Transcriptome profiling of rice seedlings under cold stress

2017 ◽  
Vol 44 (4) ◽  
pp. 419 ◽  
Author(s):  
Luciano C. da Maia ◽  
Pablo R. B. Cadore ◽  
Leticia C. Benitez ◽  
Rodrigo Danielowski ◽  
Eugenia J. B. Braga ◽  
...  
Keyword(s):  
Cold Stress ◽  
Cold Tolerance ◽  
Food Production ◽  
Genetic Model ◽  
Rice Yield ◽  
Oryza Sativa L ◽  
Abiotic Factors ◽  
Transcriptome Profiling ◽  
Important Species ◽  
Differential Expressed Genes

Rice (Oryza sativa L.) is one of the most important species for food production worldwide, besides being an excellent genetic model among the grasses. Cold is one of the major abiotic factors reducing rice yield, primarily affecting germination and reproduction phases. Currently, the RNAseq technique allows the identification of differential expressed genes in response to a given treatment, such as cold stress. In the present work, a transcriptome (RNAseq) analysis was performed in the V3 phase for contrasting genotypes Oro (tolerant) and Tio Taka (sensitive), in response to cold (13°C). A total of 241 and 244 M readings were obtained, resulting in the alignment of 25.703 and 26.963 genes in genotypes Oro and Tio Taka respectively. The analyses revealed 259 and 5579 differential expressed genes in response to cold in the genotypes Oro and Tio Taka respectively. Ontology classes with larger changes were metabolic process ~27%, cellular process ~21%, binding ~30% and catalytic activity ~22%. In the genotype Oro, 141 unique genes were identified, 118 were common between Oro and Tio Taka and 5461 were unique to Tio Taka. Genes involved in metabolic routes of signal transduction, phytohormones, antioxidant system and biotic stress were identified. These results provide an understanding that breeding for a quantitative trait, such as cold tolerance at germination, several gene loci must be simultaneously selected. In general, few genes were identified, but it was not possible to associate only one gene function as responsible for the cultivar tolerance; since different genes from different metabolic routes were identified. The genes described in the present work will be useful for future investigations and for the detailed validation in marker assisted selection projects for cold tolerance in the germination of rice.

scholarly journals Molecular and Phenotypic Characterization for Cold Tolerance in Rice (Oryza sativa L.)

2020 ◽  
Vol 23 (2) ◽  
pp. 1-15
Author(s):  
PS Biswas ◽  
H Khatun ◽  
M Anisuzzaman
Keyword(s):  
Cold Stress ◽  
Cold Tolerance ◽  
Oryza Sativa L ◽  
Gene Diversity ◽  
Reproductive Stage ◽  
Seedling Stage ◽  
Phenotypic Characterization ◽  
Breeding Lines ◽  
Upgma Dendrogram ◽  
Ssr Loci

Cold stress affects growth and development of rice plants from germination to reproductive stages. Thirty breeding lines/varieties including tolerant and susceptible check varieties were evaluated for cold tolerance at seedling and reproductive stage using artificially induced low temperature situations to understand the genetic relationship among them and to identify promising donors for cold tolerance. Three breeding lines, BR8253-9-3-4-3, IR77497-31-2-3-1and IR2266-42-6-2 demonstrated higher cold tolerance for the seedling stage (LD score <3.0). Molecular analysis revealed 68% genetic similarity among the genotypes. On average 64% of the breeding lines shared common alleles at any given locus ranging from 27% (RM22870) to 97% (RM186). UPGMA dendrogram showed that majority of the breeding lines showing 4-5 degrees of LD were grouped together. Two breeding lines, BR8258-7-1-5-2B2 and BR8258-7-1-5-2B3 having 86% common alleles showed low leaf discoloration (LD: 4) at seedling stage coupled with relatively low reduction in spikelet fertility (45.8% and 48.1%) and grain yield (43.3% and 39.1%). The gene diversity and PIC value revealed that seven SSR loci (RM1282, RM600, RM5349, RM6972, RM5847, RM5911, and RM511) might be the best markers to differentiate between tolerant and susceptible genotypes at reproductive stage. The breeding lines with tolerance to cold stress at the seedling and the reproductive stages identified from this study, and the SSR markers mentioned above could be useful for developing cold tolerance rice. Bangladesh Rice j. 2019, 23(2): 1-15

scholarly journals Effects of the sludge application at different concentrations on growth and production of rice (Oryza sativa L.) using a water channel underneath soil surface

