The contribution of cis- and trans-acting variants to gene regulation in wild and domesticated barley under cold stress and control conditions

AbstractBarley, like other crops, has experienced a series of genetic changes that have impacted its architecture and growth habit to suit the needs of humans, termed the domestication syndrome. Domestication also resulted in a concomitant bottleneck that reduced sequence diversity in genes and regulatory regions. Little is known about regulatory changes resulting from domestication in barley. We used RNA-seq to examine allele-specific expression (ASE) in hybrids between wild and domesticated barley. Our results show that most genes have conserved regulation. In contrast to studies of allele specific expression in interspecific hybrids, we find almost a complete absence of trans effects. We also find that cis regulation is largely stable in response to short-term cold stress. Our study has practical implications for crop improvement using wild relatives. Genes regulated in cis are more likely to be expressed in a new genetic background at the same level as in their native background.

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Landscape and evolution of cis- and trans-regulatory divergence in chicken genome between two contrasted breeds analyzed in three tissues at one day age

10.21203/rs.2.10726/v2 ◽

2019 ◽

Author(s):

Qiong Wang ◽

Yaxiong Jia ◽

Yuan Wang ◽

Zhihua Jiang ◽

Xiang Zhou ◽

...

Keyword(s):

Chicken Genome ◽

Reproductive Traits ◽

Purifying Selection ◽

Population Divergence ◽

Specific Reference ◽

Specific Expression ◽

Allele Specific Expression ◽

Allele Specific ◽

Trans Regulation ◽

Cis And Trans

Abstract Background: Gene expression variation is an important mechanism underlying phenotypic variation, and can occur via cis- and trans-regulation. In order to understand the role of cis- and trans-regulatory variation on population divergence of chicken, we developed reciprocal crosses of two chicken breeds, White Leghorn and Cornish Game, with major differences in body size and reproductive traits, and used them to identify the degree of cis versus trans variation in brain, liver and muscle of both male and female samples at 1 day age. Results: We provided a landscape about how the transcriptomes are regulated in the hybrid progenies of two contrasted breeds by allele specific expression analysis. Our results showed that compared with the cis-regulatory divergence, trans-acted genes existed more extensively in the chicken genome. Furthermore, a widespread tendency of compensatory regulation exists in chicken genome. Most importantly, we found the evidence of stronger purifying selection on genes regulated by trans variations than the cis elements. Conclusions: We demonstrated a pipeline to explore the allele-specific expression in the hybrid progenies of inbred lines without specific reference genome. Our research performed the first study to describe the regulatory divergence between two contrasted breeds. The results suggested that artificial selection associated with domestication in chicken may have more often acted on trans-regulatory divergence than cis.

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Evolution of cis- and trans-regulatory divergence in the chicken genome between two contrasting breeds analyzed using three tissue types at one-day-old

BMC Genomics ◽

10.1186/s12864-019-6342-5 ◽

2019 ◽

Vol 20 (1) ◽

Author(s):

Qiong Wang ◽

Yaxiong Jia ◽

Yuan Wang ◽

Zhihua Jiang ◽

Xiang Zhou ◽

...

Keyword(s):

Chicken Genome ◽

Reproductive Traits ◽

Purifying Selection ◽

Population Divergence ◽

Specific Reference ◽

Specific Expression ◽

Allele Specific Expression ◽

Allele Specific ◽

Trans Regulation ◽

Cis And Trans

Abstract Background Gene expression variation is a key underlying factor influencing phenotypic variation, and can occur via cis- or trans-regulation. To understand the role of cis- and trans-regulatory variation on population divergence in chicken, we developed reciprocal crosses of two chicken breeds, White Leghorn and Cornish Game, which exhibit major differences in body size and reproductive traits, and used them to determine the degree of cis versus trans variation in the brain, liver, and muscle tissue of male and female 1-day-old specimens. Results We provided an overview of how transcriptomes are regulated in hybrid progenies of two contrasting breeds based on allele specific expression analysis. Compared with cis-regulatory divergence, trans-acting genes were more extensive in the chicken genome. In addition, considerable compensatory cis- and trans-regulatory changes exist in the chicken genome. Most importantly, stronger purifying selection was observed on genes regulated by trans-variations than in genes regulated by the cis elements. Conclusions We present a pipeline to explore allele-specific expression in hybrid progenies of inbred lines without a specific reference genome. Our research is the first study to describe the regulatory divergence between two contrasting breeds. The results suggest that artificial selection associated with domestication in chicken could have acted more on trans-regulatory divergence than on cis-regulatory divergence.

