scholarly journals Genome-Wide Identification and Analysis of Genes, Conserved between japonica and indica Rice Cultivars, that Respond to Low-Temperature Stress at the Vegetative Growth Stage

2017 ◽  
Vol 8 ◽  
Author(s):  
Manu Kumar ◽  
Yun-Shil Gho ◽  
Ki-Hong Jung ◽  
Seong-Ryong Kim
Keyword(s):  
Low Temperature ◽  
Temperature Stress ◽  
Vegetative Growth ◽  
Growth Stage ◽  
Indica Rice ◽  
Low Temperature Stress ◽  
Rice Cultivars ◽  
Genome Wide ◽  
Japonica And Indica Rice

Gene-Coexpression Network Analysis Identifies Specific Modules and Hub Genes Related to Cold Stress in Rice

2021 ◽  
Author(s):  
Zhichi Zeng ◽  
Sichen Zhang ◽  
Wenyan Li ◽  
Baoshan Chen ◽  
Wenlan Li
Keyword(s):  
Network Analysis ◽  
Low Temperature ◽  
Cold Stress ◽  
Cold Tolerance ◽  
Temperature Stress ◽  
Low Temperature Stress ◽  
Rice Cultivars ◽  
Hub Genes ◽  
New Genes ◽  
Short Period

Abstract Background: When plants are subjected to cold stress, they undergo a series of molecular and physiological changes to protect themselves from injury. Indica cultivars can usually withstand only mild cold stress in a relatively short period. Hormone-mediated defence response plays an important role in cold stress. Weighted gene co-expression network analysis (WGCNA) is a very useful tool for studying the correlation between genes, identifying modules with high phenotype correlation, and identifying Hub genes in different modules. Many studies have elucidated the molecular mechanisms of cold tolerance in different plants, but little information about the recovery process after cold stress is available.Results: To understand the molecular mechanism of cold tolerance in rice, we performed comprehensive transcriptome analyses during cold treatment and recovery stage in two cultivars of near-isogenic lines (9311 and DC907). Twelve transcriptomes in two rice cultivars were determined. A total of 2509 new genes were predicted by fragment splicing and assembly, and 7506 differentially expressed genes were identified by pairwise comparison. A total of 26 modules were obtained by expression-network analysis, 12 of which were highly correlated with cold stress or recovery treatment. We further identified candidate Hub genes associated with specific modules and analysed their regulatory relationships based on coexpression data. Results showed that various plant-hormone regulatory genes acted together to protect plants from physiological damage under short-term low-temperature stress. We speculated that this may be common in rice. Under long-term cold stress, rice improved the tolerance to low-temperature stress by promoting autophagy, sugar synthesis, and metabolism.Conclusion: Through WGCNA analysis at the transcriptome level, we provided a potential regulatory mechanism for the cold stress and recovery of rice cultivars and identified candidate central genes. Our findings provided an important reference for the future cultivation of rice strains with good tolerance.

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 Transcriptomic, proteomic, and physiological comparative analyses of flooding mitigation of the damage induced by low-temperature stress in direct seeded early indica rice at the seedling stage

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wenxia Wang ◽  
Jie Du ◽  
Liming Chen ◽  
Yongjun Zeng ◽  
Xueming Tan ◽  
...  
Keyword(s):  
Low Temperature ◽  
Temperature Stress ◽  
Molecular Mechanisms ◽  
Tricarboxylic Acid Cycle ◽  
Indica Rice ◽  
Low Temperature Stress ◽  
Seedling Stage ◽  
Differentially Expressed ◽  
Rice Seedlings ◽  
Direct Seeded