2021 ◽  
Vol 74 (1) ◽  
Author(s):  
Arman Effendi ◽  
Elza Zuhry ◽  
Erlida Ariani
Keyword(s):  
Palm Oil ◽  
Food Production ◽  
Agricultural Development ◽  
Rice Yield ◽  
Oryza Sativa L ◽  
Water Channel ◽  
Aerobic Condition ◽  
Soil Surface ◽  
Waste Sludge ◽  
High Level

Indonesia’s strategies are focus on improving food production using environmentally-friendly measures in its agricultural development. This research was designed in accordance with the national strategies on increasing the productivity of rice using efficient water while reducing methane emissions from rice fields. A low rice yield is obtained when the conventional anaerobic methods (flooded soil) are used. Additional to the water, sludge from palm oil factories was also applied. This research aimed to establish a proper concentration of sludge to increase the productivity of rice sown in aerobic condition with the water level at 5 cm below soil surface. The study was conducted by making experiments with 5 levels. Waste sludge from palm oil factories was applied on the soils tested with concentrations of 0 t ha-1, 10 t ha-1, 15 t ha-1, 20 t ha-1 and 25 t ha-1. Height of the plant, total number of tillers, number of productive tillers, number of filled grains, percentage of filled grains, weight of 1000 grains and weight of filled grain per plot were studied. Application of 25 t ha-1 organic sludge showed a high level of productivity increasing the total number of tillers, the number of productive tillers and weight of filled grain per plot.

Rice-cold tolerance across reproductive stages

2016 ◽  
Vol 67 (8) ◽  
pp. 823 ◽  
Author(s):  
J. H. Mitchell ◽  
S. L. Zulkafli ◽  
J. Bosse ◽  
B. Campbell ◽  
P. Snell ◽  
...  
Keyword(s):  
Cold Stress ◽  
Cold Tolerance ◽  
Oryza Sativa L ◽  
Genotypic Variation ◽  
Flowering Stage ◽  
Spikelet Sterility ◽  
Booting Stage ◽  
Cold Tolerant ◽  
Tolerance Response ◽  
F2 Generation

Cold temperature stress at the reproductive stage, particularly at booting and flowering stages can cause significant reductions in rice (Oryza sativa L.) yield particularly at high latitudes and elevation. Although genotypic variation for cold tolerance is known to exist, the tolerance mechanisms and genotypic consistency across the stages are yet to be understood for segregating populations. Three experiments were conducted under controlled temperature glasshouse conditions to determine floral characteristics that were associated with cold tolerance at the flowering stage and to determine genotypic consistency at the booting and flowering stages. Twenty F5 Reiziq × Lijiangheigu lines from two extreme phenotypic bulks selected for cold tolerance at booting stage in the F2 generation were utilised. Spikelet sterility under cold stress at booting was significantly correlated with spikelet sterility under cold stress at flowering (r = 0.62**) with five lines identified as cold tolerant across reproductive stages. There was also a positive correlation (r = 0.47*) between spikelet sterility under cold stress at booting at the F5 and at the F2 generation. The quantitative trait loci (QTL; qLTSPKST10.1) previously identified on chromosome 10 contributing to spikelet sterility within the F2 generation, was also identified in the F5 generation. Additionally, genomic regions displaying significant segregation between the progenies contrasting for their cold tolerance response phenotype were identified on chromosomes 5 and 7 with Lijiangheigu as allelic donor and an estimated reduction in spikelet sterility of 25% and 27%, respectively. Although genotypic variation in spikelet sterility at the booting stage was not related to the development rate for heading or flowering, those cold-tolerant genotypes at the flowering stage were the quickest to complete flowering. Cold-tolerant genotypes at the flowering stage had larger numbers of dehisced anthers and subsequently pollen number on stigma, which contributed to reduced spikelet sterility. It is concluded that enhanced anther dehiscence plays a significant role in improved cold tolerance at the flowering stage.

