Phenotypic Variation and Selection for Cold-Tolerant Rice (Oryza sativa L.) at Germination and Seedling Stages

Owing to its origin in tropical and subtropical areas, rice is susceptible to cold stress. Low temperatures at the germination and seedling stages can result in seed loss, a delayed transplanting period, and lower final yield. In this study, 181 rice varieties from around the world were investigated for cold tolerance at the germination and seedling stages. At the germination stage, the responses of different rice varieties were examined based on the germination index, coleoptile length, and radicle length at low (13 °C) and control temperatures (25 °C). Significant variations in the germination index, coleoptile length, and radicle length were observed among varieties. Low temperature significantly decreased germination ability, and coleoptile and radicle growth in the studied varieties. At the seedling stage, cold tolerance of the rice varieties was evaluated based on the leaf color score under natural low temperature. Similar to the germination stage, at the seedling stage, significant variation in root and shoot growth was observed in the response of rice varieties to low temperature conditions. Based on the results from both the germination and seedling stages, two varieties (Hei-Chiao-Chui-Li-Hsiang and Ta-Mao-Tao) were selected as the best cold-tolerant varieties. Our results also indicate the benefits of warming treatments to protect rice seedlings from low temperature conditions.

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Evaluation of rice (Oryza sativa L.) genotypes for cold tolerance at seedling stage

ORYZA- An International Journal on Rice ◽

10.35709/ory.2020.57.1.5 ◽

2020 ◽

Vol 57 (1) ◽

pp. 43-48

Author(s):

K Sumayya ◽

MP Rajanna ◽

CA Deepak ◽

KV Shivakumar ◽

GR Denesh

Keyword(s):

Oryza Sativa ◽

Low Temperature ◽

Cold Tolerance ◽

Oryza Sativa L ◽

Early Spring ◽

Seedling Stage ◽

Germination Index ◽

Coleoptile Length ◽

Crop Establishment ◽

Rice Genotypes

Cold tolerance during germination is important for ensuring fast and uniform crop establishment. Rice plants are injured at the seedling stage when they are grown in early spring in temperate or subtropical environments. The productivity of rice is particularly low during spring due to cold, which is an important abiotic constraint, where low temperature prevails below 18 ºC. The present study was taken up to evaluate cold tolerance in 86 rice genotypes based on seed and seedling parameters as per Cruz and Milach (2004). Seeds were germinated under two conditions i.e.,160C for 28 days (cold) and 280C for 7 days (control).The genotypes showed highly significant differences forparameters such as germination (%), germination index (%), percentage of seeds with coleoptile superior to 5 mm (PERCOL), percentage of reduction in coleoptile length (REDCOL) and coleoptile regrowth (COLREG, cm).Both REDCOL and COLREG seem to be the most adequate characteristics to be used to evaluate cold tolerance during the germination period in rice. Among those genotypes, AC 35548, JBT 37/164, PS 353, KMP-175 andThanu were adjudged as promising when screened for cold tolerance under laboratory conditions based on the aforementioned parameters.

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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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Cold tolerance at the germination stage of rice: methods of evaluation and characterization of genotypes

Scientia Agricola ◽

10.1590/s0103-90162004000100001 ◽

2004 ◽

Vol 61 (1) ◽

pp. 1-8 ◽

Cited By ~ 39

Author(s):

Renata Pereira da Cruz ◽

Sandra Cristina Kothe Milach

Keyword(s):

Cold Tolerance ◽

Coleoptile Length ◽

Methods Of Evaluation ◽

Cold Tolerant ◽

Measured Characteristic ◽

Method Of Evaluation ◽

Different Origins ◽

Adequate Method ◽

Germination Stage

Rice cold tolerance at the germination stage is important in Rio Grande do Sul (RS) where temperatures below 15°C prevent or reduce germination and plant establishment in early sowings. The present study aimed at identifying an adequate method for cold tolerance evaluation of the rice germination stage and at verifying the variability among 24 rice genotypes of different origins. Cold tolerance was evaluated in experiment I, germination under two conditions: 13°C for 28 days and 28°C for seven days, and in experiment II, germination under 28°C for 72 hours, 13°C for 96 hours and again 28°C for 72 hours. In experiment I measured characteristics were germination index, percentage of seeds with coleoptile length superior to 5 mm and percentage of reduction in coleoptile length due to cold. In experiment II the measured characteristic was coleoptile regrowth after the cold period. Cold tolerance varied among genotypes studied in both experiments, but only the percentage of reduction in coleoptile length and coleoptile regrowth allowed a better distinction between the tolerant checks and the susceptible one. In general, genotypes belonging to the Japonica subspecies presented higher cold tolerance than Indica, but there was variability within subspecies. The most adequate method of evaluation of cold tolerance is through percentage of reduction in coleoptile length and coleoptile regrowth. Among Japonica genotypes, Quilla 64117 and Diamante presented the highest cold tolerance, and among Indica, cultivars BR-IRGA 410 and IRGA 416 were the most cold tolerant at the germination stage.

