scholarly journals Allele specific expression analysis identifies regulatory variation associated with stress-related genes in the Mexican highland maize landrace Palomero Toluqueño

2017 ◽  
Author(s):  
M. Rocío Aguilar-Rangel ◽  
Ricardo A. Chávez Montes ◽  
Eric Gonzalez-Segovia ◽  
Jeffrey Ross-Ibarra ◽  
June K. Simpson ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Stress Response ◽  
Local Adaptation ◽  
Expression Analysis ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Regulatory Variation ◽  
Highland Maize ◽  
Allele Specific ◽  
Stress Related Genes

ABSTRACTBackgroundGene regulatory variation has been proposed to play an important role in the adaptation of plants to environmental stress. In the central highlands of Mexico, farmer selection has generated a unique group of maize landraces adapted the challenges of the highland niche. In this study, gene expression in Mexican highland maize and a reference maize breeding line were compared to identify evidence of regulatory variation in stress-related genes. It was hypothesised that local adaptation in Mexican highland maize would be associated with a transcriptional signature observable even under benign conditions.MethodsAllele specific expression analysis was performed using the seedling-leaf transcriptome of an F1 individual generated from the cross between the highland adapted Mexican landrace Palomero Toluqueño and the reference line B73, grown under benign conditions. Results were compared with a published dataset describing the transcriptional response of B73 seedlings to cold, heat, salt and UV treatments.ResultsA total of 2386 genes were identified to show allele specific expression. Of these, 277 showed an expression difference between Palomero Toluqueño and B73 alleles that mirrored the response of B73 cold, heat, salt and/or UV treatments, and, as such, were considered to display a constitutive stress response. Constitutive stress response candidates included genes associated with plant hormone signaling and a number of transcription factors. Construction of a gene co-expression network revealed further signaling and stress-related genes to be among the potential targets of the transcription factors candidates.DiscussionConstitutive activation of responses may represent the best strategy when stresses are severe but predictable. Expression differences observed here between PT and B73 alleles indicate the presence of cis-acting regulatory variation linked to stress-related genes in PT. Considered alongside gene annotation and population data, allele specific expression analysis of plants grown under benign conditions provides an attractive strategy to identify functional variation potentially linked to local adaptation.

scholarly journals Allele specific expression analysis identifies regulatory variation associated with stress-related genes in the Mexican highland maize landrace Palomero Toluqueño

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3737 ◽  
Author(s):  
M. Rocío Aguilar-Rangel ◽  
Ricardo A. Chávez Montes ◽  
Eric González-Segovia ◽  
Jeffrey Ross-Ibarra ◽  
June K. Simpson ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Stress Response ◽  
Expression Analysis ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Regulatory Variation ◽  
Highland Maize ◽  
Allele Specific ◽  
Stress Related Genes ◽  
Prior Stress

BackgroundGene regulatory variation has been proposed to play an important role in the adaptation of plants to environmental stress. In the central highlands of Mexico, farmer selection has generated a unique group of maize landraces adapted to the challenges of the highland niche. In this study, gene expression in Mexican highland maize and a reference maize breeding line were compared to identify evidence of regulatory variation in stress-related genes. It was hypothesised that local adaptation in Mexican highland maize would be associated with a transcriptional signature observable even under benign conditions.MethodsAllele specific expression analysis was performed using the seedling-leaf transcriptome of an F1individual generated from the cross between the highland adapted Mexican landrace Palomero Toluqueño and the reference line B73, grown under benign conditions. Results were compared with a published dataset describing the transcriptional response of B73 seedlings to cold, heat, salt and UV treatments.ResultsA total of 2,386 genes were identified to show allele specific expression. Of these, 277 showed an expression difference between Palomero Toluqueño and B73 alleles under benign conditions that anticipated the response of B73 cold, heat, salt and/or UV treatments, and, as such, were considered to display a prior stress response. Prior stress response candidates included genes associated with plant hormone signaling and a number of transcription factors. Construction of a gene co-expression network revealed further signaling and stress-related genes to be among the potential targets of the transcription factors candidates.DiscussionPrior activation of responses may represent the best strategy when stresses are severe but predictable. Expression differences observed here between Palomero Toluqueño and B73 alleles indicate the presence ofcis-acting regulatory variation linked to stress-related genes in Palomero Toluqueño. Considered alongside gene annotation and population data, allele specific expression analysis of plants grown under benign conditions provides an attractive strategy to identify functional variation potentially linked to local adaptation.

scholarly journals Genome-Wide Regulatory Interactions in the Early Stages of Drosophila Speciation

2020 ◽  
Author(s):  
◽  
Alwyn Clark Go
Keyword(s):  
Reproductive Isolation ◽  
Expression Analysis ◽  
Regulatory Elements ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Regulatory Interactions ◽  
Early Stages ◽  
Genome Wide ◽  
Allele Specific ◽  
Incomplete Reproductive Isolation