scholarly journals Cold tolerance of ScCBL6 is associated with photosynthesis and tonoplast transporters in Arabidopsis

2019 ◽  
Author(s):  
Yanli Zhou ◽  
Changhong Zhao ◽  
Guangqiang Long ◽  
Chengli Zhou ◽  
Xudong Sun ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Cold Stress ◽  
Cold Tolerance ◽  
Ectopic Expression ◽  
Tibet Plateau ◽  
Integrated Analysis ◽  
Rna Seq ◽  
Stipa Purpurea ◽  
Multiple Processes ◽  
Differential Expressed Genes

Abstract Plant adapted in the fragile zone offer enormous opportunity to understand the stress biology under ecological scenario . Stipa capillacea is widely distributed in the frigid and arid region of Tibet Plateau, but its signal system has never been investigated yet. In this study, we isolated a signal transduction gene, ScCBL6 , in Stipa capillacea , to characterize its cold tolerance capacity by ectopic expression in Arabidopsis . The results suggested that full length ScCBL6 encodes 227 amino acids, and phylogenetically clustered with CBL6 protein in Stipa purpurea and Oryza sativa . In comparison with wild type (WT) plants, ScCBL6 overexpressing plants ( ScCBL6- OXP) are tolerant to cold stress but not drought stress, which attested by the higher photosynthetic capacity (Fv/Fm) and survival rate of ScCBL6- OXP under cold stress. We further compared their cold-responsive transcriptome profiles through RNA-Seq. Totally, 3931 genes were differentially expressed by introduction of ScCBL6. They are participated in multiple processes like immune system, lipid catabolic, secondary metabolic and mainly enriched in plant hormone signal transduction and biomacro-molecule metabolism as regard to KEGG pathway. Differential expressed genes (DEGs) were predicted to locate in chloroplast, mitochondrion, vacuole, and so on, suggesting multitudinous function of ScCBL6. Based on the integrated analysis of ScCBL6-OXP, we inferred that ScCBL6 improve plant cold stress tolerance via regulate photosynthesis redox and vacuole metabolites transport in Arabidopsis .

scholarly journals Genome-wide analysis of Dof transcription factors and their response to cold stress in rice (Oryza sativa L.)

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jia Liu ◽  
Qinglin Meng ◽  
Hongtao Xiang ◽  
Fengmei Shi ◽  
Ligong Ma ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Transcription Factors ◽  
Plant Growth ◽  
Cold Stress ◽  
Cold Tolerance ◽  
Oryza Sativa L ◽  
Evolutionary Relationship ◽  
Diverse Range ◽  
Genome Wide ◽  
Duplication Events

Abstract Background Rice (Oryza sativa L.) is a food crop for humans worldwide. However, temperature has an effect during the vegetative and reproductive stages. In high-latitude regions where rice is cultivated, cold stress is a major cause of yield loss and plant death. Research has identified a group of plant-specific transcription factors, DNA binding with one zinc fingers (DOFs), with a diverse range of functions, including stress signaling and stress response during plant growth. The aim of this study was to identify Dof genes in two rice subspecies, indica and japonica, and screen for Dof genes that may be involved in cold tolerance during plant growth. Results A total of 30 rice Dofs (OsDofs) were identified using bioinformatics and genome-wide analyses and phylogenetically analyzed. The 30 OsDOFs were classified into six subfamilies, and 24 motifs were identified based on protein sequence alignment. The chromosome locations of OsDofs were determined and nine gene duplication events were identified. A joint phylogenetic analysis was performed on DOF protein sequences obtained from four monocotyledon species to examine the evolutionary relationship of DOF proteins. Expression profiling of OsDofs from two japonica cultivars (Longdao5, which is cold-tolerant, and Longjing11, which is cold-sensitive) revealed that OsDof1 and OsDof19 are cold-inducible genes. We examined the seed setting rates in OsDof1- and OsDof19-overexpression and RNAi lines and found that OsDof1 showed a response to cold stress. Conclusions Our investigation identified OsDof1 as a potential target for genetic breeding of rice with enhanced cold tolerance.

