidia deliciosa Planch Kiwifruit Plants

Xing,

Huang,

Zhang

et al. 2023

IJMS

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“…Within the Italian kiwifruit sector, this practice has not been widely used before. We have, therefore, screened genotypes of different Actinidia species intended for use as rootstocks or for breeding programs for their putative resistance or tolerance to KVDS [27,29,45,46].…”

Section: Discussionmentioning

confidence: 99%

Potential of Different Actinidia Genotypes as Resistant Rootstocks for Preventing Kiwifruit Vine Decline Syndrome

et al. 2022

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Kiwifruit Vine Decline Syndrome (KVDS) is currently affecting Italian kiwifruit cultivation, causing dramatic yield and economic losses. The syndrome’s aetiology is due to soil-borne pathogens and waterlogging, leading to the decay of roots and then the canopy. Current knowledge about the disease is limited, and the techniques to control the syndrome are ineffective. The use of tolerant rootstocks is one of the most promising tools. Six genotypes of Actinidia were tested for two years at four infected experimental sites in Friuli Venezia Giulia (NE Italy). Plant evaluation and analysis were carried out on the root system and the vegetative parts. At all experimental sites, three genotypes, all belonging to the A. macrosperma group, grew normally. In contrast, plants of A. polygama died earlier and those of A. chinensis var. deliciosa ‘Hayward’ declined during the first year. A. arguta ‘Miss Green’ survived the first year but started to decline during the second year. After two years of study, we were able to identify three putative resistant genotypes: A. macrosperma accession numbers 176 and 183, and ‘Bounty71’, which will be a useful resource as rootstocks or as parents for breeding owing to their potential genetic resistance traits.

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“…Third-generation sequencing technology holds great potential for improved transcript detection compared to second-generation sequencing techniques such as RNA-seq. This has been demonstrated through its successful applications in a variety of plants [31][32][33][34]. The current study provided comprehensive landscapes of isoform full-length sequences, gene structures, lncRNAs, and AS events.…”

Section: High-quality Data Obtained From Pacbio Transcriptome Sequencingmentioning

confidence: 87%

The Landscapes of Gluten Regulatory Network in Elite Wheat Cultivars Contrasting in Gluten Strength

Liu

Zhu

et al. 2023

IJMS

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Yangmai-13 (YM13) is a wheat cultivar with weak gluten fractions. In contrast, Zhenmai-168 (ZM168) is an elite wheat cultivar known for its strong gluten fractions and has been widely used in a number of breeding programs. However, the genetic mechanisms underlying the gluten signatures of ZM168 remain largely unclear. To address this, we combined RNA-seq and PacBio full-length sequencing technology to unveil the potential mechanisms of ZM168 grain quality. A total of 44,709 transcripts were identified in Y13N (YM13 treated with nitrogen) and 51,942 transcripts in Z168N (ZM168 treated with nitrogen), including 28,016 and 28,626 novel isoforms in Y13N and Z168N, respectively. Five hundred and eighty-four differential alternative splicing (AS) events and 491 long noncoding RNAs (lncRNAs) were discovered. Incorporating the sodium-dodecyl-sulfate (SDS) sedimentation volume (SSV) trait, both weighted gene coexpression network analysis (WGCNA) and multiscale embedded gene coexpression network analysis (MEGENA) were employed for network construction and prediction of key drivers. Fifteen new candidates have emerged in association with SSV, including 4 transcription factors (TFs) and 11 transcripts that partake in the post-translational modification pathway. The transcriptome atlas provides new perspectives on wheat grain quality and would be beneficial for developing promising strategies for breeding programs.

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Full-Length Transcriptome and RNA-Seq Analyses Reveal the Mechanisms Underlying Waterlogging Tolerance in Kiwifruit (Actinidia valvata)

Cited by 24 publications

References 97 publications

Transcriptome Analysis Reveals the Molecular Mechanism and Responsive Genes of Waterlogging Stress in Actinidia deliciosa Planch Kiwifruit Plants

Transcriptome Analysis Reveals the Molecular Mechanism and Responsive Genes of Waterlogging Stress in Actinidia deliciosa Planch Kiwifruit Plants

Potential of Different Actinidia Genotypes as Resistant Rootstocks for Preventing Kiwifruit Vine Decline Syndrome

The Landscapes of Gluten Regulatory Network in Elite Wheat Cultivars Contrasting in Gluten Strength

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