scholarly journals Balancing selection maintains diversity in a cold tolerance gene in broadly distributed live oaks

Genome ◽  
2017 ◽  
Vol 60 (9) ◽  
pp. 762-769 ◽  
Author(s):  
Jose Eduardo Meireles ◽  
Anne Beulke ◽  
Daniel S. Borkowski ◽  
Jeanne Romero-Severson ◽  
Jeannine Cavender-Bares
Keyword(s):  
Cold Acclimation ◽  
Cold Tolerance ◽  
Freezing Tolerance ◽  
Negative Selection ◽  
Balancing Selection ◽  
Variable Temperature ◽  
Purifying Selection ◽  
Housekeeping Genes ◽  
Cold Response ◽  
Tolerance Gene

Cold poses major physiological challenges to plants, especially long-lived trees. In trees occurring along variable temperature clines, the expected direction and consequences of selection on cold acclimation ability and freezing tolerance are not straightforward. Here we estimated selection in cold acclimation genes at two evolutionary timescales in all seven species of the American live oaks (Quercus subsection Virentes). Two cold response candidate genes were chosen: ICE1, a key gene in the cold acclimation pathway, and HOS1, which modulates cold response by negatively regulating ICE1. Two housekeeping genes, GAPDB and CHR11, were also analyzed. At the shallow evolutionary timescale, we demonstrate that HOS1 experienced recent balancing selection in the two most broadly distributed species, Q. virginiana and Q. oleoides. At a deeper evolutionary scale, a codon-based model of evolution revealed the signature of negative selection in ICE1. In contrast, three positively selected codons have been identified in HOS1, possibly a signature of the diversification of Virentes into warmer climates from a freezing adapted lineage of oaks. Our findings indicate that evolution has favored diversity in cold tolerance modulation through balancing selection in HOS1 while maintaining core cold acclimation ability, as evidenced by purifying selection in ICE1.

scholarly journals Physiological and transcriptome analysis of Magnolia denudata leaf buds during long-term cold acclimation

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Kunjing Wu ◽  
Xiaojing Duan ◽  
Zhonglong Zhu ◽  
Ziyang Sang ◽  
Jie Duan ◽  
...  
Keyword(s):  
Cold Acclimation ◽  
Cold Tolerance ◽  
Transcriptome Analysis ◽  
Average Length ◽  
Cold Response ◽  
Helix Loop Helix ◽  
Smoke Pollution ◽  
Magnolia Denudata ◽  
Pathway Analyses

Abstract Background Magonlia denudata is an important perennial tree species of the Magnoliaceae family, known for its ornamental value, resistance to smoke pollution and wind, role in air purification, and robust cold tolerance. In this study, a high-throughput transcriptome analysis of leaf buds was performed, and gene expression following artificial acclimation 22 °C, 4 °C and 0 °C, was compared by RNA sequencing. Results Over 426 million clean reads were produced from three libraries (22 °C, 4 °C and 0 °C). A total of 74,503 non-redundant unigenes were generated, with an average length of 1173.7 bp (N50 = 1548). Based on transcriptional results, 357 and 235 unigenes were identified as being upregulated and downregulated under cold stress conditions, respectively. Differentially expressed genes were annotated using Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes pathway analyses. The transcriptomic analysis focused on carbon metabolism and plant hormone signal transduction associated with cold acclimation. Transcription factors such as those in the basic helix-loop-helix and AP2/ERF families were found to play an important role in M. denudata cold acclimation. Conclusion M. denudata exhibits responses to non-freezing cold temperature (4 °C) to increase its cold tolerance. Cold resistance was further strengthened with cold acclimation under freezing conditions (0 °C). Cold tolerance genes, and cold signaling transcriptional pathways, and potential functional key components for the regulation of the cold response were identified in M. denudata. These results provide a basis for further studies, and the verification of key genes involved in cold acclimation responses in M. denudata lays a foundation for developing breeding programs for Magnoliaceae species.

scholarly journals 905 PB 526 DIFFERENTIAL EXPRESSION OF DEHYDRIN (47 KD) “BOILING STABLE” PROTEIN WITHIN POPULATIONS OF TWO DIPLOID POTATO SPECIES SEGREGATING FOR COLD TOLERANCE AND ACCLIMATION CAPACITY