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Evolution of cis- and trans-regulatory divergence in the chicken genome between two contrasting breeds analyzed using three tissue types at one-day-old

10.21203/rs.2.10726/v3 ◽

2019 ◽

Author(s):

Qiong Wang ◽

Yaxiong Jia ◽

Yuan Wang ◽

Zhihua Jiang ◽

Xiang Zhou ◽

...

Keyword(s):

Chicken Genome ◽

Reproductive Traits ◽

Purifying Selection ◽

Population Divergence ◽

Specific Reference ◽

Specific Expression ◽

Allele Specific Expression ◽

Allele Specific ◽

Trans Regulation ◽

Cis And Trans

Abstract Background: Gene expression variation is a key underlying factor influencing phenotypic variation, and can occur via cis- or trans-regulation. To understand the role of cis- and trans-regulatory variation on population divergence in chicken, we developed reciprocal crosses of two chicken breeds, White Leghorn and Cornish Game, which exhibit major differences in body size and reproductive traits, and used them to determine the degree of cis versus trans variation in the brain, liver, and muscle tissue of male and female 1-day-old specimens.Results: We provided an overview of how transcriptomes are regulated in hybrid progenies of two contrasting breeds based on allele specific expression analysis. Compared with cis-regulatory divergence, trans-acting genes were more extensive in the chicken genome. In addition, considerable compensatory cis- and trans-regulatory changes exist in the chicken genome. Most importantly, stronger purifying selection was observed on genes regulated by trans-variations than in genes regulated by the cis elements.Conclusions: We present a pipeline to explore allele-specific expression in hybrid progenies of inbred lines without a specific reference genome. Our research is the first study to describe the regulatory divergence between two contrasting breeds. The results suggest that artificial selection associated with domestication in chicken could have acted more on trans-regulatory divergence than on cis-regulatory divergence.

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Cis-regulatory changes in locomotor genes are associated with the evolution of burrowing behavior

10.1101/2021.09.27.462036 ◽

2021 ◽

Author(s):

Caroline K. Hu ◽

Ryan A. York ◽

Hillery C. Metz ◽

Nicole L. Bedford ◽

Hunter B. Fraser ◽

...

Keyword(s):

Gene Expression ◽

Candidate Genes ◽

Sister Species ◽

Behavioral Context ◽

Specific Expression ◽

Allele Specific Expression ◽

Regulatory Changes ◽

Allele Specific ◽

Burrowing Behavior ◽

Regulated Gene Expression

SummaryHow evolution modifies complex, innate behaviors is largely unknown. Divergence in many morphological traits has been linked, at least in part, to cis-regulatory changes in gene expression, a pattern also observed in some behaviors of recently diverged populations. Given this, we compared the gene expression in the brains of two interfertile sister species of Peromyscus mice, including allele-specific expression (ASE) of their F1 hybrids, that show large and heritable differences in burrowing behavior. Because cis-regulation may contribute to constitutive as well as activity-dependent gene expression, we also captured a molecular signature of burrowing circuit divergence by quantifying gene expression in mice shortly after burrowing. We found that several thousand genes were differentially expressed between the two sister species regardless of behavioral context, with several thousand more showing behavior-dependent differences. Allele-specific expression in F1 hybrids showed a similar pattern, suggesting that much of the differential expression is driven by cis-regulatory divergence. Genes related to locomotor coordination showed the strongest signals of lineage-specific selection on burrowing-induced cis-regulatory changes. By comparing these candidate genes to independent quantitative trait locus (QTL) mapping data, we found that the closest QTL markers to these candidate genes are associated with variation in burrow shape, demonstrating an enrichment for candidate locomotor genes near segregating causal loci. Together, our results provide insight into how cis-regulated gene expression can depend on behavioral context as well as how this dynamic regulatory divergence between species can be integrated with forward genetics to enrich our understanding of the genetic basis of behavioral evolution.