scholarly journals Combining QTL-seq and linkage mapping to fine map a candidate gene in qCTS6 for cold tolerance at the seedling stage in rice

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Luomiao Yang ◽  
Jingguo Wang ◽  
Zhenghong Han ◽  
Lei Lei ◽  
Hua Long Liu ◽  
...  
Keyword(s):  
Cold Stress ◽  
Cold Tolerance ◽  
Regulatory Gene ◽  
Snp Markers ◽  
Seedling Stage ◽  
Pcr Analysis ◽  
Sequencing Data ◽  
Coding Region ◽  
Rice Varieties ◽  
Major Qtl

Abstract Background Cold stress caused by low temperatures is an important factor restricting rice production. Identification of cold-tolerance genes that can stably express in cold environments is crucial for molecular rice breeding. Results In this study, we employed high-throughput quantitative trait locus sequencing (QTL-seq) analyses in a 460-individual F2:3 mapping population to identify major QTL genomic regions governing cold tolerance at the seedling stage in rice. A novel major QTL (qCTS6) controlling the survival rate (SR) under low-temperature conditions of 9°C/10 days was mapped on the 2.60-Mb interval on chromosome 6. Twenty-seven single-nucleotide polymorphism (SNP) markers were designed for the qCST6 region based on re-sequencing data, and local QTL mapping was conducted using traditional linkage analysis. Eventually, we mapped qCTS6 to a 96.6-kb region containing 13 annotated genes, of which seven predicted genes contained 13 non-synonymous SNP loci. Quantitative reverse transcription PCR analysis revealed that only Os06g0719500, an OsbZIP54 transcription factor, was strongly induced by cold stress. Haplotype analysis confirmed that +376 bp (T>A) in the OsbZIP54 coding region played a key role in regulating cold tolerance in rice. Conclusion We identified OsbZIP54 as a novel regulatory gene associated with rice cold-responsive traits, with its Dongfu-104 allele showing specific cold-induction expression serving as an important molecular variation for rice improvement. This result is expected to further exploration of the genetic mechanism of rice cold tolerance at the seedling stage and improve cold tolerance in rice varieties by marker-assisted selection.

scholarly journals Transcriptomic Analysis of Short-Term Salt-Stress Response in Mega Hybrid Rice Seedlings

Agronomy ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1328
Author(s):  
Noushin Jahan ◽  
Yang Lv ◽  
Mengqiu Song ◽  
Yu Zhang ◽  
Liangguang Shang ◽  
...  
Keyword(s):  
Salt Stress ◽  
Molecular Mechanisms ◽  
Oryza Sativa L ◽  
Transcriptome Profiling ◽  
Bhlh Transcription Factor ◽  
F1 Hybrid ◽  
Salt Stress Response ◽  
Productivity Losses ◽  
Expression Of Genes ◽  
Trait Locus

