scholarly journals Genetic Dissection of Germinability under Low Temperature by Building a Resequencing Linkage Map in japonica Rice

2020 ◽  
Vol 21 (4) ◽  
pp. 1284 ◽  
Author(s):  
Shukun Jiang ◽  
Chao Yang ◽  
Quan Xu ◽  
Lizhi Wang ◽  
Xianli Yang ◽  
...  
Keyword(s):  
Low Temperature ◽  
Genetic Distance ◽  
Recombinant Inbred Lines ◽  
Seed Vigor ◽  
Japonica Rice ◽  
Rice Breeding ◽  
Positive Effects ◽  
Comparison Results ◽  
Cold Tolerant ◽  
Bin Map

Among all cereals, rice is highly sensitive to cold stress, especially at the germination stage, which adversely impacts its germination ability, seed vigor, crop stand establishment, and, ultimately, grain yield. The dissection of novel quantitative trait loci (QTLs) or genes conferring a low-temperature germination (LTG) ability can significantly accelerate cold-tolerant rice breeding to ensure the wide application of rice cultivation through the direct seeding method. In this study, we identified 11 QTLs for LTG using 144 recombinant inbred lines (RILs) derived from a cross between a cold-tolerant variety, Lijiangxintuanheigu (LTH), and a cold-sensitive variety, Shennong265 (SN265). By resequencing two parents and RIL lines, a high-density bin map, including 2,828 bin markers, was constructed using 123,859 single-nucleotide polymorphisms (SNPs) between two parents. The total genetic distance corresponding to all 12 chromosome linkage maps was 2,840.12 cm. Adjacent markers were marked by an average genetic distance of 1.01 cm, corresponding to a 128.80 kb physical distance. Eight and three QTL alleles had positive effects inherited from LTH and SN265, respectively. Moreover, a pleiotropic QTL was identified for a higher number of erected panicles and a higher grain number on Chr-9 near the previously cloned DEP1 gene. Among the LTG QTLs, qLTG3 and qLTG7b were also located at relatively small genetic intervals that define two known LTG genes, qLTG3-1 and OsSAP16. Sequencing comparisons between the two parents demonstrated that LTH possesses qLTG3-1 and OsSAP16 genes, and SN-265 owns the DEP1 gene. These comparison results strengthen the accuracy and mapping resolution power of the bin map and population. Later, fine mapping was done for qLTG6 at 45.80 kb through four key homozygous recombinant lines derived from a population with 1569 segregating plants. Finally, LOC_Os06g01320 was identified as the most possible candidate gene for qLTG6, which contains a missense mutation and a 32-bp deletion/insertion at the promoter between the two parents. LTH was observed to have lower expression levels in comparison with SN265 and was commonly detected at low temperatures. In conclusion, these results strengthen our understanding of the impacts of cold temperature stress on seed vigor and germination abilities and help improve the mechanisms of rice breeding programs to breed cold-tolerant varieties.

scholarly journals Near-Isogenic Lines of Japonica Rice Revealed New QTLs for Cold Tolerance at Booting Stage

Agronomy ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 40 ◽  
Author(s):  
Zhenghai Sun ◽  
Juan Du ◽  
Xiaoying Pu ◽  
Muhammad Kazim Ali ◽  
Xiaomeng Yang ◽  
...  
Keyword(s):  
Low Temperature ◽  
Cold Tolerance ◽  
Temperature Stress ◽  
Mixed Linear Model ◽  
Low Temperature Stress ◽  
Japonica Rice ◽  
Near Isogenic Lines ◽  
Booting Stage ◽  
Isogenic Lines ◽  
Cold Tolerant

