OsGATA16, a GATA Transcription Factor, Confers Cold Tolerance by Repressing OsWRKY45-1 at the Seedling Stage in Rice

Abstract BackgroundCold stress in rice is a major abiotic stress that adversely affects growth and substantially reduces rice yield. Identification of cold-related functional rice genes is important for breeding programs aimed at increasing resilience and yield in rice crops. GATA-family transcription factors involve diverse function in rice, however, their roles in the response to low-temperature stress remain unclear.ResultsA GATA-type zinc finger transcription factor, OsGATA16, that increases cold tolerance in rice. OsGATA16 is an OsGATA subfamily-II protein and contains eleven putative phosphorylation sites, NLS, and several conserved domains. Overexpression of OsGATA16 increased tolerance to cold stress at seedling stage. Transcriptional analysis showed that OsGATA16 was induced by cold and ABA treatments, but was repressed by drought, cytokinin, and JA. OsGATA16 was expressed in all plant tissues, with highest expression in panicles. Subcellular localization and transcriptional analysis indicated that OsGATA16 acted as a nuclear-targeted transcriptional suppressor. Four cold-related genes (OsWRKY45-1, OsSRFP1, OsCYL4, and OsMYB30) were repressed in OsGATA16-overexpression lines compared with wild type after low-temperature exposure. Yeast one-hybrid and Dual-luciferase reporter assays showed that OsGATA16 bound to the promoter of OsWRKY45-1 and repressed its expression. Eleven SNPs within OsGATA16 were identified and haplotype analysis showed a polarization between Japonica and Indicia subspecies. A non-synonymous SNP was identified that explained differences in cold tolerance among the 137 rice accessions.ConclusionA novel GATA transcription factor, OsGATA16, plays a positive role in cold tolerance at the seedling stage in rice by direct repression of OsWRKY45-1 expression. One SNP was identified that explained cold tolerance differences among rice accessions. These results support future breeding programs to improve cold tolerance in commercial rice crops.

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OsGATA16, a GATA Transcription Factor, Confers Cold Tolerance by Repressing OsWRKY45–1 at the Seedling Stage in Rice

Rice ◽

10.1186/s12284-021-00485-w ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Hongjia Zhang ◽

Tao Wu ◽

Zhao Li ◽

Kai Huang ◽

Na-Eun Kim ◽

...

Keyword(s):

Transcription Factor ◽

Cold Stress ◽

Cold Tolerance ◽

Haplotype Analysis ◽

Seedling Stage ◽

Growth And Yield ◽

Wild Type ◽

Gata Transcription Factor ◽

Localization Signal ◽

New Germplasm

Abstract Background Cold stress is the main abiotic stress in rice, which seriously affects the growth and yield of rice. Identification of cold tolerance genes is of great significance for rice to solve these problems. GATA-family transcription factors involve diverse biological functions, however, their role in cold tolerance in rice remains unclear. Results In this study, a GATA-type zinc finger transcription factor OsGATA16, which can improve cold tolerance, was isolated and characterized from rice. OsGATA16 belongs to OsGATA subfamily-II and contains 11 putative phosphorylation sites, a nuclear localization signal (NLS), and other several conserved domains. OsGATA16 was expressed in all plant tissues, with the strongest in panicles. It was induced by cold and ABA treatments, but was repressed by drought, cytokinin and JA, and acted as a transcriptional suppressor in the nucleus. Overexpression of OsGATA16 improves cold tolerance of rice at seedling stage. Under cold stress treatments, the transcription of four cold-related genes OsWRKY45–1, OsSRFP1, OsCYL4, and OsMYB30 was repressed in OsGATA16-overexpressing (OE) rice compared with wild-type (WT). Interestingly, OsGATA16 bound to the promoter of OsWRKY45–1 and repressed its expression. In addition, haplotype analysis showed that OsGATA16 polarized between the two major rice subspecies japonica and indica, and had a non-synonymous SNP8 (336G) associated with cold tolerance. Conclusion OsGATA16 is a GATA transcription factor, which improves cold tolerance at seedling stage in rice. It acts as a positive regulator of cold tolerance by repressing some cold-related genes such as OsWRKY45–1, OsSRFP1, OsCYL4 and OsMYB30. Additionally, OsGATA16 has a non-synonymous SNP8 (336G) associated with cold tolerance on CDS region. This study provides a theoretical basis for elucidating the mechanism of cold tolerance in rice and new germplasm resources for rice breeding.

