Transcriptome analysis of grapevine shoots exposed to chilling temperature for four weeks

Kim, Seon Ae; Ahn, Soon Young; Yun, Hae Keun

doi:10.1007/s13580-015-0118-5

Cited by 14 publications

(11 citation statements)

References 49 publications

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“…Many metabolomics [ 12 , 35 ], functional genomics [ 36 , 37 ], high-throughput sequencing [ 23 ], and proteomics [ 38 ] studies have identified the molecular mechanisms of plant cold tolerance. However, the current understanding of the complex mechanisms of winter rapeseed resistance to cold is still limited.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome Analysis Reveals Key Cold-Stress-Responsive Genes in Winter Rapeseed (Brassica rapa L.)

Coulter

Liu³

et al. 2019

IJMS

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Low ambient air temperature limits the growth and selection of crops in cold regions, and cold tolerance is a survival strategy for overwintering plants in cold winters. Studies of differences in transcriptional levels of winter rapeseed (Brassica rapa L.) under cold stress can improve our understanding of transcript-mediated cold stress responses. In this study, two winter rapeseed varieties, Longyou-7 (cold-tolerant) and Lenox (cold-sensitive), were used to reveal morphological, physiological, and transcriptome levels after 24 h of cold stress, and 24 h at room temperature, to identify the mechanism of tolerance to cold stress. Compared to Lenox, Longyou-7 has a shorter growth period and greater belowground mass, and exhibits stronger physiological activity after cold stress. Subsequently, more complete genomic annotation was obtained by sequencing. A total of 10,251 and 10,972 differentially expressed genes (DEG) were identified in Longyou-7 and Lenox, respectively. Six terms closely related to cold stress were found by the Gene Ontology (GO) function annotation. Some of these terms had greater upregulated expression in Longyou-7, and the expression of these genes was verified by qRT-PCR. Most of these DEGs are involved in phenylpropanoid biosynthesis, plant hormone signal transduction, ribosome biogenesis, MAPK signaling pathway, basal transcription factors, and photosynthesis. Analysis of the genes involved in the peroxisome pathway revealed that Longyou-7 and Lenox may have different metabolic patterns. Some transcription factors may play an important role in winter rapeseed tolerance to cold stress, and Longyou-7 is slightly slower than Lenox. Our results provide a transcriptome database and candidate genes for further study of winter rapeseed cold stress.

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Section: Discussionmentioning

confidence: 99%

Transcriptome Analysis Reveals Key Cold-Stress-Responsive Genes in Winter Rapeseed (Brassica rapa L.)

Coulter

Liu³

et al. 2019

IJMS

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“…Core-2/I-branching beta-1, 6-N-acetylglucosaminyltransferase is a member of Core-2/I-Branching enzyme family that has been shown to be inhibited in response to a long exposure to low temperature in grapevine ( Vitis spp.) (Kim et al, 2016 ). Markers S1_102344252 and S1_102344288 on chromosome 3 were linked to a RING/U-box protein.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Association Mapping of Loci Associated with Plant Growth and Forage Production under Salt Stress in Alfalfa (Medicago sativa L.)

Liu

2017

Front. Plant Sci.

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Salinity tolerance is highly desirable to sustain alfalfa production in marginal lands that have been rendered saline. In this study, we used a diverse panel of 198 alfalfa accessions for mapping loci associated with plant growth and forage production under salt stress using genome-wide association studies (GWAS). The plants were genotyped using genotyping-by-sequencing (GBS). A greenhouse procedure was used for phenotyping four agronomic and physiological traits affected by salt stress, including dry weight (DW), plant height (PH), leaf chlorophyll content (LCC), and stomatal conductance (SC). For each trait, a stress susceptibility index (SSI) was used to evaluate plant performance under stressed and non-stressed conditions. Marker-trait association identified a total of 42 markers significantly associated with salt tolerance. They were located on all chromosomes except chromosome 2 based on the alignment of their flanking sequences to the reference genome (Medicago truncatula). Of those identified, 13 were associated with multiple traits. Several loci identified in the present study were also identified in previous reports. BLAST search revealed that 19 putative candidate genes linked to 24 significant markers. Among them, B3 DNA-binding protein, Thiaminepyrophosphokinase and IQ calmodulin-binding motif protein were identified among multiple traits in the present and previous studies. With further investigation, these markers and candidates would be useful for developing markers for marker-assisted selection in breeding programs to improve alfalfa cultivars with enhanced tolerance to salt stress.

