scholarly journals QTL Mapping Low-Temperature Germination Ability in the Maize IBM Syn10 DH Population

Plants ◽  
2022 ◽  
Vol 11 (2) ◽  
pp. 214
Author(s):  
Qinghui Han ◽  
Qingxiang Zhu ◽  
Yao Shen ◽  
Michael Lee ◽  
Thomas Lübberstedt ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Low Temperature ◽  
Candidate Genes ◽  
Temperature Tolerance ◽  
Bhlh Transcription Factor ◽  
Rna Seq ◽  
Dh Population ◽  
Low Temperature Tolerance ◽  
Germination Ability ◽  
Upregulated Genes

Chilling injury poses a serious threat to seed emergence of spring-sowing maize in China, which has become one of the main climatic limiting factors affecting maize production in China. It is of great significance to mine the key genes controlling low-temperature tolerance during seed germination and study their functions for breeding new maize varieties with strong low-temperature tolerance during germination. In this study, 176 lines of the intermated B73 × Mo17 (IBM) Syn10 doubled haploid (DH) population, which comprised 6618 bin markers, were used for QTL analysis of low-temperature germination ability. The results showed significant differences in germination related traits under optimum-temperature condition (25 °C) and low-temperature condition (10 °C) between two parental lines. In total, 13 QTLs were detected on all chromosomes, except for chromosome 5, 7, 10. Among them, seven QTLs formed five QTL clusters on chromosomes 1, 2, 3, 4, and 9 under the low-temperature condition, which suggested that there may be some genes regulating multiple germination traits at the same time. A total of 39 candidate genes were extracted from five QTL clusters based on the maize GDB under the low-temperature condition. To further screen candidate genes controlling low-temperature germination, RNA-Seq, in which RNA was extracted from the germination seeds of B73 and Mo17 at 10 °C, was conducted, and three B73 upregulated genes and five Mo17 upregulated genes were found by combined analysis of RNA-Seq and QTL located genes. Additionally, the variations of Zm00001d027976 (GLABRA2), Zm00001d007311 (bHLH transcription factor), and Zm00001d053703 (bZIP transcription factor) were found by comparison of amino sequence between B73 and Mo17. This study will provide a theoretical basis for marker-assisted breeding and lay a foundation for further revealing molecular mechanism of low-temperature germination tolerance in maize.

scholarly journals Full-length transcriptome sequencing reveals the low-temperature-tolerance mechanism of Medicago falcata roots

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Guowen Cui ◽  
Hua Chai ◽  
Hang Yin ◽  
Mei Yang ◽  
Guofu Hu ◽  
...  
Keyword(s):  
Low Temperature ◽  
Temperature Stress ◽  
Electrolyte Leakage ◽  
Temperature Tolerance ◽  
Low Temperature Stress ◽  
Full Length ◽  
Rna Seq ◽  
Smrt Sequencing ◽  
Tolerance Mechanism ◽  
Low Temperature Tolerance

Abstract Background Low temperature is one of the main environmental factors that limits crop growth, development, and production. Medicago falcata is an important leguminous herb that is widely distributed worldwide. M. falcata is related to alfalfa but is more tolerant to low temperature than alfalfa. Understanding the low temperature tolerance mechanism of M. falcata is important for the genetic improvement of alfalfa. Results In this study, we explored the transcriptomic changes in the roots of low-temperature-treated M. falcata plants by combining SMRT sequencing and NGS technologies. A total of 115,153 nonredundant sequences were obtained, and 8849 AS events, 73,149 SSRs, and 4189 lncRNAs were predicted. A total of 111,587 genes from SMRT sequencing were annotated, and 11,369 DEGs involved in plant hormone signal transduction, protein processing in endoplasmic reticulum, carbon metabolism, glycolysis/gluconeogenesis, starch and sucrose metabolism, and endocytosis pathways were identified. We characterized 1538 TF genes into 45 TF gene families, and the most abundant TF family was the WRKY family, followed by the ERF, MYB, bHLH and NAC families. A total of 134 genes, including 101 whose expression was upregulated and 33 whose expression was downregulated, were differentially coexpressed at all five temperature points. PB40804, PB75011, PB110405 and PB108808 were found to play crucial roles in the tolerance of M. falcata to low temperature. WGCNA revealed that the MEbrown module was significantly correlated with low-temperature stress in M. falcata. Electrolyte leakage was correlated with most genetic modules and verified that electrolyte leakage can be used as a direct stress marker in physiological assays to indicate cell membrane damage from low-temperature stress. The consistency between the qRT-PCR results and RNA-seq analyses confirmed the validity of the RNA-seq data and the analysis of the regulatory mechanism of low-temperature stress on the basis of the transcriptome. Conclusions The full-length transcripts generated in this study provide a full characterization of the transcriptome of M. falcata and may be useful for mining new low-temperature stress-related genes specific to M. falcata. These new findings could facilitate the understanding of the low-temperature-tolerance mechanism of M. falcata.