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Mapping quantitative trait loci for cold tolerance in rice at seedling stage

Bangladesh Journal of Botany ◽

10.3329/bjb.v48i4.49050 ◽

2019 ◽

Vol 48 (4) ◽

pp. 1021-1028

Author(s):

Nomita Das ◽

Nazmul Alam ◽

Kamal Hossain ◽

Partha S Biswas

Keyword(s):

Quantitative Trait Loci ◽

Cold Tolerance ◽

Quantitative Trait ◽

Interval Mapping ◽

Seedling Stage ◽

Growth Stages ◽

Rice Varieties ◽

Significant Qtls ◽

Trait Loci ◽

Cold Tolerant

Rice plants are sensitive to cold stress at various growth stages starting from germination to maturity. Exploitation of cold tolerance for the development of cold tolerant varieties may help in saving crop loss or cost of production in the cold prone environment. Introgression of quantitative trait loci (QTLs) conferring cold tolerance in the elite variety may be the most effective and sustainable approach to address this issue. A F2:3 mapping population of a cross between a cold susceptible variety (BR1) and a cold tolerant variety (BR18) was used to map QTLs for cold tolerance at seedling stage. Three significant QTLs on chromosomes 1, 3 and 12 associated with cold tolerance were mapped between the markers intervals of RM220-RM10829, RM546-RM7 and RM27877-RM463, respectively at a threshold LOD of 4.3 through composite interval mapping. Phenotypic contributions of these QTLs were 50.7, 39 and 52.7%, respectively. Marker information of such a large effect QTL could be used in the breeding program after necessary validation to develop cold tolerant high yielding rice varieties.

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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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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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Genome-Wide Association Study (GWAS) For Cold Tolerance at The Bud Burst Stage in Rice Using SNP Markers

10.21203/rs.3.rs-311085/v1 ◽

2021 ◽

Author(s):

Caijing Li ◽

Jindong Liu ◽

Jianxin Bian ◽

Tao Jin ◽

Baoli Zou ◽

...

Keyword(s):

Low Temperature ◽

Association Study ◽

Cold Tolerance ◽

Genetic Basis ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Bud Burst ◽

Rice Varieties ◽

Rice Landraces ◽

Genome Wide

Abstract Background: Rice is a crop that is very sensitive to low temperature, and its morphological development and production are greatly affected by low temperature. Therefore, understanding the genetic basis of cold tolerance in rice is of great significance for mining favorable genes and cultivating excellent rice varieties. However, there were limited studies focusing on cold tolerance at the bud burst stage, therefore, considerable attention should be paid to the genetic basis of cold tolerance at the bud burst stage (CTBB).Results: In this study, a natural population consisting of 211 rice landraces collected from 15 provinces of China and other countries were firstly used to evaluate the cold tolerance at the bud burst stage. Population structure analysis showed that this population divided into three groups and was rich in genetic diversity. Our evaluation results confered that the japonica rice was more tolerance to cold at the bud burst stage than indica rice. Genome-wide association study (GWAS) were performed through the phenotypic data of 211 rice landraces and 36,727 SNPs dataset under a mixed linear model, and 12 QTLs (P < 0.0001) were identified according to the seedling survival rate (SSR) treated at 4 ℃, in which there are five QTLs (qSSR2-2, qSSR3-1, qSSR3-2, qSSR3-3 and qSSR9) which were co-located with previous studies, and seven QTLs (qSSR2-1, qSSR3-4, qSSR3-5, qSSR3-6, qSSR3-7, qSSR4 and qSSR7) which were reported for the first time. Among these QTLs, qSSR9, harboring the highest-peak SNP, explained biggest phenotypic variation. Through bioinformatics analysis, five genes (LOC_Os09g12440, LOC_Os09g12470, LOC_Os09g12520, LOC_Os09g12580 and LOC_Os09g12720) were nominated as candidates for qSSR9. Conclusion: This natural population consisting of 211 rice landraces with high density SNPs will serve as a better choice for identifying rice QTLs/genes in future, and the detected QTLs associated with cold tolerance in rice bud burst stage will be conducive to further mining favorable genes and breeding of rice varieties under cold stress.