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“…Moreover, TOPLESS (TPL) was involved in mutual adjustment between hormones via NO in Petunia hybrida [ 36 ]. Additionally, genes encoding a non-specific serine/threonine protein kinase were down-regulated expressed during response to low temperature in two grapevine varieties [ 37 ]. Recent research indicated that phytochrome B (PHYB) and PHYA antagonistically regulated tomato low-temperature tolerance, in a process involving far-red light-induced PHYA activation to induce ABA signaling and eventually lead to cold response [ 38 ].…”

Section: Resultsmentioning

confidence: 99%

Gene expression profile indicates involvement of NO in Camellia sinensis pollen tube growth at low temperature

Pan

Wang

et al. 2016

BMC Genomics

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BackgroundNitric oxide (NO) functions as a critical signaling molecule in the low-temperature stress responses in plants, including polarized pollen tube growth in Camellia sinensis. Despite this, the potential mechanisms underlying the participation of NO in pollen tube responses to low temperature remain unclear. Here, we investigate alterations to gene expression in C. sinensis pollen tubes exposed to low-temperature stress and NO using RNA-Seq technology, in order to find the potential candidate genes related to the regulation of pollen tube elongation by NO under low-temperature stress.ResultsThree libraries were generated from C. sinensis cv. ‘Longjingchangye’ pollen tubes cultured at 25 °C (CsPT-CK) and 4 °C (CsPT-LT) or with 25 μM DEA NONOate (CsPT-NO). The number of unigenes found for the three biological replications were 39,726, 40,440 and 41,626 for CsPT-CK; 36,993, 39,070 and 39,439 for CsPT-LT; and 39,514, 38,298 and 39,061 for CsPT-NO. A total of 36,097 unique assembled and annotated sequences from C. sinensis pollen tube reads were found in a BLAST search of the following databases: NCBI non-redundant nucleotide, Swiss-prot protein, Kyoto Encyclopedia of Genes and Genomes, Cluster of Orthologous Groups of proteins, and Gene Ontology. The absolute values of log2Ratio > 1 and probability > 0.7 were used as the thresholds for significantly differential gene expression, and 766, 497 and 929 differentially expressed genes (DEGs) were found from the comparison analyses of the CK-VS-LT, CK-VS-NO and LT-VS-NO libraries, respectively. Genes related to metabolism and signaling pathways of plant hormones, transcription factors (TFs), vesicle polarized trafficking, cell wall biosynthesis, the ubiquitination machinery of the ubiquitin system and species-specific secondary metabolite pathways were mainly observed in the CK-VS-LT and CK-VS-NO libraries.ConclusionDifferentially expressed unigenes related to the inhibition of C. sinensis pollen tube growth under low temperature and NO are identified in this study. The transcriptomic gene expression profiles present a valuable genomic tool to improve studying the molecular mechanisms underlying low-temperature tolerance in pollen tube.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3158-4) contains supplementary material, which is available to authorized users.

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Transcriptome analysis of grapevine shoots exposed to chilling temperature for four weeks

Cited by 14 publications

References 49 publications

Transcriptome Analysis Reveals Key Cold-Stress-Responsive Genes in Winter Rapeseed (Brassica rapa L.)

Transcriptome Analysis Reveals Key Cold-Stress-Responsive Genes in Winter Rapeseed (Brassica rapa L.)

Genome-Wide Association Mapping of Loci Associated with Plant Growth and Forage Production under Salt Stress in Alfalfa (Medicago sativa L.)

Gene expression profile indicates involvement of NO in Camellia sinensis pollen tube growth at low temperature

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