scholarly journals Full-length transcriptome sequencing reveals a low-temperature-tolerance mechanism in Medicago falcata roots

2019 ◽  
Author(s):  
Guowen Cui ◽  
Hua Chai ◽  
Hang Yin ◽  
Mei Yang ◽  
Guofu Hu ◽  
...  
Keyword(s):  
Low Temperature ◽  
Temperature Stress ◽  
Electrolyte Leakage ◽  
Temperature Tolerance ◽  
Low Temperature Stress ◽  
Full Length ◽  
Rna Seq ◽  
Tolerance Mechanism ◽  
Medicago Falcata ◽  
Low Temperature Tolerance

Abstract Background Low temperature is one of the main environmental factors that limits crop growth, development and production. Medicago falcata is an economically and ecologically important legume that is closely related to alfalfa and exhibits better tolerance to low temperature than alfalfa. Understanding the low-temperature-tolerance mechanism of M. falcata is important for the genetic improvement of alfalfa. Results In this study, we explored the transcriptomic changes in low-temperature-treated M. falcata roots by combining SMRT and NGS technologies. A total of 115,153 nonredundant sequences were obtained, and 8,849 AS events, 73,149 SSRs and 4,189 LncRNAs were predicted. A total of 111,587 genes from SMRT were annotated, and 11,369 DEGs were identified in this paper that are involved in plant hormone signal transduction, protein processing in endoplasmic reticulum, carbon metabolism, glycolysis/gluconeogenesis, starch and sucrose metabolism, and endocytosis pathways. We characterized 1,538 TF genes into 45 TF gene families, and the most abundant TF family was WRKY, followed by ERF, MYB, bHLH and NAC. A total of 134 genes were differentially coexpressed at all five temperature points, including 101 upregulated genes and 33 downregulated genes. PB40804, PB75011, PB110405 and PB108808 were found to play crucial roles in the tolerance of M. falcata to low temperature. The WGCNA results showed that the MEbrown module was significantly correlated with low-temperature stress in M. falcata. Electrolyte leakage was correlated with most genetic modules and corroborated that electrolyte leakage can be used as direct stress markers to reflect cell membrane damage from low-temperature stress in physiological assays. The consistency between the qRT-PCR results and RNA-Seq analyses confirm the validity of the RNA-Seq data and the analysis of the regulation of low-temperature stress in the transcriptome. Conclusions The full-length transcripts generated in this study provided a full characterization of the gene transcription of M. falcata and are useful for mining new low-temperature stress-related genes specific to M. falcata. These new findings facilitate the understanding of low-temperature-tolerance mechanisms in M. falcata.

scholarly journals Low temperature seed germination of cucumber: genetic basis of the tolerance trait

2013 ◽  
Vol 21 (2) ◽  
pp. 125-130 ◽  
Author(s):  
Urszula Kłosińska ◽  
Elżbieta U. Kozik ◽  
Marcin Nowicki ◽  
Todd C. Wehner
Keyword(s):  
Low Temperature ◽  
Genetic Basis ◽  
Recessive Gene ◽  
Temperature Tolerance ◽  
Gene Model ◽  
Cucumis Sativus L ◽  
F2 Population ◽  
Low Temperature Tolerance ◽  
Germination Ability ◽  
Cold Tolerant

ABSTRACT Cucumber (Cucumis sativus L.) germinates in an optimal temperature ranging from 24 to 28 °C. In order to develop cultivars with low temperature germination ability, knowledge regarding its genetic basis is needed. In our earlier study, we identified the accession PI 390953 as chilling tolerant and a good cold germinator. The objective of our present study was to compare cold germinability of cold tolerant breeding line B 5669 with PI 390953, and to measure the inheritance of this trait. At 13 °C, both tested cultigens (B 5669, PI 390953) showed the highest germinability and we found no significant differences between them regarding the rate of germination, days to germination (DTG), or germination index (GI). We also observed differences in the germination ability at 13 °C among seven hybrid populations of cucumber, derived from the cross between good cold germinator B 5669 (P1) and B 6115 (P2) lacking cold-germination ability. The fastest low temperature germination and the highest low temperature germination percentages were observed in B 5669 (P1) with germination of 78 and 100% on the 6th and 10th day of the test, respectively. In addition, the cultigen B 5669 exhibited the fastest germination, reaching on average of DTG = 5.7. B 6115 (P2) and BC1P2 proved unable to germinate at 13 °C even within 21 days. The seed germinability of F2 population fits a three-recessive gene model. Cucumber cultigens B 5669, PI 390953, and PI 246903 showed low temperature tolerance, but of them B 5669 may become the most desirable to breeders since it exhibits cold germinability combined with good fruit quality traits.