Speciation occurs when reproductive barriers prevent the exchange of genetic information between individuals. A common form of reproductive barrier between species capable of interbreeding is hybrid sterility. Genomic incompatibilities between the divergent genomes of different species contribute to a reduction in hybrid fitness. These incompatibilities continue to accumulate after speciation, therefore, young divergent taxa with incomplete reproductive isolation are important in understating the genetics leading to speciation. Here, I use two Drosophila subspecies pairs. The first is D. willistoni consisting of D. w. willistoni and D. w. winge. The second subspecies pair is D. pseudoobscura, which is composed of D. p. pseudoobscura and D. p. bogotana. Both subspecies pairs are at the early stages of speciation and show incomplete reproductive isolation through unidirectional hybrid male sterility. In this thesis, I performed an exploratory survey of genome-wide expression analysis using RNA-sequencing on D. willistoni and determined the extent of regulatory divergence between the subspecies using allele-specific expression analysis. I found that misexpressed genes showed a degree of tissue specificity and that the sterile male hybrids had a higher proportion of misexpressed genes in the testes relative to the fertile hybrids. The analysis of regulatory divergence between this subspecies pair found a large (66-70%) proportion of genes with conserved regulatory elements. Of the genes showing evidence or regulatory divergence between subspecies, cis-regulatory divergence was more common than other types. In the D. pseudoobscura subspecies pair, I compared sequence and expression divergence and found no support for directional selection driving gene misexpression in their hybrids. Allele-specific expression analysis revealed that compensatory cis-trans mutations partly explained gene misexpression in the hybrids. The remaining hybrid misexpression occurs due to interacting gene networks or possible co-option of cis-regulatory elements by divergent transacting factors. Overall, the results of this thesis highlight the role of regulatory interactions in a hybrid genome and how these interactions could lead to hybrid breakdown by disrupting gene interaction networks.

Allele-Specific Expression and Evolution of Gene Regulation Underlying Acute Heat Stress Response and Local Adaptation in the Copepod Tigriopus californicus

2020 ◽  
Vol 111 (6) ◽  
pp. 539-547
Author(s):  
Sumaetee Tangwancharoen ◽  
Brice X Semmens ◽  
Ronald S Burton
Keyword(s):  
Gene Expression ◽  
Heat Stress ◽  
Stress Response ◽  
Local Adaptation ◽  
F1 Hybrids ◽  
Specific Expression ◽  
Heat Stress Response ◽  
Acute Heat Stress ◽  
Number Of Genes ◽  
Allele Specific

Abstract Geographic variation in environmental temperature can select for local adaptation among conspecific populations. Divergence in gene expression across the transcriptome is a key mechanism for evolution of local thermal adaptation in many systems, yet the genetic mechanisms underlying this regulatory evolution remain poorly understood. Here we examine gene expression in 2 locally adapted Tigriopus californicus populations (heat tolerant San Diego, SD, and less tolerant Santa Cruz, SC) and their F1 hybrids during acute heat stress response. Allele-specific expression (ASE) in F1 hybrids was used to determine cis-regulatory divergence. We found that the number of genes showing significant allelic imbalance increased under heat stress compared to unstressed controls. This suggests that there is significant population divergence in cis-regulatory elements underlying heat stress response. Specifically, the number of genes showing an excess of transcripts from the more thermal tolerant (SD) population increased with heat stress while that number of genes with an SC excess was similar in both treatments. Inheritance patterns of gene expression also revealed that genes displaying SD-dominant expression phenotypes increase in number in response to heat stress; that is, across loci, gene expression in F1’s following heat stress showed more similarity to SD than SC, a pattern that was absent in the control treatment. The observed patterns of ASE and inheritance of gene expression provide insight into the complex processes underlying local adaptation and thermal stress response.

Allele-specific expression of the serotonin transporter and its transcription factors following lamotrigine treatment in vitro

2013 ◽  
Vol 162 (5) ◽  
pp. 474-483 ◽  
Author(s):  
Ursula M. D'Souza ◽  
Georgia Powell-Smith ◽  
Kate Haddley ◽  
Timothy R. Powell ◽  
Vivien J. Bubb ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Serotonin Transporter ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Allele Specific

scholarly journals Comprehensively Evaluating cis -Regulatory Variation in the Human Prostate Transcriptome by Using Gene-Level Allele-Specific Expression

2015 ◽  
Vol 96 (6) ◽  
pp. 869-882 ◽  
Author(s):  
Nicholas B. Larson ◽  
Shannon McDonnell ◽  
Amy J. French ◽  
Zach Fogarty ◽  
John Cheville ◽  
...  
Keyword(s):  
Human Prostate ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Regulatory Variation ◽  
Gene Level ◽  
Allele Specific
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