Comparative transcriptome profiling of tuberous roots of two sweetpotato lines with contrasting low temperature tolerance during storage

Ji, Cheng; Kim, Ho Soo; Lee, Chan-Ju; Kim, So-Eun; Lee, Hyeong-Un; Nam, Sang-Sik; Li, Qiang; Ma, Daifu; Kwak, Sang‐Soo

doi:10.1016/j.gene.2019.144244

Cited by 23 publications

(18 citation statements)

References 46 publications

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“…Fibrous roots (S1, root diameter of 2 mm), pencil roots (S2, root diameter of 5 mm) and storage roots at two stages (S3 and S4; root diameters of 15 mm and 25 mm, respectively) were collected from the sweet potato plants in early November to cover the entire storage root initiation and development processes. Then, for low-temperature treatment, the collected storage roots (S4) were stored at 4 °C as described [ 47 ]. Tuberous roots were collected at 0 (control), 1, and 2 weeks after treatment.…”

Section: Methodsmentioning

confidence: 99%

Genome-wide identification, phylogeny and expression analysis of AP2/ERF transcription factors family in sweet potato

Hao

et al. 2021

BMC Genomics

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Background In recent years, much attention has been given to AP2/ERF transcription factors because they play indispensable roles in many biological processes, such as plant development and biotic and abiotic stress responses. Although AP2/ERFs have been thoroughly characterised in many plant species, the knowledge about this family in the sweet potato, which is a vital edible and medicinal crop, is still limited. In this study, a comprehensive genome-wide investigation was conducted to characterise the AP2/ERF gene family in the sweet potato. Results Here, 198 IbAP2/ERF transcription factors were obtained. Phylogenetic analysis classified the members of the IbAP2/ERF family into three groups, namely, ERF (172 members), AP2 (21 members) and RAV (5 members), which was consistent with the analysis of gene structure and conserved protein domains. The evolutionary characteristics of these IbAP2/ERF genes were systematically investigated by analysing chromosome location, conserved protein motifs and gene duplication events, indicating that the expansion of the IbAP2/ERF gene family may have been caused by tandem duplication. Furthermore, the analysis of cis-acting elements in IbAP2/ERF gene promoters implied that these genes may play crucial roles in plant growth, development and stress responses. Additionally, the available RNA-seq data and quantitative real-time PCR (qRT-PCR) were used to investigate the expression patterns of IbAP2/ERF genes during sweet potato root development as well as under multiple forms of abiotic stress, and we identified several developmental stage-specific and stress-responsive IbAP2/ERF genes. Furthermore, g59127 was differentially expressed under various stress conditions and was identified as a nuclear protein, which was in line with predicted subcellular localization results. Conclusions This study originally revealed the characteristics of the IbAP2/ERF superfamily and provides valuable resources for further evolutionary and functional investigations of IbAP2/ERF genes in the sweet potato.

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Section: Methodsmentioning

confidence: 99%

Genome-wide identification, phylogeny and expression analysis of AP2/ERF transcription factors family in sweet potato

Hao

et al. 2021

BMC Genomics

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“…Transcriptome technology has been used to reveal differences in the molecular mechanisms of cold tolerance among different varieties [33,[50][51][52][53]. Previous studies have shown that there are more constitutive expression genes in the tolerant variety than the sensitive one before cold stress treatment [54,55].…”

Section: Transcriptional Differences In Cotyledons Of Varieties With mentioning

confidence: 99%

Transcriptomic Profiling of Young Cotyledons Response to Chilling Stress in Two Contrasting Cotton (Gossypium hirsutum L.) Genotypes at the Seedling Stage

Cheng

Zhang

Wang

et al. 2020

IJMS

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Young cotyledons of cotton seedlings are most susceptible to chilling stress. To gain insight into the potential mechanism of cold tolerance of young cotton cotyledons, we conducted physiological and comparative transcriptome analysis of two varieties with contrasting phenotypes. The evaluation of chilling injury of young cotyledons among 74 cotton varieties revealed that H559 was the most tolerant and YM21 was the most sensitive. The physiological analysis found that the ROS scavenging ability was lower, and cell membrane damage was more severe in the cotyledons of YM21 than that of H559 under chilling stress. RNA-seq analysis identified a total of 44,998 expressed genes and 19,982 differentially expressed genes (DEGs) in young cotyledons of the two varieties under chilling stress. Weighted gene coexpression network analysis (WGCNA) of all DEGs revealed four significant modules with close correlation with specific samples. The GO-term enrichment analysis found that lots of genes in H559-specific modules were involved in plant resistance to abiotic stress. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that pathways such as plant hormone signal transduction, MAPK signaling, and plant–pathogen interaction were related to chilling stress response. A total of 574 transcription factors and 936 hub genes in these modules were identified. Twenty hub genes were selected for qRT-PCR verification, revealing the reliability and accuracy of transcriptome data. These findings will lay a foundation for future research on the molecular mechanism of cold tolerance in cotyledons of cotton.