Low temperature stress severely hampers rice productivity, and hence elaborating chilling-mediated physiochemical alterations and unravelling cold tolerance pathways will facilitate cold resilient rice breeding. Various cold tolerant Near-isogenic lines (NILs) selected at the booting stage through backcrossing of a japonica landrace Lijing2 (cold tolerant) with cold sensitive Towada (a japonica cultivar). The cold tolerance attributes of NILs was validated over two years by evaluating the spikelet fertility followed by correlation of nineteen morphological traits with the rate of seed setting (RSS). Results revealed BG, FG, 1-2IL, RSLL, and UIL were significantly correlated with RSS and had nearer marker interval distance with cold tolerance in QTL analysis. Two QTLs, qCTB-7-a and qCTB-7-b, were found for RSS based on a mixed linear model. Alleles of two QTLs were contributed by Lijing2 and genetic distances between the peaks were 0.00 and 0.06cM, which explained 5.70% and 8.36% variation, respectively, One QTL for 1-2IL, RSLL, and ILBS, while two QTLs for FG, BG, and UIL were also identified. These findings can be exploited to engineer low temperature stress tolerant rice in times of climate change.

scholarly journals Breeding for Low Temperature Germinability in Temperate Japonica Rice Varieties: Analysis of Candidate Genes in Associated QTLs

Agronomy ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 2125
Author(s):  
Ester Sales ◽  
Eva Miedes ◽  
Luis Marqués
Keyword(s):  
Low Temperature ◽  
Genome Wide Association Study ◽  
Recombinant Inbred Lines ◽  
Rice Chromosome ◽  
Temperature Tolerance ◽  
Chromosome 3 ◽  
Japonica Rice ◽  
Rice Cultivars ◽  
Rice Varieties ◽  
Low Temperature Tolerance

In temperate areas, rice deals with low temperatures that can affect plant growth and crop yield. Rapid germination is required for adequate plant establishment in the field, therefore obtaining cultivars that maintain this phenotype under suboptimal temperature conditions is a challenge for rice breeders. Our study aimed to investigate temperature-induced expression changes in genes underlying quantitative trait loci (QTLs) associated to this trait (low temperature germinability, LTG) that were detected in a previous genome wide association study (GWAS). In the context of a breeding program for japonica rice cultivars adapted to cultivation in Spain, we obtained two biparental families of lines derived from hybridization with two cold tolerant Italian cultivars, and we have studied the effect on the LTG phenotype of introgressing these QTLs. A wide region in chromosome 3 was related to significant increases in seedling growth rate at 15 °C, although the extent of the effect depended on the analyzed family. In parallel, we studied the pattern of expression during germination at different temperatures of 10 genes located in the LTG-associated QTLs, in five japonica rice cultivars and in a biparental family of recombinant inbred lines (RILs). Cold induced changes in the expression of the 10 analyzed genes, with significant differences among genotypes. Variation in LTG phenotype was consistently associated with changes in the pattern of expression of five genes from the tagged regions in rice chromosome 3, which encoded for enzymes implicated in phytohormone metabolism (OsFBK12, Os3Bglu6), oxidative stress (SPL35, OsSRO1c) and Mn homeostasis maintenance (OsMTP8.1). Differential expression induced by cold in two regulatory genes (Os02g0824000 and Os06g06400) also contributed to explain low temperature tolerance during rice germination. In conclusion, introgression in defective cultivars of favorable alleles for these genes would contribute to the genetic improvement of LTG in japonica rice varieties.

scholarly journals Effects of seed priming treatments on the germination and development of two rapeseed (Brassica napus L.) varieties under the co-influence of low temperature and drought

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0257236
Author(s):  
Zong He Zhu ◽  
Abdul Sami ◽  
Qing Qing Xu ◽  
Ling Ling Wu ◽  
Wen Yin Zheng ◽  
...  
Keyword(s):  
Low Temperature ◽  
Germination Rate ◽  
Seed Priming ◽  
Seed Vigor ◽  
Stress Conditions ◽  
Stem Length ◽  
Activity Levels ◽  
Sod Activity ◽  
Germination Time ◽  
Rape Seedlings

