Transcriptome Analysis Reveals Candidate Genes Involved in Low Temperature Stress in Bell Pepper

2020 ◽  
Vol 67 (6) ◽  
pp. 1116-1125
Author(s):  
L. Ji ◽  
P. Li ◽  
Zh. Su ◽  
M. Li ◽  
H. Wang
Keyword(s):  
Low Temperature ◽  
Candidate Genes ◽  
Temperature Stress ◽  
Transcriptome Analysis ◽  
Low Temperature Stress ◽  
Bell Pepper

Root transcriptome analysis of Saccharum spontaneum uncovers key genes and pathways in response to low-temperature stress

2020 ◽  
Vol 171 ◽  
pp. 103935
Author(s):  
S. Dharshini ◽  
Nam V. Hoang ◽  
C. Mahadevaiah ◽  
T.S. Sarath Padmanabhan ◽  
G. Alagarasan ◽  
...  
Keyword(s):  
Low Temperature ◽  
Temperature Stress ◽  
Transcriptome Analysis ◽  
Low Temperature Stress ◽  
Saccharum Spontaneum ◽  
Root Transcriptome ◽  
Key Genes

scholarly journals Genome-Wide Association Mapping Unravels the Genetic Control of Seed Vigor under Low-Temperature Conditions in Rapeseed (Brassica napus L.)

Plants ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 426
Author(s):  
Tao Luo ◽  
Yuting Zhang ◽  
Chunni Zhang ◽  
Matthew N. Nelson ◽  
Jinzhan Yuan ◽  
...  
Keyword(s):  
Low Temperature ◽  
Stress Tolerance ◽  
Candidate Genes ◽  
Temperature Stress ◽  
Seed Vigor ◽  
Low Temperature Stress ◽  
Brassica Napus L ◽  
Temperature Conditions ◽  
Genome Wide ◽  
Tolerance Indices

Low temperature inhibits rapid germination and successful seedling establishment of rapeseed (Brassica napus L.), leading to significant productivity losses. Little is known about the genetic diversity for seed vigor under low-temperature conditions in rapeseed, which motivated our investigation of 13 seed germination- and emergence-related traits under normal and low-temperature conditions for 442 diverse rapeseed accessions. The stress tolerance index was calculated for each trait based on performance under non-stress and low-temperature stress conditions. Principal component analysis of the low-temperature stress tolerance indices identified five principal components that captured 100% of the seedling response to low temperature. A genome-wide association study using ~8 million SNP (single-nucleotide polymorphism) markers identified from genome resequencing was undertaken to uncover the genetic basis of seed vigor related traits in rapeseed. We detected 22 quantitative trait loci (QTLs) significantly associated with stress tolerance indices regarding seed vigor under low-temperature stress. Scrutiny of the genes in these QTL regions identified 62 candidate genes related to specific stress tolerance indices of seed vigor, and the majority were involved in DNA repair, RNA translation, mitochondrial activation and energy generation, ubiquitination and degradation of protein reserve, antioxidant system, and plant hormone and signal transduction. The high effect variation and haplotype-based effect of these candidate genes were evaluated, and high priority could be given to the candidate genes BnaA03g40290D, BnaA06g07530D, BnaA09g06240D, BnaA09g06250D, and BnaC02g10720D in further study. These findings should be useful for marker-assisted breeding and genomic selection of rapeseed to increase seed vigor under low-temperature stress.

scholarly journals Genetics and Breeding of Low-Temperature Stress Tolerance in Rice

2021 ◽  
pp. 221-280
Author(s):  
Sofi Najeeb ◽  
Anumalla Mahender ◽  
Annamalai Anandan ◽  
Waseem Hussain ◽  
Zhikang Li ◽  
...  
Keyword(s):  
Low Temperature ◽  
Stress Tolerance ◽  
Candidate Genes ◽  
Temperature Stress ◽  
Association Studies ◽  
Low Temperature Stress ◽  
Growth Stages ◽  
Rice Varieties ◽  
Long Time ◽  
Mapping Populations