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

BMC Plant Biology ◽

10.1186/s12870-021-03076-5 ◽

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.

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

Plant Physiology ◽

10.1093/plphys/kiab142 ◽

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.

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Identification of cold stress responsive microRNAs in cold tolerant and susceptible Hemerocallis fulva by high throughput sequencing

10.21203/rs.3.rs-41470/v1 ◽

2020 ◽

Author(s):

Changbing Huang ◽

Chun Jiang ◽

limin Jin ◽

Huanchao Zhang

Keyword(s):

Low Temperature ◽

Cold Stress ◽

Cold Tolerance ◽

Temperature Stress ◽

Stress Responses ◽

Target Genes ◽

Low Temperature Stress ◽

Differentially Expressed ◽

Differentially Expressed Mirnas ◽

Cold Tolerant

Abstract Background:Hemerocallis fulva is a perennial herb belonging to Hemerocallis of Hemerocallis. Because of the large and bright colors, it is often used as a garden ornamental plant. But most varieties of H. fulva on the market will wither in winter, which will affect their beauty. It is very important to study the effect of low temperature stress on the physiological indexes of H. fulva and understand the cold tolerance of different H. fulva. MiRNA is a kind of endogenous non coding small molecular RNA with length of 21-24nt. It mainly inhibits protein translation by cutting target genes, and plays an important role in the development of organisms, gene expression and biological stress. Low temperature is the main abiotic stress affecting the production of H. fulva in China, which hinders the growth and development of plants. A comprehensive understanding of the expression pattern of microRNA in H. fulva under low temperature stress can improve our understanding of microRNA mediated stress response. Although there are many studies on miRNAs of various plants under cold stress at home and abroad, there are few studies on miRNAs related to cold stress of H. fulva. It is of great significance to explore the cold stress resistant gene resources of H. fulva, especially the identification and functional research of miRNA closely related to cold stress, for the breeding of excellent H. fulva.Results A total of 5619 cold-responsive miRNAs, 315 putative novel and 5 304 conserved miRNAs, were identified from the leaves and roots of two different varieties ‘Jinyan’ (cold-tolerant) and ‘Lucretius ’ (cold-sensitive), which were stressed under -4 oC for 24 h. Twelve conserved and three novel miRNAs (novel-miR10, novel-miR19 and novel-miR48) were differentially expressed in leaves of ‘Jinyan’ under cold stress. Novel-miR19, novel-miR29 and novel-miR30 were up-regulated in roots of ‘Jinyan’ under cold stress. Thirteen and two conserved miRNAs were deferentially expressed in leaves and roots of ‘Lucretius’ after cold stress. The deferentially expressed miRNAs between two cultivars under cold stress include novel miRNAs and the members of the miR156, miR166 and miR319 families. A total of 6 598 target genes for 6 516 known miRNAs and 82 novel miRNAs were predicted by bioinformatic analysis, mainly involved in metabolic processes and stress responses. Ten differentially expressed miRNAs and predicted target genes were confirmed by quantitative reverse transcription PCR(q-PCR), and the expressional changes of target genes were negatively correlated to differentially expressed miRNAs. Our data indicated that some candidate miRNAs (e.g., miR156a-3-p, miR319a, and novel-miR19) may play important roles in plant response to cold stress.Conclusions Our study indicates that some putative target genes and miRNA mediated metabolic processes and stress responses are significant to cold tolerance in H. fulva.

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

Bangladesh Rice Journal ◽

10.3329/brj.v23i2.48243 ◽

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

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Different Responses of Cytoplasmic and Endoplasmic Reticulum Hsp90 Genes from Eogystia hippophaecola (Lepidoptera: Cossidae) to Cold Stress

Forests ◽

10.3390/f10111039 ◽

2019 ◽

Vol 10 (11) ◽

pp. 1039

Author(s):

Qianqian Wang ◽

Jing Tao ◽

Yurong Li ◽

Yabei Xu ◽

Xinhai Liu ◽

...