The present study was performed to evaluate the effects of seed priming. This was done by soaking the seeds of two rapeseed cultivars, namely, ZY15 (tolerant to low temperature and drought) and HY49 (sensitive to low temperature and drought), for 12 h in varying solutions: distilled water, 138 mg/L salicylic acid (SA), 300 mg/L gibberellic acid (GA), 89.4 mg/L sodium nitroprusside (SNP), 3000 mg/L calcium chloride (CaCl2), and 30 mg/L abscisic acid (ABA). Primed and non-primed seeds were left to germinate at 15°C and -0.15 MPa (T15W15) and at 25°C and 0 MPa (T25W0), respectively. The results showed that SA, GA, SNP, CaCl2, and ABA significantly improved the germination potential (GP), germination rate (GR), germination index (GI), stem fresh weight (SFW), stem dry weight (SDW), root length (RL), stem length (SL), and seed vigor index (SVI) under T15W15. For ZY15 seeds under T25W0, GA, SNP, CaCl2, and ABA priming reduced the average germination time (96% after 5 days) compared to that of the control (88% after 5 days). For ZY15 seeds under T15W15, SA, SNP, CaCl2, and ABA priming, with respect to the control and water-treated groups, shortened the average germination time (92% after 5 days) compared to that of the control (80% after 5 days). For HY49 seeds under T25W0, GA, SNP, CaCl2, and ABA priming reduced the average germination time (92% after 5 days) compared to that of the control (85% after 5 days). Similarly, for HY49 seeds under T15W15, GA priming shortened the average germination time (89% after 5 days) compared to that of the control (83% after 5 days). These priming agents increased the net photosynthesis, stomatal conductivity, and transpiration rate of rape seedlings under conditions of low temperature and drought stress, while also decreasing intercellular carbon dioxide (CO2) concentrations. Additionally, SA, GA, SNP, CaCl2, and ABA increased superoxide dismutase concentrations (SOD) and ascorbic peroxidase (APX) activities of rape seedlings under stress conditions, while decreasing catalase (CAT) and peroxidase (POD) activities in ZY15 seedlings. In HY49, which is sensitive to low temperature and drought, all priming solutions, except for SNP, led to an increase in SOD activity levels and a decrease in CAT activity levels. Overall, SA, GA, SNP, and CaCl2 increased the concentrations of indoleacetic acid (IAA), GA, ABA, and cytokinin (CTK) in seedlings under stress conditions. Moreover, compared to SA, CaCl2, and ABA, GA (300 mg/L) and SNP (300 mol/L) showed improved priming effects for ZY15 and HY49 under stress conditions.

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

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.

scholarly journals Identification of quantitative trait loci for leaf traits in rice

Genetika ◽  
2016 ◽  
Vol 48 (2) ◽  
pp. 643-652 ◽  
Author(s):  
Baoyan Jia ◽  
Xinhua Zhao ◽  
Yang Qin ◽  
Muhammad Irfan ◽  
Tae-Heon Kim ◽  
...  
Keyword(s):  
Recombinant Inbred Lines ◽  
Leaf Traits ◽  
Rice Cultivar ◽  
Interval Mapping ◽  
Mapping Method ◽  
Japonica Rice ◽  
Phenotypic Variance ◽  
Simple Sequence ◽  
Variance Explained ◽  
Map Distance

A recombinant inbred lines (RILs) population of 90 lines were developed from a subspecies cross between an indica type cultivar, ?Cheongcheong?, and a japonica rice cultivar, ?Nagdong? was evaluated for leaf traits in 2009. A genetic linkage map consisting of 154 simple sequence repeat (SSR) markers was constructed, covering 1973.6 cM of 12 chromosomes with an average map distance of 13.9 cM between markers. By composite interval mapping method a total of 19 QTLs were identified for the leaf traits on 5 chromosomes (Chr.1, Chr.3, Chr.6, Chr.8 and Chr.11). The percentage of phenotypic variance explained by each QTL varied from 8.1% to 29.4%. Five pleiotropic effects loci were identified on chromosomes 1,6.

scholarly journals Comparative transcriptome analysis of the cold resistance of the sterile rice line 33S