AbstractLow-temperature stress (LTS) is one of the major abiotic stresses that affect crop growth and ultimately decrease grain yield. The development of rice varieties with low-temperature stress tolerance has been a severe challenge for rice breeders for a long time. The lack of consistency of the quantitative trait loci (QTLs) governing LTS tolerance for any given growth stage over different genetic backgrounds of mapping populations under different low-temperature stress conditions remains a crucial barrier for adopting marker-assisted selection (MAS). In this review, we discuss the ideal location and phenotyping for agromorphological and physiological parameters as indicators for LTS tolerance and also the traits associated with QTLs that were identified from biparental mapping populations and diverse rice accessions. We highlight the progress made in the fields of genome editing, genetic transformation, transcriptomics, and metabolomics to elucidate the molecular mechanisms of cold tolerance in rice. The stage-specific QTLs and candidate genes for LTS tolerance brought out valuable information toward identifying and improving LTS tolerance in rice varieties. We showed 578 QTLs and 38 functionally characterized genes involved in LTS tolerance. Among these, 29 QTLs were found to be colocalized at different growth stages of rice. The combination of stage-specific QTLs and genes from biparental mapping populations and genome-wide association studies provide potential information for developing LTS-tolerant rice varieties. The identified colocalized stage-specific LTS-tolerance QTLs will be useful for MAS and QTL pyramiding and for accelerating mapping and cloning of the possible candidate genes, revealing the underlying LTS-tolerance mechanisms in rice.

scholarly journals Comparative transcriptome analysis of sweet corn seedlings under low-temperature stress

2017 ◽  
Vol 5 (5) ◽  
pp. 396-406 ◽  
Author(s):  
Jihua Mao ◽  
Yongtao Yu ◽  
Jing Yang ◽  
Gaoke Li ◽  
Chunyan Li ◽  
...  
Keyword(s):  
Low Temperature ◽  
Temperature Stress ◽  
Transcriptome Analysis ◽  
Sweet Corn ◽  
Low Temperature Stress ◽  
Comparative Transcriptome ◽  
Comparative Transcriptome Analysis

scholarly journals Transcriptome analysis of chrysanthemum (Dendranthema grandiflorum) in response to low temperature stress

BMC Genomics ◽  
2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Ke Wang ◽  
Zhen-yu Bai ◽  
Qian-yu Liang ◽  
Qing-lin Liu ◽  
Lei Zhang ◽  
...  
Keyword(s):  
Low Temperature ◽  
Temperature Stress ◽  
Transcriptome Analysis ◽  
Low Temperature Stress ◽  
Dendranthema Grandiflorum

Comparative Transcriptome Analysis Between Cold-Tolerant and Sensitive Brassica Oleracea L. in Response to Low Temperature Stress

2021 ◽  
Author(s):  
Shuhan Jiang ◽  
Dongjian Xia ◽  
Qian Dai ◽  
Yuxia Luo ◽  
Yao Chen ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Low Temperature ◽  
Brassica Oleracea ◽  
Cold Tolerance ◽  
Temperature Stress ◽  
Transcriptome Analysis ◽  
Low Temperature Stress ◽  
Biological Processes ◽  
The Common ◽  
Go Terms

Abstract Background: Brassica oleracea L. occupies an important position in the annual production of vegetables. But during winter Brassica oleracea L. often suffers from low temperatures and even sub-zero temperatures. Through transcriptome analysis and identification, the pathways involved in cold tolerance of Brassica oleracea L. were analyzed and candidate genes related to cold tolerance of Brassica oleracea L. were identified.Results: Under low temperature stress, a large number of significantly different genes were found in Zhonggan1229 (ZG, low temperature tolerance) and Yingchun (YN, low temperature sensitive). There were 3902 significantly up-regulated genes and 5309 significantly down-regulated genes in ZG, and 4253 significantly up-regulated genes and 5938 significantly down-regulated genes in YN. Among them, 1844 different genes are the specific different genes in ZG and 6089 genes are the common different genes to response the low temperature stress. By annotating the specific different genes in ZG, 26 of the top 30 enriched GO terms belonged to biological processes, 4 terms belonged to molecular functions. By annotating the common different genes, 23 GO terms belonged to biological processes, 1 GO term belonged to molecular functions, and 6 GO terms belonged to cellular components. Circadian rhythms of plants and Plant hormone signal transduction were not only significantly enriched in the two analyzed genes, but also the effects of low temperature stress were most significant. Among the unique different genes in ZG, 154 genes were annotated into transcription factor families, and 79 genes were up-regulated and 75 genes were down-regulated, the encoding of MYB-related proteins was the largest group. Among the different genes shared by the two varieties, 516 genes were annotated into corresponding transcription factor families, 211 genes were up-regulated and 296 genes were down-regulated, however, there were 4 genes that were up-regulated in ZG but down-regulated in YN, and 5 genes that were down-regulated in ZG but up-regulated in YN, the largest group was the protein encoding ERF.Conclusions: The results identified important genes, pathways, and transcription factors that respond to low temperature stress, provided cold tolerance gene resources for the subsequent cold tolerance breeding research of Brassica oleracea L..

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