scholarly journals Genome-Wide Analysis of NAC Gene Family in Betula pendula

Forests ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 741 ◽  
Author(s):  
Song Chen ◽  
Xin Lin ◽  
Dawei Zhang ◽  
Qi Li ◽  
Xiyang Zhao ◽  
...  
Keyword(s):  
Low Temperature ◽  
Gene Family ◽  
Temperature Stress ◽  
Betula Pendula ◽  
Low Temperature Stress ◽  
Specific Expression ◽  
Genome Wide ◽  
Nac Gene Family ◽  
Cold Responses ◽  
Insight Into

NACs (NAM, ATAF1/2, and CUC2) are plant-specific transcription factors that play diverse roles in various plant developmental processes. In this study, we identified the NAC gene family in birch (Betula pendula) and further analyzed the function of BpNACs. Phylogenetic analysis reveals that the 114 BpNACs can be divided into seven subfamilies. We investigated the expression levels of these BpNACs in different tissues of birch including roots, xylem, leaves, and flowers, and the results showed that the BpNACs seem to be expressed higher in xylem and roots than leaves and flowers. In addition to tissue-specific expression analysis, we investigated the expression of BpNACs under low-temperature stress. A total of 21 BpNACs were differentially expressed under low-temperature stress, of which 17 were up-regulated, and four were down-regulated. Using the gene expression data, we reconstructed the gene co-expression network for the 21 low-temperature-responsive BpNACs. In conclusion, our results provide insight into the evolution of NAC genes in the B. pendula genome, and provide a basis for understanding the molecular mechanism for BpNAC-mediated cold responses in birch.

scholarly journals Identification of proteins involved in response to cold stress and genome-wide identification and analysis of the APX gene family in winter rapeseed (Brassica rapa L.)

2021 ◽  
Author(s):  
Li Ma ◽  
Jing Bai ◽  
Jia Xu ◽  
Weiliang Qi ◽  
Haiyun Li ◽  
...  
Keyword(s):  
Low Temperature ◽  
Gene Family ◽  
Temperature Stress ◽  
Brassica Rapa ◽  
Cold Resistance ◽  
Resistance Mechanism ◽  
Northern China ◽  
Low Temperature Stress ◽  
Oilseed Crop ◽  
Cold Response

Abstract Winter Brassica rapa is an important oilseed crop in northern China, but the mechanism of its cold resistance remains unclear. APX plays important roles in response of this plant to abiotic stress and in scavenging free radicals. In this study, 59 DEPs were isolated and identified from winter B. rapa and B. napus using bidirectional electrophoresis, and APX was found to be differentially expressed in these two species. Therefore, the roles of APX proteins in the cold response and superoxide metabolism pathways in both rapeseed species were further investigated. And comprehensive analysis of phylogeny, chromosome distribution, motif identification, sequence structure, gene duplication, and RNA-seq expression profile in APX gene family. Most of the BrAPX genes were specifically expressed under low temperature stress and behaved significantly differently in cold-tolerant and cold-sensitive varieties. qPCR was also used to verify the differences in expression between these two varieties under cold, freezing, drought and heat stress, and these candidate genes and proteins may play important roles in the response of B. rapa to low temperature stress and provide new information for the elucidation of the cold resistance mechanism in B. rapa.

scholarly journals Genome-Wide Association Mapping Unravels the Genetic Control of Seed Vigor under Low-Temperature Conditions in Rapeseed (Brassica napus L.)

Plants ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 426
Author(s):  
Tao Luo ◽  
Yuting Zhang ◽  
Chunni Zhang ◽  
Matthew N. Nelson ◽  
Jinzhan Yuan ◽  
...  
Keyword(s):  
Low Temperature ◽  
Stress Tolerance ◽  
Candidate Genes ◽  
Temperature Stress ◽  
Seed Vigor ◽  
Low Temperature Stress ◽  
Brassica Napus L ◽  
Temperature Conditions ◽  
Genome Wide ◽  
Tolerance Indices

Low temperature inhibits rapid germination and successful seedling establishment of rapeseed (Brassica napus L.), leading to significant productivity losses. Little is known about the genetic diversity for seed vigor under low-temperature conditions in rapeseed, which motivated our investigation of 13 seed germination- and emergence-related traits under normal and low-temperature conditions for 442 diverse rapeseed accessions. The stress tolerance index was calculated for each trait based on performance under non-stress and low-temperature stress conditions. Principal component analysis of the low-temperature stress tolerance indices identified five principal components that captured 100% of the seedling response to low temperature. A genome-wide association study using ~8 million SNP (single-nucleotide polymorphism) markers identified from genome resequencing was undertaken to uncover the genetic basis of seed vigor related traits in rapeseed. We detected 22 quantitative trait loci (QTLs) significantly associated with stress tolerance indices regarding seed vigor under low-temperature stress. Scrutiny of the genes in these QTL regions identified 62 candidate genes related to specific stress tolerance indices of seed vigor, and the majority were involved in DNA repair, RNA translation, mitochondrial activation and energy generation, ubiquitination and degradation of protein reserve, antioxidant system, and plant hormone and signal transduction. The high effect variation and haplotype-based effect of these candidate genes were evaluated, and high priority could be given to the candidate genes BnaA03g40290D, BnaA06g07530D, BnaA09g06240D, BnaA09g06250D, and BnaC02g10720D in further study. These findings should be useful for marker-assisted breeding and genomic selection of rapeseed to increase seed vigor under low-temperature stress.