HortScience ◽  
1994 ◽  
Vol 29 (5) ◽  
pp. 563f-563
Author(s):  
Bjorn H. Karlsson ◽  
Jiwan P. Palta ◽  
Laurie S. Weiss ◽  
James F. Harbage ◽  
John B. Bamber
Keyword(s):  
Cold Acclimation ◽  
Cold Tolerance ◽  
Freezing Tolerance ◽  
Residual Activity ◽  
Backcross Progeny ◽  
Ion Leakage ◽  
Heritable Trait ◽  
Cold Tolerant ◽  
Cold Sensitive ◽  
Induced Changes

Cold-induced changes in gene expression have been demonstrated in a number of species that vary in freezing tolerance and acclimation capacity. Relative freezing tolerance was measured based on ion leakage for both nonacclimated and acclimated S. commersonii and S. cardiophyllum parents, F1 and backcross progeny segregating for cold tolerance and acclimation capacity. Western blot analyses showed increase in a dehydrin band (47 kD)(antisera courtesy of T. Close) following cold acclimation of cold tolerant S. commersonii, and a slight increase in cold sensitive S. cardiophyllum. Expression of 47 kD cosegregated with non acclimated freezing tolerance but not with acclimated freezing tolerance. Our results show that (i) expression of dehydrins is a heritable trait in the Solanum diploid population, (ii) there is no direct relationship between relative freezing tolerance and the presence or absence of dehydrm protein following cold acclimation and (iii) based on assays measuring the residual activity of the lactate dehydrogenase (LDH) enzyme following freezing, the cryoprotective influence of `boiling stable' proteins was species dependent and is related to the freezing tolerance of the species. Supported by USDA/NRI grant 91-3700-6636 to J.P.P. and J.B.B..

scholarly journals Expression of Heat-stable and Putative Dehydrin Proteins during Nonacclimated and Cold-acclimated Conditions in Several Tuber-bearing Solanum Species

1999 ◽  
Vol 124 (3) ◽  
pp. 245-251 ◽  
Author(s):  
Björn H. Karlsson ◽  
Jiwan P. Palta
Keyword(s):  
Cold Acclimation ◽  
Freezing Tolerance ◽  
Cold Treatment ◽  
Solanum Species ◽  
Cold Response ◽  
Quantitative Expression ◽  
Stressful Environment ◽  
Heat Stable ◽  
Heat Stable Protein ◽  
Cold Sensitive

Recent studies suggest cold-regulated heat-stable proteins mitigate the potential damaging effects of low water activity associated with freezing. A proposed function of these proteins is stabilization of enzymes during exposure of plants to subzero temperatures. To test this hypothesis for tuber-bearing Solanum L. species we determined the quantitative expression of heat-stable proteins, the qualitative changes in dehydrin proteins, and the capacity of heat-stable proteins to cryoprotect a freeze-thaw labile enzyme lactate dehydrogenase (LDH). We used five tuber-bearing Solanum species (S. tuberosum L. `Red Pontiac', S. acaule Bitter, S. sanctae rosea Hawkes, S. commersonii Dunal, and S. cardiophyllum Bitter), which vary in nonacclimated relative freezing tolerance (NA RFT), acclimated relative freezing tolerance (AC RFT), and acclimation capacity (ACC). The protein fraction containing a mixture of heat-stable proteins demonstrated cryoprotective capacities greater or equal to other cryoprotective compounds (bovine serum albumin, polyethylene glycol, glycerol, and sucrose). Heat-stable proteins extracted from acclimated S. commersonii had superior cryoprotective capacity than those extracted from nonacclimated S. commersonii plants. Interestingly, in the presence of these proteins extracted from acclimated plants (in S. commersonii and S. sanctae rosea), LDH activity was elevated above that of unfrozen controls. No quantitative relationships were found between heat-stable protein concentration and NA RFT, AC RFT, or ACC among the five species. This was also true for dehydrin protein expression. Cold acclimation treatment resulted in increased dehydrin expression for acclimating and nonacclimating species. In three of the cold acclimating species (S. acaule, S. sanctae rosea, and S. commersonii), an increase in dehydrin expression may play a role in increased freezing tolerance during cold acclimation. In the cold sensitive, nonacclimating species (S. tuberosum and S. cardiophyllum), however, an increase in dehydrin level maybe related to the response of these species to changed (perhaps stressful) environment during cold treatment. By exploiting the genetic variation in NA RFT and ACC for five tuber-bearing species, we were able to gain new insight into the complexity of the relationship between heat-stable protein and cold response.

