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 Identification of Candidate Genes Conferring Cold Tolerance to Rice (Oryza sativa L.) at the Bud-Bursting Stage Using Bulk Segregant Analysis Sequencing and Linkage Mapping

2021 ◽  
Vol 12 ◽  
Author(s):  
Luomiao Yang ◽  
Lei Lei ◽  
Peng Li ◽  
Jingguo Wang ◽  
Chao Wang ◽  
...  
Keyword(s):  
Low Temperature ◽  
Cold Tolerance ◽  
Oryza Sativa L ◽  
Chromosome 9 ◽  
Pcr Analysis ◽  
Potential Candidate ◽  
Sequencing Data ◽  
Coding Region ◽  
Rice Varieties ◽  
Major Qtl

Low-temperature tolerance during the bud-bursting stage is an important characteristic of direct-seeded rice. The identification of cold-tolerance quantitative trait loci (QTL) in species that can stably tolerate cold environments is crucial for the molecular breeding of rice with such traits. In our study, high-throughput QTL-sequencing analyses were performed in a 460-individual F2:3 mapping population to identify the major QTL genomic regions governing cold tolerance at the bud-bursting (CTBB) stage in rice. A novel major QTL, qCTBB9, which controls seed survival rate (SR) under low-temperature conditions of 5°C/9 days, was mapped on the 5.40-Mb interval on chromosome 9. Twenty-six non-synonymous single-nucleotide polymorphism (nSNP) markers were designed for the qCTBB9 region based on re-sequencing data and local QTL mapping conducted using traditional linkage analysis. We mapped qCTBB9 to a 483.87-kb region containing 58 annotated genes, among which six predicted genes contained nine nSNP loci. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis revealed that only Os09g0444200 was strongly induced by cold stress. Haplotype analysis further confirmed that the SNP 1,654,225 bp in the Os09g0444200 coding region plays a key role in regulating the cold tolerance of rice. These results suggest that Os09g0444200 is a potential candidate for qCTBB9. Our results are of great significance to explore the genetic mechanism of rice CTBB and to improve the cold tolerance of rice varieties by marker-assisted selection.

scholarly journals Jasmonate and Melatonin Act Synergistically to Potentiate Cold Tolerance in Tomato Plants

2022 ◽  
Vol 12 ◽  
Author(s):  
Fei Ding ◽  
Liming Ren ◽  
Fang Xie ◽  
Meiling Wang ◽  
Shuoxin Zhang
Keyword(s):  
Cold Stress ◽  
Cold Tolerance ◽  
Feedback Loop ◽  
Pcr Analysis ◽  
Tomato Plants ◽  
Qrt Pcr ◽  
Cold Condition ◽  
Tomato Cultivars ◽  
Cold Responses ◽  
Ja Signaling

Both jasmonic acid (JA) and melatonin (MT) have been demonstrated to play positive roles in cold tolerance, however, whether and how they crosstalk in the cold responses in plants remain elusive. Here, we report that JA and MT act synergistically in the cold tolerance in tomato plants (Solanum lycopersicum). It was found that JA and MT were both substantially accumulated in response to cold stress and foliar applications of methyl jasmonate (MeJA) and MT promoted cold tolerance as evidenced by increased Fv/Fm, decreased relative electrolyte leakage (EL) and declined H2O2 accumulation in tomato plants. Inhibition of MT biosynthesis attenuated MeJA-induced cold tolerance, while inhibition of JA biosynthesis reduced MT accumulation in tomato plants under cold conditions. Furthermore, qRT-PCR analysis showed that the expressions of two MT biosynthetic genes, SlSNAT and SlAMST, were strongly induced by MeJA, whereas suppression of SlMYC2, a master JA signaling regulator, abated the expressions of SlSNAT and SlAMST under cold stress. Additionally, suppression of SlMYC2 reduced MT accumulation, decreased Fv/Fm and increased EL in cold-stressed tomato plants. Interestingly, exogenous MT promoted JA accumulation, while inhibition of MT biosynthesis significantly reduced JA accumulation in tomato plants under the cold condition. Taken together, these results suggest that JA and MT act cooperatively in cold tolerance and form a positive feedback loop, amplifying the cold responses of tomato plants. Our findings might be translated into the development of cold-resistant tomato cultivars by genetically manipulating JA and MT pathways.

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

Cold tolerance in rice varieties at different growth stages

2009 ◽  
Vol 60 (4) ◽  
pp. 328 ◽  
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.

A major QTL associated with cold tolerance at seedling stage in rice (Oryza sativa L.)

