scholarly journals Screening of the candidate genes related to low-temperature tolerance of Fenneropenaeus chinensis based on high-throughput transcriptome sequencing

PLoS ONE ◽  
2019 ◽  
Vol 14 (4) ◽  
pp. e0211182 ◽  
Author(s):  
Xianhong Meng ◽  
Lijun Dong ◽  
Xiaoli Shi ◽  
Xupeng Li ◽  
Juan Sui ◽  
...  
Keyword(s):  
Low Temperature ◽  
Candidate Genes ◽  
High Throughput ◽  
Transcriptome Sequencing ◽  
Fenneropenaeus Chinensis ◽  
Temperature Tolerance ◽  
Low Temperature Tolerance

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 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 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.

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