PLoS ONE ◽  
2022 ◽  
Vol 17 (1) ◽  
pp. e0261822
Author(s):  
Hongjun Xie ◽  
Mingdong Zhu ◽  
Yaying Yu ◽  
Xiaoshan Zeng ◽  
Guohua Tang ◽  
...  
Keyword(s):  
Low Temperature ◽  
Cold Resistance ◽  
Temperature Response ◽  
Enrichment Analysis ◽  
Abiotic Factor ◽  
Comparative Transcriptome ◽  
Important Species ◽  
Expression Of Genes ◽  
Nutrient Reserve ◽  
Cold Tolerant

Rice (Oryza sativa L.) is one of the most important species for food production worldwide. Low temperature is a major abiotic factor that affects rice germination and reproduction. Here, the underlying regulatory mechanism in seedlings of a TGMS variety (33S) and a cold-sensitive variety (Nipponbare) was investigated by comparative transcriptome. There were 795 differentially expressed genes (DEGs) identified only in cold-treated 33S, suggesting that 33S had a unique cold-resistance system. Functional and enrichment analysis of these DEGs revealed that, in 33S, several metabolic pathways, such as photosynthesis, amino acid metabolism, secondary metabolite biosynthesis, were significantly repressed. Moreover, pathways related to growth and development, including starch and sucrose metabolism, and DNA biosynthesis and damage response/repair, were significantly enhanced. The expression of genes related to nutrient reserve activity were significantly up-regulated in 33S. Finally, three NAC and several ERF transcription factors were predicted to be important in this transcriptional reprogramming. This present work provides valuable information for future investigations of low-temperature response mechanisms and genetic improvement of cold-tolerant rice seedlings.

Effects of root characteristics on panicle formation in japonica rice under low temperature water stress at the reproductive stage

2022 ◽  
Vol 277 ◽  
pp. 108395
Author(s):  
Yan Jia ◽  
Hualong Liu ◽  
Hao Wang ◽  
Detang Zou ◽  
Zhaojun Qu ◽  
...  
Keyword(s):  
Water Stress ◽  
Low Temperature ◽  
Reproductive Stage ◽  
Japonica Rice ◽  
Root Characteristics ◽  
Temperature Water

scholarly journals Effects of Putrescine Application on Peach Fruit during Storage

2019 ◽  
Vol 11 (7) ◽  
pp. 2013 ◽  
Author(s):  
Nadeem Abbasi ◽  
Irfan Ali ◽  
Ishfaq Hafiz ◽  
Mekhled Alenazi ◽  
Muhammad Shafiq
Keyword(s):  
Low Temperature ◽  
Quality Characteristics ◽  
Fruit Growth ◽  
Economic Losses ◽  
Spray Application ◽  
Peach Fruit ◽  
Colour Perception ◽  
Low Temperature Storage ◽  
Positive Effects ◽  
Temperature Storage

The peach industry faces serious economic losses because of the short “green” life of the fruit at postharvest. In the present study, we investigated the effects of putrescine (PUT) application on the quality characteristics, pattern of ripening, storage behaviour and shelf life of peach fruit during low-temperature storage. The aqueous solution of PUT (0, 1, 2 and 3 mM) was applied to the peach trees at three distinctive stages of fruit growth and development. The fruits, harvested at the commercial stage of maturity, were stored at 1 ± 1 °C and 90 ± 2% relative humidity for 6 weeks. The data for fruit firmness, total soluble solids (SSC), titratable acidity (TA), ascorbic acid (AsA) content, rate of ethylene production, chilling injury (CI) index and colour perception were collected at harvest and then on a weekly basis throughout the storage period. The results showed that spray application of PUT significantly reduced the incidence of CI and reduced the rates of fruit softening, loss in fruit weight, SSC, TA, AsA content and fading of skin colour during storage, regardless of the doses of PUT applied, or the time of application. However, the positive effects on the quality characteristics of peach fruit, including CI, were more pronounced with the higher doses of PUT, specifically when applied at 2 mM. In conclusion, CI in peach fruit may be substantially alleviated by the spray application of 1–3 mM PUT during fruit growth without compromising the quality of the fruit for up to 6 weeks in low-temperature storage.

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