scholarly journals Arabidopsis thaliana eIF4E1 and eIF(iso)4E Participate in Cold Response and Promote Translation of Some Stress-Related mRNAs

2021 ◽  
Vol 12 ◽  
Author(s):  
Kenia Salazar-Díaz ◽  
Mayra Aquino-Luna ◽  
Eloísa Hernández-Lucero ◽  
Brenda Nieto-Rivera ◽  
Marlon A. Pulido-Torres ◽  
...  
Keyword(s):  
Cold Acclimation ◽  
Freezing Tolerance ◽  
Translation Initiation ◽  
Mrna Translation ◽  
Cold Response ◽  
Cold Temperatures ◽  
Gene Expression Control ◽  
And Shifts ◽  
Processing Stability

Plant defense and adaptation to adverse environmental conditions rely on gene expression control, such as mRNA transcription, processing, stability, and translation. Sudden temperature changes are common in the era of global warming; thus, understanding plant acclimation responses at the molecular level becomes imperative. mRNA translation initiation regulation has a pivotal role in achieving the synthesis of the appropriate battery of proteins needed to cope with temperature stress. In this study, we analyzed the role of translation initiation factors belonging to the eIF4E family in Arabidopsis acclimation to cold temperatures and freezing tolerance. Using knockout (KO) and overexpressing mutants of AteIF4E1 or AteIF(iso)4E, we found that AteIF4E1 but not AteIF(iso)4E overexpressing lines displayed enhanced tolerance to freezing without previous acclimation at 4°C. However, KO mutant lines, eif(iso)4e-1 and eif4e1-KO, were more sensitive to the stress. Cold acclimation in wild-type plants was accompanied by increased levels of eIF4E1 and eIF(iso)4E transcript levels, polysomes (P) enrichment, and shifts of these factors from translationally non-active to active fractions. Transcripts, previously found as candidates for eIF(iso)4E or eIF4E1 selective translation, changed their distribution in both P and total RNA in the presence of cold. Some of these transcripts changed their polysomal distribution in the mutant and one eIF4E1 overexpressing line. According to this, we propose a role of eIF4E1 and eIF(iso)4E in cold acclimation and freezing tolerance by regulating the expression of stress-related genes.

Growth, freezing tolerance, and yield performance of alfalfa (Medicago sativaL.) cultivars grown under controlled and field conditions in northern latitudes

2018 ◽  
Vol 98 (5) ◽  
pp. 1109-1118 ◽  
Author(s):  
Mervi M. Seppänen ◽  
Ville Alitalo ◽  
Hanna K. Bäckström ◽  
Kirsi Mäkiniemi ◽  
Venla Jokela ◽  
...  
Keyword(s):  
Field Experiment ◽  
Cold Acclimation ◽  
Freezing Tolerance ◽  
Field Experiments ◽  
Starch Content ◽  
Day Length ◽  
Forage Legume ◽  
Northern Latitudes ◽  
Medicago Sativa L ◽  
Second Year

Alfalfa (Medicago sativa L.) is one of the most popular forage legume crops worldwide. Its cultivation in the boreal and sub-boreal zone is restricted by inadequate winter hardiness, but global warming may increase its adaptability in these latitudes. Here, we examined variation in growth and freezing tolerance of four alfalfa cultivars recommended for the northern temperate climates of Europe (Alexis, Lavo, Live, and Nexus) and two cultivars with adaptation to milder or Mediterranean climates (Rangelander and Hunter River). Two experiments under controlled conditions (growth cessation and cold acclimation experiments) along with a 2-yr field experiment were conducted. Lavo was the most freezing-tolerant cultivar in both the cold acclimation and field experiments. Both Rangelander and Hunter River showed poor freezing tolerance. Lavo responded to decreasing temperatures, unlike the response to shorter day length, by allocating biomass to the roots. In general, better freezing tolerance was associated with high total nonstructural carbohydrate and low starch content. The field experiment results revealed that the more freezing-tolerant cultivars may have some advantages regarding yield, especially in the second year, but the differences between the cultivars were modest.