Keyword(s):

Endoplasmic Reticulum ◽

Amino Acid ◽

Low Temperature ◽

Cold Stress ◽

Cold Tolerance ◽

Response Times ◽

Expression Patterns ◽

Amino Acid Sequences ◽

Sea Buckthorn ◽

Open Reading Frames

Eogystia hippophaecola Hua, Chou, Fang et Chen (Lepidoptera: Cossidae) is an important borer pest of the sea buckthorn forest (Hippophae rhamnoides L.) in China. Its larvae, which are highly cold tolerant, mainly overwinter in sea buckthorn roots. Heat shock proteins (Hsps) are important molecular chaperones that have been linked to cold tolerance in insects. In this study, we cloned the open reading frames (ORFs) of two Hsp90 genes from E. hippophaecola, EhHsp90-1 and EhHsp90-2, and analyzed their expression under cold stress by qRT-PCR. EhHsp90-1 and EhHsp90-2 are 2154 and 2346 bp in length, respectively, encoding 717 and 781 amino acids. The deduced amino acid sequences contain the conserved signature sequences of the Hsp90 family and the C-terminus characteristic sequence of cytoplasmic or endoplasmic reticulum Hsp90 protein. Phylogenetic analysis revealed the amino acid sequences of EhHsp90-1 and EhHsp90-2 were very similar to the corresponding proteins from Lepidoptera. Under various low-temperature treatments lasting 2 h, EhHsp90-1 and EhHsp90-2 exhibited similar expression patterns, increasing first and then decreasing. At −5 °C, EhHsp90-1 was significantly up-regulated after 12 h, whereas EhHsp90-2 was up-regulated after just 1 h and reached its highest level at 2 h; however, the overall degree of upregulation was greater for EhHsp90-1. Subsequently, the expression level of EhHsp90-2 fluctuated with time. Our results suggest that the two Hsp90s play important roles in E. hippophaecola larvae response to cold stress, but that their response times and the magnitudes of their responses to low-temperature stress differed significantly, providing a theoretical basis for further studying the molecular mechanism of cold tolerance in E. hippophaecola larvae.

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RNA-seq analysis provides insights into cold stress responses of Xanthomonas citri pv. citri

BMC Genomics ◽

10.1186/s12864-019-6193-0 ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 1

Author(s):

Jin-Xing Liao ◽

Kai-Huai Li ◽

Jin-Pei Wang ◽

Jia-Ru Deng ◽

Qiong-Guang Liu ◽

...

Keyword(s):

Fatty Acid ◽

Low Temperature ◽

Cold Stress ◽

Stress Responses ◽

Citrus Canker ◽

Transcriptional Analysis ◽

Adaptive Responses ◽

Xanthomonas Citri ◽

Type Iv ◽

Expression Of Genes

Abstract Background Xanthomonas citri pv. citri (Xcc) is a citrus canker causing Gram-negative bacteria. Currently, little is known about the biological and molecular responses of Xcc to low temperatures. Results Results depicted that low temperature significantly reduced growth and increased biofilm formation and unsaturated fatty acid (UFA) ratio in Xcc. At low temperature Xcc formed branching structured motility. Global transcriptome analysis revealed that low temperature modulates multiple signaling networks and essential cellular processes such as carbon, nitrogen and fatty acid metabolism in Xcc. Differential expression of genes associated with type IV pilus system and pathogenesis are important cellular adaptive responses of Xcc to cold stress. Conclusions Study provides clear insights into biological characteristics and genome-wide transcriptional analysis based molecular mechanism of Xcc in response to low temperature.

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Identification of QTLs controlling low-temperature germinability and cold tolerance at the seedling stage in rice (Oryza Sativa L.)

Euphytica ◽

10.1007/s10681-017-2092-0 ◽

2017 ◽

Vol 214 (1) ◽

Cited By ~ 8

Author(s):

L. M. Yang ◽

H. L. Liu ◽

L. Lei ◽

H. W. Zhao ◽

J. G. Wang ◽

...