Salinity is a major abiotic stressor that leads to productivity losses in rice (Oryza sativa L.). In this study, transcriptome profiling and heterosis-related genes were analyzed by ribonucleic acid sequencing (RNA-Seq) in seedlings of a mega rice hybrid, Liang-You-Pei-Jiu (LYP9), and its two parents 93–11 and Pei-ai64s (PA64s), under control and two different salinity levels, where we found 8292, 8037, and 631 salt-induced differentially expressed genes (DEGs), respectively. Heterosis-related DEGs were obtained higher after 14 days of salt treatment than after 7 days. There were 631 and 4237 salt-induced DEGs related to heterosis under 7-day and 14-day salt stresses, respectively. Gene functional classification showed the expression of genes involved in photosynthesis activity after 7-day stress treatment, and in metabolic and catabolic activity after 14 days. In addition, we correlated the concurrence of an expression of DEGs for the bHLH transcription factor and a shoot length/salinity-related quantitative trait locus qSL7 that we fine-mapped previously, providing a confirmed case of heterosis-related genes. This experiment reveals the transcriptomic divergence of the rice F1 hybrid and its parental lines under control and salt stress state, and enlightens about the significant molecular mechanisms developed over time in response to salt stress.

scholarly journals Comparative Transcriptome Analysis Reveals Potential Gene Modules Associated with Cold Tolerance in Sugarcane (Saccharum officinarum L.)

2021 ◽  
Author(s):  
Xing Huang ◽  
Yongsheng Liang ◽  
Baoqing Zhang ◽  
Xiupeng Song ◽  
Yangrui Li ◽  
...  
Keyword(s):  
Cold Stress ◽  
Cold Tolerance ◽  
Cold Resistance ◽  
Soluble Sugar ◽  
Resistance Mechanism ◽  
Saccharum Officinarum ◽  
Calcium Signal ◽  
Protein Kinase Activity ◽  
Comparative Transcriptome ◽  
Climate Conditions

AbstractSugarcane is an important crop worldwide, and most sugar is derived directly from sugarcane. Due to its thermophilic nature, the yield of sugarcane is largely influenced by extreme climate conditions, especially cold stress. Therefore, the development of sugarcane with improved cold tolerance is an important goal. However, little is known about the multiple mechanisms underlying cold acclimation at the bud stage in sugarcane. In this study, we emphasized that sensitivity to cold stress was higher for the sugarcane variety ROC22 than for GT42, as determined by physical signs, including bud growth capacity, relative conductivity, malonaldehyde contents, and soluble sugar contents. To understand the factors contributing to the difference in cold tolerance between ROC22 and GT42, comparative transcriptome analyses were performed. We found that genes involved in the regulation of the stability of the membrane system were the relative determinants of difference in cold tolerance. Additionally, genes related to protein kinase activity, starch metabolism, and calcium signal transduction were associated with cold tolerance. Finally, 25 candidate genes, including 23 variety-specific and 2 common genes, and 7 transcription factors were screened out for understanding the possible cold resistance mechanism. The findings of this study provide candidate gene resources for cold resistance and will improve our understanding of the regulation of cold tolerance at the bud stage in sugarcane.

GRAS-domain transcription factor PAT1 regulates jasmonic acid biosynthesis in grape cold stress response

2021 ◽  
Author(s):  
Zemin Wang ◽  
Darren Chern Jan Wong ◽  
Yi Wang ◽  
Guangzhao Xu ◽  
Chong Ren ◽  
...  
Keyword(s):  
Stress Response ◽  
Cold Stress ◽  
Cold Tolerance ◽  
Cold Treatment ◽  
Ectopic Expression ◽  
Bimolecular Fluorescence Complementation ◽  
Luciferase Reporter ◽  
Vitis Amurensis ◽  
Mobility Shift