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Biplot analysis of diallel crosses for cold tolerance in rice at the germination stage

Crop and Pasture Science ◽

10.1071/cp10207 ◽

2011 ◽

Vol 62 (2) ◽

pp. 169 ◽

Cited By ~ 2

Author(s):

Peyman Sharifi ◽

Mohammad Reza Safari Motlagh

Keyword(s):

Cold Tolerance ◽

Combining Ability ◽

Graphical Representation ◽

Principal Component ◽

Environment Interaction ◽

Coleoptile Length ◽

Heterotic Groups ◽

Diallel Crosses ◽

Biplot Analysis ◽

Germination Stage

This paper reports analysis of 7 × 7 diallel crosses using a genotype main effect plus genotype-by-environment interaction biplot for determining cold tolerance at the germination stage in rice. ANOVA indicated that there were highly significant differences among the replications, genotypes, general combining ability (GCA) and specific combining ability (SCA) for percentage of reduction in radicle length (RL), coleoptile length (CL) and germination percentage (GP). The hybrid Neda × Hassani had the highest mid-parent heterosis for RL, CL and GP (–58.84, –68.47 and –80.77%, respectively). This result indicated that the reduction of three traits in crosses of Neda × Hassani was lower than their parents. The graphical representation by biplot analysis allowed a rapid and effective overview of GCA and reveals that Deilamani was an ideal general combiner for all traits and this parent is a superior variety for these three traits. Three potential heterotic groups are suggested for RL reduction. Four potential heterotic groups were identified for the two other traits, in the biplot. The first two principal component (PC) axes in the biplot for reduction in GP explained 85% of the variation with first and second principal components (PC1 and PC2, respectively). An important inference that can be drawn from these results is that cross combinations involving Hassani and Deilamani as one of the parents recorded desirable SCA effects for all or most of the studied traits. The information obtained from this experiment can facilitate the identification of hybrids that combine cold resistance traits in rice.

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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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Tetraploidy enhances the cold-resistance in yellow kiwifruit (Actinidia chinensis)

10.21203/rs.2.21136/v1 ◽

2020 ◽

Author(s):

Yipei Li ◽

Xiaozhen Liu ◽

Zhou Wei ◽

Zhimin Zhang ◽

Wen Bian ◽

...

Keyword(s):

Survival Rate ◽

Low Temperature ◽

Cold Tolerance ◽

Regulatory Networks ◽

Temperature Tolerance ◽

Temperature Treatment ◽

Actinidia Chinensis ◽

Low Temperature Tolerance ◽

Low Temperature Treatment ◽

Cold Tolerant

Abstract Yellow kiwifruit ( Actinidia chinensis ) is highly susceptible to severe weather, such as low temperature and frost, which may affect the production in the coming year. And the cold-resistant mechanism of kiwifruit associated with gene regulation is poorly investigated. To botain cold-resistant germplam, to provide insight into the causes of differences in low temperature tolerance due to ploidy and to better understand cold-adaptive mechanisms in tetraploid kiwifruit, the diploid yellow kiwifruit ‘SWFU03’ and its tetraploid plantlets were subjected to cold-tolerant screening with L-hydroxyproline (L-Hyp) and low temperature, the selected ones were then analyzed by transcriptome data and confirmed by RT-qPCR. The results showed that the survival rate of tetraploid plants was 62.22% when treated with 8 mmol/L L-Hyp for 30 days, while all the diploid ones died. After treated with 0°C for 12 h, then at room temperature for seven days, the survival rate of tetraploid plantlets was 42.22%, while all diploidy died. Hence, cold tolerance of the tetraploid plantlets was stronger than that of the diploid genotypes. Using these two screening systems, 126 cold-resistant tetraploid tissue culture plantlets were obtained. A total of 1630 differentially expressed genes (DEGs) were identified, of which 619 were up-regulated and 1011 were down-regulated in the low temperature treatment goup. The DEGs enriched in the cold-tolerance related pathways mainly included plant hormone signal transduction, and starch and sucrose metabolism pathway. RT-qPCR analysis confirmed the expression levels of eight up-regulated genes in these pathways in the cold-resistant mutants. In conclusion, this study has identified cold-resistant yellow kiwifruit plantlets and cold-tolerance related genes. Moreover, the dataset got in this study advances our knowledge of the cold-adaptive genes in the regulatory networks and leads to understand the cold tolerance mechanisms in the tetraploid yellow kiwifruit.

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