scholarly journals Perspectives on Low Temperature Tolerance and Vernalization Sensitivity in Barley: Prospects for Facultative Growth Habit

2020 ◽  
Vol 11 ◽  
Author(s):  
María Muñoz-Amatriaín ◽  
Javier Hernandez ◽  
Dustin Herb ◽  
P. Stephen Baenziger ◽  
Anne Marie Bochard ◽  
...  
Keyword(s):  
Low Temperature ◽  
Candidate Genes ◽  
Growth Habit ◽  
Association Studies ◽  
Meta Analysis ◽  
Field Tests ◽  
Temperature Tolerance ◽  
Genome Wide Association Studies ◽  
Low Temperature Tolerance ◽  
A Genome

One option to achieving greater resiliency for barley production in the face of climate change is to explore the potential of winter and facultative growth habits: for both types, low temperature tolerance (LTT) and vernalization sensitivity are key traits. Sensitivity to short-day photoperiod is a desirable attribute for facultative types. In order to broaden our understanding of the genetics of these phenotypes, we mapped quantitative trait loci (QTLs) and identified candidate genes using a genome-wide association studies (GWAS) panel composed of 882 barley accessions that was genotyped with the Illumina 9K single-nucleotide polymorphism (SNP) chip. Fifteen loci including 5 known and 10 novel QTL/genes were identified for LTT—assessed as winter survival in 10 field tests and mapped using a GWAS meta-analysis. FR-H1, FR-H2, and FR-H3 were major drivers of LTT, and candidate genes were identified for FR-H3. The principal determinants of vernalization sensitivity were VRN-H1, VRN-H2, and PPD-H1. VRN-H2 deletions conferred insensitive or intermediate sensitivity to vernalization. A subset of accessions with maximum LTT were identified as a resource for allele mining and further characterization. Facultative types comprised a small portion of the GWAS panel but may be useful for developing germplasm with this growth habit.

scholarly journals Full-length transcriptome sequencing reveals the low-temperature-tolerance mechanism of Medicago falcata roots

2019 ◽  
Author(s):  
Guowen Cui ◽  
Hua Chai ◽  
Hang Yin ◽  
Mei Yang ◽  
Guofu Hu ◽  
...  
Keyword(s):  
Low Temperature ◽  
Temperature Stress ◽  
Electrolyte Leakage ◽  
Temperature Tolerance ◽  
Low Temperature Stress ◽  
Full Length ◽  
Rna Seq ◽  
Smrt Sequencing ◽  
Tolerance Mechanism ◽  
Low Temperature Tolerance

Abstract Background: Low temperature is one of the main environmental factors that limits crop growth, development, and production. Medicago falcata is an important leguminous herb that is widely distributed worldwide. M. falcata is related to alfalfa but is more tolerant to low temperature than alfalfa. Understanding the low temperature tolerance mechanism of M. falcata is important for the genetic improvement of alfalfa. Results: In this study, we explored the transcriptomic changes in the roots of low-temperature-treated M. falcata plants by combining SMRT sequencing and NGS technologies. A total of 115,153 nonredundant sequences were obtained, and 8,849 AS events, 73,149 SSRs, and 4,189 lncRNAs were predicted. A total of 111,587 genes from SMRT sequencing were annotated, and 11,369 DEGs involved in plant hormone signal transduction, protein processing in endoplasmic reticulum, carbon metabolism, glycolysis/gluconeogenesis, starch and sucrose metabolism, and endocytosis pathways were identified. We characterized 1,538 TF genes into 45 TF gene families, and the most abundant TF family was the WRKY family, followed by the ERF, MYB, bHLH and NAC families. A total of 134 genes, including 101 whose expression was upregulated and 33 whose expression was downregulated, were differentially coexpressed at all five temperature points. PB40804, PB75011, PB110405 and PB108808 were found to play crucial roles in the tolerance of M. falcata to low temperature. WGCNA revealed that the MEbrown module was significantly correlated with low-temperature stress in M. falcata. Electrolyte leakage was correlated with most genetic modules and verified that electrolyte leakage can be used as a direct stress marker in physiological assays to indicate cell membrane damage from low-temperature stress. The consistency between the qRT-PCR results and RNA-seq analyses confirmed the validity of the RNA-seq data and the analysis of the regulatory mechanism of low-temperature stress on the basis of the transcriptome. Conclusions: The full-length transcripts generated in this study provide a full characterization of the transcriptome of M. falcata and may be useful for mining new low-temperature stress-related genes specific to M. falcata. These new findings could facilitate the understanding of the low-temperature-tolerance mechanism of M. falcata.