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Evolution of cis- and trans-regulatory divergence in the chicken genome between two contrasting breeds analyzed using three tissue types at one-day-old

10.21203/rs.2.10726/v4 ◽

2019 ◽

Author(s):

Qiong Wang ◽

Yaxiong Jia ◽

Yuan Wang ◽

Zhihua Jiang ◽

Xiang Zhou ◽

...

Keyword(s):

Chicken Genome ◽

Reproductive Traits ◽

Purifying Selection ◽

Population Divergence ◽

Specific Reference ◽

Specific Expression ◽

Allele Specific Expression ◽

Allele Specific ◽

Trans Regulation ◽

Cis And Trans

Abstract Background: Gene expression variation is a key underlying factor influencing phenotypic variation, and can occur via cis- or trans-regulation. To understand the role of cis- and trans-regulatory variation on population divergence in chicken, we developed reciprocal crosses of two chicken breeds, White Leghorn and Cornish Game, which exhibit major differences in body size and reproductive traits, and used them to determine the degree of cis versus trans variation in the brain, liver, and muscle tissue of male and female 1-day-old specimens.Results: We provided an overview of how transcriptomes are regulated in hybrid progenies of two contrasting breeds based on allele specific expression analysis. Compared with cis-regulatory divergence, trans-acting genes were more extensive in the chicken genome. In addition, considerable compensatory cis- and trans-regulatory changes exist in the chicken genome. Most importantly, stronger purifying selection was observed on genes regulated by trans-variations than in genes regulated by the cis elements.Conclusions: We present a pipeline to explore allele-specific expression in hybrid progenies of inbred lines without a specific reference genome. Our research is the first study to describe the regulatory divergence between two contrasting breeds. The results suggest that artificial selection associated with domestication in chicken could have acted more on trans-regulatory divergence than on cis-regulatory divergence.

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Genome-Wide Identification and Quantification of cis- and trans-Regulated Genes Responding to Marek’s Disease Virus Infection via Analysis of Allele-Specific Expression

Frontiers in Genetics ◽

10.3389/fgene.2011.00113 ◽

2012 ◽

Vol 2 ◽

Cited By ~ 6

Author(s):

Sean MacEachern ◽

William M. Muir ◽

Seth D. Crosby ◽

Hans H. Cheng

Keyword(s):

Virus Infection ◽

Disease Virus ◽

Marek's Disease Virus ◽

Marek's Disease ◽

Specific Expression ◽

Allele Specific Expression ◽

Genome Wide ◽

Allele Specific ◽

Cis And Trans ◽

Identification And Quantification

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Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT

Scientific Reports ◽

10.1038/s41598-021-83459-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

M. Joseph Tomlinson ◽

Shawn W. Polson ◽

Jing Qiu ◽

Juniper A. Lake ◽

William Lee ◽

...

Keyword(s):

Broiler Chickens ◽

Nucleotide Polymorphisms ◽

Rna Seq ◽

Specific Expression ◽

Single Nucleotide ◽

Allele Specific Expression ◽

Detection Tool ◽

Commercial Broiler ◽

Significant Phenomenon ◽

Allele Specific

AbstractDifferential abundance of allelic transcripts in a diploid organism, commonly referred to as allele specific expression (ASE), is a biologically significant phenomenon and can be examined using single nucleotide polymorphisms (SNPs) from RNA-seq. Quantifying ASE aids in our ability to identify and understand cis-regulatory mechanisms that influence gene expression, and thereby assist in identifying causal mutations. This study examines ASE in breast muscle, abdominal fat, and liver of commercial broiler chickens using variants called from a large sub-set of the samples (n = 68). ASE analysis was performed using a custom software called VCF ASE Detection Tool (VADT), which detects ASE of biallelic SNPs using a binomial test. On average ~ 174,000 SNPs in each tissue passed our filtering criteria and were considered informative, of which ~ 24,000 (~ 14%) showed ASE. Of all ASE SNPs, only 3.7% exhibited ASE in all three tissues, with ~ 83% showing ASE specific to a single tissue. When ASE genes (genes containing ASE SNPs) were compared between tissues, the overlap among all three tissues increased to 20.1%. Our results indicate that ASE genes show tissue-specific enrichment patterns, but all three tissues showed enrichment for pathways involved in translation.

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