Cold Response of Dedifferentiated Barley Cells at the Gene Expression, Hormone Composition, and Freezing Tolerance Levels: Studies on Callus Cultures

2012 ◽  
Vol 54 (2) ◽  
pp. 337-349 ◽  
Author(s):  
Ildikó Vashegyi ◽  
Zsuzsa Marozsán-Tóth ◽  
Gábor Galiba ◽  
Petre I. Dobrev ◽  
Radomira Vankova ◽  
...  
Keyword(s):  
Gene Expression ◽  
Freezing Tolerance ◽  
Callus Cultures ◽  
Cold Response

scholarly journals Divergent and convergent evolution of housekeeping genes in human–pig lineage

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4840 ◽  
Author(s):  
Kai Wei ◽  
Tingting Zhang ◽  
Lei Ma
Keyword(s):  
Active Sites ◽  
Evolutionary Dynamics ◽  
Purifying Selection ◽  
Housekeeping Genes ◽  
Neutral Evolution ◽  
Structure Evolution ◽  
Tissue Cell ◽  
Sequencing Data ◽  
Cellular Functions ◽  
Species Specific

Housekeeping genes are ubiquitously expressed and maintain basic cellular functions across tissue/cell type conditions. The present study aimed to develop a set of pig housekeeping genes and compare the structure, evolution and function of housekeeping genes in the human–pig lineage. By using RNA sequencing data, we identified 3,136 pig housekeeping genes. Compared with human housekeeping genes, we found that pig housekeeping genes were longer and subjected to slightly weaker purifying selection pressure and faster neutral evolution. Common housekeeping genes, shared by the two species, achieve stronger purifying selection than species-specific genes. However, pig- and human-specific housekeeping genes have similar functions. Some species-specific housekeeping genes have evolved independently to form similar protein active sites or structure, such as the classical catalytic serine–histidine–aspartate triad, implying that they have converged for maintaining the basic cellular function, which allows them to adapt to the environment. Human and pig housekeeping genes have varied structures and gene lists, but they have converged to maintain basic cellular functions essential for the existence of a cell, regardless of its specific role in the species. The results of our study shed light on the evolutionary dynamics of housekeeping genes.

scholarly journals Molecular population genetics of sequence length diversity in the Adh region of Drosophila pseudoobscura

2002 ◽  
Vol 80 (3) ◽  
pp. 163-175 ◽  
Author(s):  
STEPHEN W. SCHAEFFER
Keyword(s):  
Negative Selection ◽  
Genome Rearrangement ◽  
Rare Variants ◽  
Natural Populations ◽  
Population Expansion ◽  
Purifying Selection ◽  
Sequence Length ◽  
Nucleotide Sequence Analysis ◽  
Drosophila Pseudoobscura ◽  
Indel Variation

Positive and negative selection on indel variation may explain the correlation between intron length and recombination levels in natural populations of Drosophila. A nucleotide sequence analysis of the 3·5 kilobase sequence of the alcohol dehydrogenase (Adh) region from 139 Drosophila pseudoobscura strains and one D. miranda strain was used to determine whether positive or negative selection acts on indel variation in a gene that experiences high levels of recombination. A total of 30 deletion and 36 insertion polymorphisms were segregating within D. pseudoobscura populations and no indels were fixed between D. pseudoobscura and its two sibling species D. miranda and D. persimilis. The ratio of Tajima's D to its theoretical minimum value (Dmin) was proposed as a metric to assess the heterogeneity in D among D. pseudoobscura loci when the number of segregating sites differs among loci. The magnitude of the D/Dmin ratio was found to increase as the rate of population expansion increases, allowing one to assess which loci have an excess of rare variants due to population expansion versus purifying selection. D. pseudoobscura populations appear to have had modest increases in size accounting for some of the observed excess of rare variants. The D/Dmin ratio rejected a neutral model for deletion polymorphisms. Linkage disequilibrium among pairs of indels was greater than between pairs of segregating nucleotides. These results suggest that purifying selection removes deletion variation from intron sequences, but not insertion polymorphisms. Genome rearrangement and size-dependent intron evolution are proposed as mechanisms that limit runaway intron expansion.

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