scholarly journals Identification of candidate genes for low temperature tolerance during germination of maize using a genome-wide association study and RNA-sequencing

2020 ◽  
Author(s):  
Hong Zhang ◽  
Jiayue Zhang ◽  
Qingyu Xu ◽  
Dandan Wang ◽  
Hong Di ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Low Temperature ◽  
Candidate Genes ◽  
Rna Sequencing ◽  
Temperature Tolerance ◽  
Genome Wide Association ◽  
Phenotypic Traits ◽  
Agricultural Crop ◽  
Low Temperature Tolerance ◽  
Genome Wide

Abstract Background: Maize ( Zea mays L.) is the largest agricultural crop in the world based on acreage and yield, however, it is inherently sensitive to low temperatures. The growth and yield of maize can be affected by low temperature during its whole growth period, particularly during germination. Therefore, it is urgent to identify the new gene(s) related to the low temperature tolerance during maize germination. Results: In this study, 14 phenotypic traits related to seed germination were used to explore the genetic architecture of maize through genome-wide association analysis (GWAS). A total of 30 single nucleotide polymorphisms (SNPs) associated with low temperature tolerance were detected (–log10( P ) > 4); 14 candidate genes were detected as being directly associated with these SNPs and 81 candidate genes were identified when the screen was extended to a distance of 30 kb from these SNPs. The candidate genes were predicted by conjoint analysis with RNA-sequencing (RNA-seq) to evaluate whole-genome gene expression levels. A total of nine differentially expressed genes (DEGs) (|log2foldchange|≥0.585， P <0.05) were found within distance of 30 kb, including two DEGs ( GRMZM2G101383 and GRMZM2G402584 ), which were associated with SNPs directly. The differential expression of these candidate genes was verified using qRT-PCR. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) terms of DEGs GRMZM2G052129 and GRMZM2G038964 were, ‘fatty acid metabolic process’, ‘Mitogen-activated protein kinase (MAPK) signal transduction’, and so on, which are related to the fluidity of the cell membrane and low temperature signal transduction. Conclusion: Therefore, further functional analysis of GRMZM2G052129 and GRMZM2G038964 will provide valuable information for understanding the genetic mechanism of low temperature tolerance during germination in maize.

scholarly journals OsmiR528 Enhances Cold Stress Tolerance by Repressing Expression of Stress Response-related Transcription Factor Genes in Plant Cells

2019 ◽  
Vol 20 (2) ◽  
pp. 100-114 ◽  
Author(s):  
Wei Tang ◽  
Wells A. Thompson
Keyword(s):  
Transcription Factor ◽  
Stress Response ◽  
Low Temperature ◽  
Cold Stress ◽  
Stress Tolerance ◽  
Molecular Mechanisms ◽  
Plant Cells ◽  
Temperature Tolerance ◽  
Low Temperature Tolerance ◽  
Related Transcription Factor

Background: MicroRNAs participate in many molecular mechanisms and signaling transduction pathways that are associated with plant stress tolerance by repressing expression of their target genes. However, how microRNAs enhance tolerance to low temperature stress in plant cells remains elusive. Objective: In this investigation, we demonstrated that overexpression of the rice microRNA528 (OsmiR528) increases cell viability, growth rate, antioxidants content, ascorbate peroxidase (APOX) activity, and superoxide dismutase (SOD) activity and decreases ion leakage rate and thiobarbituric acid reactive substances (TBARS) under low temperature stress in Arabidopsis (Arabidopsis thaliana), pine (Pinus elliottii), and rice (Oryza sativa). Methods: To investigate the potential mechanism of OsmiR528 in increasing cold stress tolerance, we examined expression of stress-associated MYB transcription factors OsGAMYB-like1, OsMYBS3, OsMYB4, OsMYB3R-2, OsMYB5, OsMYB59, OsMYB30, OsMYB1R, and OsMYB20 in rice cells by qRT-PCR. Results: Our experiments demonstrated that OsmiR528 decreases expression of transcription factor OsMYB30 by targeting a F-box domain containing protein gene (Os06g06050), which is a positive regulator of OsMYB30. In OsmiR528 transgenic rice, reduced OsMYB30 expression results in increased expression of BMY genes OsBMY2, OsBMY6, and OsBMY10. The transcript levels of the OsBMY2, OsBMY6, and OsBMY10 were elevated by OsMYB30 knockdown, but decreased by Os- MYB30 overexpression in OsmiR528 transgenic cell lines, suggesting that OsmiR528 increases low temperature tolerance by modulating expression of stress response-related transcription factor. Conclusion: Our experiments provide novel information in increasing our understanding in molecular mechanisms of microRNAs-associated low temperature tolerance and are valuable in plant molecular breeding from monocotyledonous, dicotyledonous, and gymnosperm plants.

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