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“…4 and 47 • C represented chilling and heat treatment and 25 • C served as controls. 4 • C were the temperature commonly used for the low temperature treatment (Ji et al, 2020;Vyse et al, 2020). Sweetpotato grows at summer hot season, it may suffer from the 40s • C. To study the impact of extreme hot temperature, we treated sweetpotato seedlings using 47 • C. Each group had a total of 60 plants.…”

Section: Sweetpotato Culture and Temperature Treatmentsmentioning

confidence: 99%

“…There are also several studies on the impact of temperature stress on sweetpotato gene expression. These studies show that low temperature treatment induced aberrant expression of many coded and non-coded genes (Ji et al, 2017a(Ji et al, , 2019(Ji et al, , 2020Xie et al, 2017Xie et al, , 2019. Several studies over-expressed an individual gene to enhance the tolerance to low temperature stress in sweetpotato (Kim et al, 2011;Fan et al, 2012;Ji et al, 2017b;Jin et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

“…Both heat and chilling temperature potentially affects sweetpotato growth and development and further affect sweetpotato yield and biomass. Although there are several reports on impact of extreme temperatures on sweetpotato (Kim et al, 2011;Fan et al, 2012;Ji et al, 2017aJi et al, , 2019Ji et al, , 2020Xie et al, 2017Xie et al, , 2019Wang et al, 2019), but these studies majorly focused on gene expression analysis and the impact during the sweetpotato storage. There is few study on the impact of temperature stress on sweetpotato seedlings, particularly on the oxidative stress.…”

Section: Introductionmentioning

confidence: 99%

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Chilling and Heat Stress-Induced Physiological Changes and MicroRNA-Related Mechanism in Sweetpotato (Ipomoea batatas L.)

Yang

et al. 2020

Front. Plant Sci.

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Sweetpotato (Ipomoea batatas (L.) Lam.) is an important industrial and food crop. Both chilling and heat stress inhibits sweetpotato growth and development and then affects yield. However, the physiological and molecular mechanisms of sweetpotato response to chilling and heat stress is unclear. In this study, we investigated the effect of extreme temperature on sweetpotato physiological response, with a focus on oxidative stress and the potential microRNA (miRNA)-mediated molecular mechanism. Our results showed that both chilling and heat stress resulted in accumulation of reactive oxygen species (ROS), including H 2 O 2 and O 2 − , and caused oxidative stress in sweetpotato. This further affected the activities of oxidative stress-related enzymes and products, including SOD, POD, and MDA. Both chilling and heat stress inhibited POD activities but induced the enzyme activities of SOD and MDA. This suggests that sweetpotato cells initiated its own defense mechanism to handle extreme temperature-caused oxidative damage. Oxidative damage and repair are one mechanism that sweetpotato plants respond to extreme temperatures. Another potential mechanism is miRNA-mediated gene response. Chilling and heat stress altered the expression of stress-responsive miRNAs in sweetpotato seedlings. These miRNAs regulate sweetpotato response to extreme stress through targeting individual protein-coding genes.

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Comparative transcriptome profiling of tuberous roots of two sweetpotato lines with contrasting low temperature tolerance during storage

Cited by 23 publications

References 46 publications

Genome-wide identification, phylogeny and expression analysis of AP2/ERF transcription factors family in sweet potato

Genome-wide identification, phylogeny and expression analysis of AP2/ERF transcription factors family in sweet potato

Transcriptomic Profiling of Young Cotyledons Response to Chilling Stress in Two Contrasting Cotton (Gossypium hirsutum L.) Genotypes at the Seedling Stage

Chilling and Heat Stress-Induced Physiological Changes and MicroRNA-Related Mechanism in Sweetpotato (Ipomoea batatas L.)

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