Euphytica ◽  
2007 ◽  
Vol 158 (1-2) ◽  
pp. 87-94 ◽  
Author(s):  
Qiaojun Lou ◽  
Liang Chen ◽  
Zongxiu Sun ◽  
Yongzhong Xing ◽  
Jun Li ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Cold Tolerance ◽  
Oryza Sativa L ◽  
Seedling Stage ◽  
Major Qtl

The pleitropic regulator AdpAch is required for natamycin biosynthesis and morphological differentiation in Streptomyces chattanoogensis

Microbiology ◽  
2011 ◽  
Vol 157 (5) ◽  
pp. 1300-1311 ◽  
Author(s):  
Yi-Ling Du ◽  
Shan-Zhen Li ◽  
Zhan Zhou ◽  
Shi-Fei Chen ◽  
Wei-Ming Fan ◽  
...  
Keyword(s):  
Genetic Manipulation ◽  
Regulatory Gene ◽  
Gene Clusters ◽  
Transcriptional Analysis ◽  
Pcr Analysis ◽  
Biosynthetic Gene ◽  
Coding Region ◽  
Mobility Shift ◽  
Intergenic Regions ◽  
Streptomyces Chattanoogensis

The complete natamycin (NTM) biosynthetic gene cluster of Streptomyces chattanoogensis was cloned and confirmed by the disruption of pathway-specific activator genes. Comparative cluster analysis with its counterpart in Streptomyces natalensis revealed different cluster architecture between these two clusters. Compared with the highly conserved coding sequences, sequence variations appear to occur frequently in the intergenic regions. The evolutionary change of nucleotide sequence in the intergenic regions has given rise to different transcriptional organizations in the two clusters and resulted in altered gene regulation. These results provide insight into the evolution of antibiotic biosynthetic gene clusters. In addition, we cloned a pleitropic regulator gene, adpAch , in S. chattanoogensis. Using the genetic system that we developed for this strain, adpAch was deleted from the genome of S. chattanoogensis. The ΔadpAch mutant showed a conditionally sparse aerial mycelium formation phenotype and defects in sporulation; it also lost the ability to produce NTM and a diffusible yellow pigment normally produced by S. chattanoogensis. RT-PCR analysis revealed that transcription of adpAch was constitutive in YEME liquid medium. By using rapid amplification of 5′ complementary DNA ends, two transcription start sites were identified upstream of the adpAch coding region. Quantitative transcriptional analysis showed that the expression level of the NTM regulatory gene scnRI decreased 20-fold in the ΔadpAch mutant strain, while the transcription of the other activator gene scnRII was not significantly affected. Electrophoretic mobility shift assay (EMSA) showed that AdpAch binds to its own promoter but fails to bind to the promoter region of scnRI, indicating that the control of scnRI by AdpAch is exerted in an indirect way. This work not only provides a platform and a new potential target for increasing the titre of NTM by genetic manipulation, but also advances the understanding of the regulation of NTM biosynthesis.

scholarly journals Genetic basis analysis for indica germinability under low temperature using a new RILs population genotyping by whole-genome resequencing

2020 ◽  
Author(s):  
Peng Wang ◽  
Guangliang Wu ◽  
Xin Luo ◽  
Ruiqi Liu ◽  
Andong Zhou ◽  
...  
Keyword(s):  
Cold Stress ◽  
Cold Tolerance ◽  
Genetic Map ◽  
Marker Assisted Selection ◽  
Genetic Basis ◽  
High Density ◽  
Genome Resequencing ◽  
Rice Varieties ◽  
Whole Genome Resequencing ◽  
Germination Stage

Abstract Background : Improving the cold tolerance of rice at germination stage is an important objective to maintain rice yields. However, less analyses were carried out to detect the quantitative trait loci (QTLs) associated with cold tolerance using indica/indica population. Therefore, the genetic basis of cold tolerance of the indica varieties should be provided considerable attentionResults: In this study, a recombinant inbred lines (RILs) population comprising 126 lines derived from two widely used double-cropped indica rice varieties Wufeng B (WFB) and Changhui T025 (CHT025) was used to construct a high-density linkage map based on whole-genome resequencing. The high-density genetic map included 2,578 bins on 12 linkage groups and was 1762.80 cM in length, with an average interlocus distance of 0.68 cM. On the basis of newly constructed high-density genetic map, a total of 18 additive QTLs ranging from 34.55 to 315.21 kb on Nipponbare genome and two pairs of epistatic QTLs associated with cold stress at germination stage were detected, which indicated that the genetic basis of cold tolerance of WFB and CHT025 at germination stage is manly due to additive effects of several QTLs. Otherwise, the phylogenetic analysis showed that WFB is a typical indica variety while CHT025 is an interphyletic rice variety. Most of the favorable QTLs harbouring in indica WFB showed different chromosomal region from the QTLs associating with cold stress from japonica rice in previous studies, which indicated that indica might have different cold stress genetic mechanism comparing to japonica subspecies. Furthermore, we can incorporate these favorable QTLs existing in WFB into rice varieties to breed new cold tolerance indica male sterile maintenance line via marker-assisted selection; CHT025 is a better source of these cold tolerance favorable QTLs only only for the improvement of indcia but also for japonica restorer line germinability under low temperature via marker-assisted selection.Conclusion : This population with high density genetic map will serve as better choice for identifying important quantitative traits of these two good indica germplasms, and these favorable QTLs exist in WFB and CHT025 can be used to breed new cold tolerance indica varieties via marker-assisted selection. These authors have contributed equally to this work

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

Agriculture ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. 162 ◽  
Author(s):  
Doan Cong Dien ◽  
Takeo Yamakawa
Keyword(s):  
Low Temperature ◽  
Cold Tolerance ◽  
Seedling Stage ◽  
Germination Index ◽  
Rice Varieties ◽  
Coleoptile Length ◽  
Temperature Conditions ◽  
Cold Tolerant ◽  
Germination Stage ◽  
Radicle Length

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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