Abstract Cultivated grapevine (Vitis) is a highly valued horticultural crop, and cold stress affects its growth and productivity. Wild Amur grape (Vitis amurensis) PAT1 (Phytochrome A signal transduction 1, VaPAT1) is induced by low temperature, and ectopic expression of VaPAT1 enhances cold tolerance in Arabidopsis (Arabidopsis thaliana). However, little is known about the molecular mechanism of VaPAT1 during the cold stress response in grapevine. Here, we confirmed the overexpression of VaPAT1 in transformed grape calli enhanced cold tolerance. Yeast two-hybrid and bimolecular fluorescence complementation assays highlighted an interaction between VaPAT1 with INDETERMINATE-DOMAIN 3 (VaIDD3). A role of VaIDD3 in cold tolerance was also indicated. Transcriptome analysis revealed VaPAT1 and VaIDD3 overexpression and cold treatment coordinately modulate the expression of stress-related genes including lipoxygenase 3 (LOX3), a gene encoding a key jasmonate biosynthesis enzyme. Co-expression network analysis indicated LOX3 might be a downstream target of VaPAT1. Both electrophoretic mobility shift and dual luciferase reporter assays showed the VaPAT1-IDD3 complex binds to the IDD-box (AGACAAA) in the VaLOX3 promoter to activate its expression. Overexpression of both VaPAT1 and VaIDD3 increased the transcription of VaLOX3 and JA levels in transgenic grape calli. Conversely, VaPAT1-SRDX (dominant repression) and CRISPR/Cas9-mediated mutagenesis of PAT1-ED causing the loss of the C-terminus in grape calli dramatically prohibited the accumulation of VaLOX3 and JA levels during cold treatment. Together, these findings point to a pivotal role of VaPAT1 in the cold stress response in grape by regulating JA biosynthesis.

scholarly journals Genome-Wide Analysis of the NAC Transcription Factor Gene Family Reveals Differential Expression Patterns and Cold-Stress Responses in the Woody Plant Prunus mume

Genes ◽  
2018 ◽  
Vol 9 (10) ◽  
pp. 494 ◽  
Author(s):  
Xiaokang Zhuo ◽  
Tangchun Zheng ◽  
Zhiyong Zhang ◽  
Yichi Zhang ◽  
Liangbao Jiang ◽  
...  
Keyword(s):  
Cold Stress ◽  
Gene Family ◽  
Cold Tolerance ◽  
Stress Responses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Freezing Stress ◽  
Prunus Mume ◽  
Flower Bud ◽  
Freezing Resistance

NAC transcription factors (TFs) participate in multiple biological processes, including biotic and abiotic stress responses, signal transduction and development. Cold stress can adversely impact plant growth and development, thereby limiting agricultural productivity. Prunus mume, an excellent horticultural crop, is widely cultivated in Asian countries. Its flower can tolerate freezing-stress in the early spring. To investigate the putative NAC genes responsible for cold-stress, we identified and analyzed 113 high-confidence PmNAC genes and characterized them by bioinformatics tools and expression profiles. These PmNACs were clustered into 14 sub-families and distributed on eight chromosomes and scaffolds, with the highest number located on chromosome 3. Duplicated events resulted in a large gene family; 15 and 8 pairs of PmNACs were the result of tandem and segmental duplicates, respectively. Moreover, three membrane-bound proteins (PmNAC59/66/73) and three miRNA-targeted genes (PmNAC40/41/83) were identified. Most PmNAC genes presented tissue-specific and time-specific expression patterns. Sixteen PmNACs (PmNAC11/19/20/23/41/48/58/74/75/76/78/79/85/86/103/111) exhibited down-regulation during flower bud opening and are, therefore, putative candidates for dormancy and cold-tolerance. Seventeen genes (PmNAC11/12/17/21/29/42/30/48/59/66/73/75/85/86/93/99/111) were highly expressed in stem during winter and are putative candidates for freezing resistance. The cold-stress response pattern of 15 putative PmNACs was observed under 4 °C at different treatment times. The expression of 10 genes (PmNAC11/20/23/40/42/48/57/60/66/86) was upregulated, while 5 genes (PmNAC59/61/82/85/107) were significantly inhibited. The putative candidates, thus identified, have the potential for breeding the cold-tolerant horticultural plants. This study increases our understanding of functions of the NAC gene family in cold tolerance, thereby potentially intensifying the molecular breeding programs of woody plants.

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