Abstract Background Low temperature (LT) often occurs at the seedling stage in the early rice-growing season, especially for direct seeded early-season indica rice, and using flooding irrigation can mitigate LT damage in rice seedlings. The molecular mechanism by which flooding mitigates the damage induced by LT stress has not been fully elucidated. Thus, LT stress at 8 °C, LT accompanied by flooding (LTF) and CK (control) treatments were established for 3 days to determine the transcriptomic, proteomic and physiological response in direct seeded rice seedlings at the seedling stage. Results LT damaged chloroplasts, and thylakoid lamellae, and increased osmiophilic bodies and starch grains compared to CK, but LTF alleviated the damage to chloroplast structure caused by LT. The physiological characteristics of treated plants showed that compared with LT, LTF significantly increased the contents of rubisco, chlorophyll, PEPCK, ATP and GA3 but significantly decreased soluble protein, MDA and ABA contents. 4D-label-free quantitative proteomic profiling showed that photosynthesis-responsive proteins, such as phytochrome, as well as chlorophyll and the tricarboxylic acid cycle were significantly downregulated in LT/CK and LTF/CK comparison groups. However, compared with LT, phytochrome, chlorophyllide oxygenase activity and the glucan branching enzyme in LTF were significantly upregulated in rice leaves. Transcriptomic and proteomic studies identified 72,818 transcripts and 5639 proteins, and 4983 genes that were identified at both the transcriptome and proteome levels. Differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) were significantly enriched in glycine, serine and threonine metabolism, biosynthesis of secondary metabolites, glycolysis/gluconeogenesis and metabolic pathways. Conclusion Through transcriptomic, proteomic and physiological analyses, we determined that a variety of metabolic pathway changes were induced by LT and LTF. GO and KEGG enrichment analyses demonstrated that DEGs and DEPs were associated with photosynthesis pathways, antioxidant enzymes and energy metabolism pathway-related proteins. Our study provided new insights for efforts to reduce the damage to direct seeded rice caused by low-temperature stress and provided a breeding target for low temperature flooding-resistant cultivars. Further analysis of translational regulation and metabolites may help to elucidate the molecular mechanisms by which flooding mitigates low-temperature stress in direct seeded early indica rice at the seedling stage.

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 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 Assessment of cold stress tolerance in maize through quantitative trait locus, genome-wide association study and transcriptome analysis

2021 ◽  
Vol 49 (4) ◽  
pp. 12525
Author(s):  
Syed F.A. GILLANI ◽  
Adnan RASHEED ◽  
Gai YUHONG ◽  
Wei JIAN ◽  
Wang Y. XIA ◽  
...  
Keyword(s):  
Low Temperature ◽  
Association Study ◽  
Temperature Stress ◽  
Genome Wide Association Study ◽  
Grain Filling ◽  
Low Temperature Stress ◽  
Genome Wide Association ◽  
Ps Ii ◽  
Genome Wide ◽  
Trait Locus

Genome-wide association study (GWAS) has become a widely accepted strategy for decoding genotype phenotype associations in many species thanks to advances in next-generation sequencing (NGS) technologies. Maize is an ideal crop for GWAS and significant progress has been made in the last decade. This review summarizes current GWAS efforts in maize functional genomics research and discusses future prospects in the omics era. The general goal of GWAS is to link genotypic variations to corresponding differences in phenotype using the most appropriate statistical model in a given population. The current review also presents perspectives for optimizing GWAS design and analysis. GWAS analysis of data from RNA, protein, and metabolite-based omics studies is discussed, along with new models and new population designs that will identify causes of phenotypic variation that have been hidden to date. The detailed that low temperature in maize seedlings altogether restricts germination and seedlings' development and destabilizes the cancer prevention agent safeguard component. Cold pressure adversely influences root morphology, photosystem II (PS II) effectiveness, chlorophyll substance, and leaf region. A short scene of low temperature stress (for example, under 10 °C for 7 days) during the V6–V9 maize development stages can fundamentally defer the anthesis commencement. Among the morphological reactions by focused on maize plants, low temperature stress causes strange tuft development in maize, along these lines influencing the fertilization and grain filling measures. Hence, problematic temperatures can cause a genuine yield decrease if happening at basic conceptive stages, as plants allocate over half of their photosynthesis to foster grains during this stage until physiological development. Low temperature stress fundamentally diminishes the plant stature and absolute yield biomass of maize. Leaf improvement turns out to be delayed in chilly focused on plants because of a drawn-out cell cycle and diminished pace of mitosis.  The joint and continuous efforts of the whole community will enhance our understanding of maize quantitative traits and boost crop molecular breeding designs.

Sign in / Sign up

Export Citation Format

Share Document