Keyword(s):

Oryza Sativa ◽

Low Temperature ◽

Cold Tolerance ◽

Oryza Sativa L ◽

Seedling Stage

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Association of qLTG3-1 with germination stage cold tolerance in diverse rice germplasm from the Indian subcontinent

Plant Genetic Resources ◽

10.1017/s1479262113000142 ◽

2013 ◽

Vol 11 (3) ◽

pp. 206-211 ◽

Cited By ~ 9

Author(s):

Clarissa Challam ◽

Gayle Alisha Kharshing ◽

Julia S. Yumnam ◽

Mayank Rai ◽

Wricha Tyagi

Keyword(s):

Low Temperature ◽

Cold Stress ◽

Cold Tolerance ◽

Indian Subcontinent ◽

Crop Productivity ◽

Climatic Conditions ◽

Superior Performance ◽

Rice Germplasm ◽

Potential Marker ◽

Rice Genotypes

Low temperature is a major constraint for crop productivity. To cope with this challenge, plants have developed several mechanisms to adapt to low temperature. Developing breeding strategies to enhance cold stress tolerance in crops requires an understanding of the mechanisms by which plants perceive and transmit cold stress-related signals to their cellular machinery, thereby activating adaptive responses. Only one quantitative trait locus for tolerance to low-temperature germination, qLTG3-1, has been narrowed down to the gene level in rice. A 71 bp indel that can be used to distinguish between tolerant and susceptible parents has been identified. We tested the 71 bp indel on 65 diverse rice genotypes including those adapted to colder climates of North and Northeastern India to find evidence of the tolerant allele (insertion) and to see whether it is associated with low-temperature germinability in these genotypes. Our results show that 48% of the rice genotypes tested carried the tolerant allele. The insertion was found to be significantly associated with cold tolerance during germination. Moreover, several landraces/improved varieties known for their superior performance in other abiotic stress conditions such as drought and high salinity conditions, and which were previously never exposed to low temperature, carry the beneficial allele for qLTG3-1, suggesting an additional role of this allele in adverse climatic conditions. This study enhances current understanding of the distribution of the tolerant allele qLTG3-1 in rice germplasm, which could help in the identification of suitable donors for potential marker-assisted breeding programmes.

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Cold tolerance in rice varieties at different growth stages

Crop and Pasture Science ◽

10.1071/cp09006 ◽

2009 ◽

Vol 60 (4) ◽

pp. 328 ◽

Cited By ~ 34

Author(s):

C. Ye ◽

S. Fukai ◽

I. Godwin ◽

R. Reinke ◽

P. Snell ◽

...

Keyword(s):

Low Temperature ◽

Cold Tolerance ◽

High Elevation ◽

Temperature Tolerance ◽

Seedling Stage ◽

Growth Stages ◽

Rice Varieties ◽

Low Temperature Tolerance ◽

Wide Range ◽

Different Growth Stages

Low temperature is a common production constraint in rice cultivation in temperate zones and high-elevation environments, with the potential to affect growth and development from germination to grain filling. There is a wide range of genotype-based differences in cold tolerance among rice varieties, these differences often reflecting growth conditions in the place of origin, as well as breeding history. However, improving low temperature tolerance of varieties has been difficult, due to a lack of clarity of the genetic basis to low temperature tolerance for different growth stages of the rice plant. Seeds or plants of 17 rice varieties of different origins were exposed to low temperature during germination (15°C), seedling, booting, and flowering stages (18.5°C), to assess their cold tolerance at different growth stages. Low temperature at the germination stage reduced both the percentage and speed of germination. Varieties from China (B55, Banjiemang, and Lijianghegu) and Hungary (HSC55) were more tolerant of low temperature than other varieties. Most of the varieties showed moderate levels of low temperature tolerance during the seedling stage, the exceptions being some varieties from Australia (Pelde, YRL39, and YRM64) and Africa (WAB160 and WAB38), which were susceptible to low temperature at the seedling stage. Low temperature at booting and flowering stages reduced plant growth and caused a significant decline in spikelet fertility. Some varieties from China (B55, Bangjiemang, Lijiangheigu), Japan (Jyoudeki), the USA (M103, M104), and Australia (Quest) were tolerant or moderately tolerant, while the remaining varieties were susceptible or moderately susceptible to low temperature at booting and flowering stages. Three varieties from China (B55, Lijianghegu, Banjiemang) and one from Hungary (HSC55) showed consistent tolerance to low temperature at all growth stages. These varieties are potentially important gene donors for breeding and genetic studies. The cold tolerance of the 17 rice varieties assessed at different growth stages was correlated. Screening for cold tolerance during early growth stages can therefore potentially be an effective way for assessing cold tolerance in breeding programs.

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