scholarly journals Transcriptome-wide identification of MAPKKK genes in bermudagrass (Cynodon dactylon L.) and their potential roles in low temperature stress responses

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10159
Author(s):  
Wei Wang ◽  
An Shao ◽  
Erick Amombo ◽  
Shugao Fan ◽  
Xiao Xu ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Low Temperature ◽  
Gene Family ◽  
Temperature Stress ◽  
Stress Responses ◽  
Cynodon Dactylon ◽  
Diploid Species ◽  
Low Temperature Stress ◽  
Biological Processes ◽  
Mapk Cascades

As upstream components of MAPK cascades, mitogen-activated protein kinase kinase kinases (MAPKKKs) act as adaptors linking upstream signaling steps to the core MAPK cascades. MAPK cascades are universal modules of signal transduction in eukaryotic organisms and play crucial roles in plant development processes and in responses to biotic and abiotic stress and signal transduction. Members of the MAPKKK gene family have been identified in several plants,however, MAPKKKs have not been systematically studied in bermudagrass (Cynodon dactylon L.). In this study, 55 potential CdMAPKKKs were produced from bermudagrass transcriptome data, of which 13 belonged to the MEKK, 38 to the Raf, and 4 to the ZIK subfamily. Multiple alignment and conserved motif analysis of CdMAPKKKs supported the evolutionary relationships inferred from phylogenetic analyses. Moreover, the distribution pattern in Poaceae species indicated that members of the MAPKKK family were conserved among almost all diploid species, and species-specific polyploidy or higher duplication ratios resulted in an expansion of the MAPKKK family. In addition, 714 co-functional links which were significantly enriched in signal transduction, responses to temperature stimuli, and other important biological processes of 55 CdMAPKKKs were identified using co-functional gene networks analysis; 30 and 19 co-functional genes involved in response to cold or heat stress, respectively, were also identified. Results of promoter analyses, and interaction network investigation of all CdMAPKKKs based on the rice homologs suggested that CdMAPKKKs are commonly associated with regulation of numerous biological processes. Furthermore, 12 and 13 CdMAPKKKs were significantly up- and downregulated, respectively, in response to low temperature stress; among them, six CdMAPKKKs were significantly induced by low temperature stress, at least at one point in time. This is the first study to conduct identification and functional analysis of the MAPKKK gene family in bermudagrass, and our results provide a foundation for further research on the functions of CdMAPKKKs in response to low temperature stress.

scholarly journals Genome-Wide Identification of Circular RNAs in Response to Low-Temperature Stress in Tomato Leaves

2020 ◽  
Vol 11 ◽  
Author(s):  
Xuedong Yang ◽  
Yahui Liu ◽  
Hui Zhang ◽  
Jinyu Wang ◽  
Gaurav Zinta ◽  
...  
Keyword(s):  
Low Temperature ◽  
Temperature Stress ◽  
Low Temperature Stress ◽  
Circular Rnas ◽  
Genome Wide

scholarly journals Transcriptome Analysis Combined With Glutathione S-transferase 1 Gene Family Whole-genome Identification Reveals the Mechanism Underlying the Exogenous Application of 5-aminolevulinic Acid to Alleviate Low Temperature Stress in Solanum Lycopersicum Seedling

2020 ◽  
Author(s):  
Zhengda Zhang ◽  
Tao Liu ◽  
Zhen Kang ◽  
Jiwen Xu ◽  
Shichun Yang ◽  
...  
Keyword(s):  
Low Temperature ◽  
Gene Family ◽  
Temperature Stress ◽  
Stress Resistance ◽  
Aminolevulinic Acid ◽  
Low Temperature Stress ◽  
Tomato Genome ◽  
Glutathione S Transferase ◽  
Cis Acting ◽  
Gst Activity

Abstract Background: Transcriptome sequencing was conducted to screen out genes that actively respond to exogenous 5-aminolevulinic acid (ALA) induction under low temperature stress. The study used two versions of the tomato genome database to strictly screen and identify tomato glutathione S-transferase (GST) gene families and carried out the related bioinformatics analysis of tomato GST gene family. The expression pattern of SlGST genes induced by exogenous application ALA under low temperature stress was also analysed. Related physiological indicators were determined, and related chemical stains were performed.Results: RNA sequencing (RNA-seq) results showed that the expression of SlGST gene was different under various treatments, and a large number of SlGST genes widely responded to ALA induction under low temperature stress. Sixty-nine full-length GST genes were identified by screening the two versions of tomato genome databases combined with protein domain analysis. Analysis of gene family phylogenetic tree divided the tomato GST gene family into eight subfamilies. Tandem replication of genes is one of the driving forces for the evolution of tomato GST gene family, and a large number of cis-acting elements are related to stress resistance on the promoter of the GST gene family. Exogenous ALA application under low temperature stress induces a broad response of tomato leaf SlGST gene (qRT-PCR verification), increases GST activity and decreases reactive oxygen species (ROS) accumulation.Conclusions: RNA sequencing results revealed that a large number of tomato GST genes are differentially expressed, and Sixty-nine GSTs are identified in the tomato genome. Tandem replication of genes is the driving force for 68 the evolution of tomato GST family, and the promoter contains a large number of cis-acting elements related to stress resistance. Test results show that exogenous ALA induces the expression of SlGST genes under low temperature stress, thereby increasing GST activity to eliminate the ROS produced under low temperature stress and increase the tomato tolerance.

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