Segregating Variation in the Transcriptome:<i>Cis</i>Regulation and Additivity of Effects

Hughes, Kimberly A.; Ayroles, Julien F.; Reedy, Melissa M.; Drnevich, Jenny; Rowe, Kevin C.; Ruedi, Elizabeth A.; Cáceres, Carla E.; Paige, Ken N.

doi:10.1534/genetics.105.051474

Cited by 66 publications

(82 citation statements)

References 40 publications

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“…Our observation that cis-and trans-eQTL are associated with different distributions of R 2 (Figure 2) was also found in Drosophila (Meiklejohn et al 2003;Wayne et al 2004;Hughes et al 2006). A potential explanation for this observation is that the transcript abundance of most genes is regulated by multiple signal transduction networks at multiple levels (e.g., transcription and transcript stability); thus a polymorphism in any one of these regulatory levels may be functionally limited to only a small change in transcript accumulation for those genes controlled in trans by that polymorphism.…”

Section: à14supporting

confidence: 74%

Global eQTL Mapping Reveals the Complex Genetic Architecture of Transcript-Level Variation in Arabidopsis

et al. 2007

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The genetic architecture of transcript-level variation is largely unknown. The genetic determinants of transcript-level variation were characterized in a recombinant inbred line (RIL) population (n ¼ 211) of Arabidopsis thaliana using whole-genome microarray analysis and expression quantitative trait loci (eQTL) mapping of transcript levels as expression traits (e-traits). Genetic control of transcription was highly complex: one-third of the quantitatively controlled transcripts/e-traits were regulated by cis-eQTL, and many trans-eQTL mapped to hotspots that regulated hundreds to thousands of e-traits. Several thousand eQTL of large phenotypic effect were detected, but almost all (93%) of the 36,871 eQTL were associated with small phenotypic effects (R 2 , 0.3). Many transcripts/e-traits were controlled by multiple eQTL with opposite allelic effects and exhibited higher heritability in the RILs than their parents, suggesting nonadditive genetic variation. To our knowledge, this is the first large-scale global eQTL study in a relatively large plant mapping population. It reveals that the genetic control of transcript level is highly variable and multifaceted and that this complexity may be a general characteristic of eukaryotes.

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Section: à14supporting

confidence: 74%

Global eQTL Mapping Reveals the Complex Genetic Architecture of Transcript-Level Variation in Arabidopsis

et al. 2007

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“…Also, variation among the RILs reflects only the homozygous effects of alleles. Neither homozygous effects nor variation in the two parental lines is necessarily representative of variation segregating within randomly mating populations (Mackay 2001, Hughes et al 2006. If variation in sperm competition is maintained by strong balancing selection on a few loci, RILs generated from two inbred lines could fail to reflect variation that persists within randomly mating populations.…”

Section: Discussionmentioning

confidence: 99%

QUANTITATIVE TRAIT LOCUS ANALYSIS OF MALE MATING SUCCESS AND SPERM COMPETITION INDROSOPHILA MELANOGASTER

Hughes¹,

Leips²

2006

Evolution

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Abstract. Much of sexual selection theory depends on assumptions about the genetic basis of variation in male mating success and sperm competitive ability. Despite intense interest in this topic, few genes have been identified that contribute to variation in these traits. Here we report the results of quantitative trait locus (QTL) analyses of mating success of male Drosophila melanogaster when exposed to virgin females, remating success of males with previously mated females, and both defense and offense components of sperm competition. We found two to four significant QTLs for remating success, but no QTLs for mating success, even though mating success was more genetically variable than remating success in the recombinant inbred lines used in this study. By combining these results with data from previous gene-expression experiments, we were able to identify three X-linked candidate genes for variation in remating ability. For two of these genes, QTL and expression data were completely concordant with respect to directionality of effects: high mating success was associated with high levels of gene expression and with beneficial QTL effects on the trait. We found equivocal evidence for genetic variation in sperm offense and defense in the recombinant inbred lines, and we did not find any significant QTLs for either sperm competition trait.

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“…Previous studies on regulatory elements have reported contrasting results regarding the overall proportions of cis vs trans effects, depending on the distance of the parental groups used to generate the crosses studied (interspecies or intraspecies) (Wayne et al, 2004;Wittkopp et al, 2004;Hughes et al, 2006;Lemos et al, 2008;Wittkopp et al, 2008b;Graze et al, 2009). However, most of these studies globally agree that cis regulation contributes more to gene expression variation than trans effects, especially in comparisons among populations relative to comparisons within populations.…”

Section: Cis-acting Regulatory Effectsmentioning

confidence: 99%

Linking transcriptomic and genomic variation to growth in brook charr hybrids (Salvelinus fontinalis, Mitchill)

Bougas¹,

Normandeau²,

Audet³

et al. 2013

Heredity

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Hybridization can lead to phenotypic differences arising from changes in gene expression patterns or new allele combinations. Variation in gene expression is thought to be controlled by differences in transcription regulation of parental alleles, either through cis-or trans-regulatory elements. A previous study among brook charr hybrids from different populations (Rupert, Laval, and domestic) showing distinct length at age during early life stages also revealed different patterns in transcription regulation inheritance of transcript abundance. In the present study, transcript abundance using RNA-sequencing and quantitative real-time PCR, single-nucleotide polymorphism (SNP) genotypes and allelic imbalance were assessed in order to understand the molecular mechanisms underlying the observed transcriptomic and differences in length at age among domestic Â Rupert hybrids and Laval Â domestic hybrids. We found 198 differentially expressed genes between the two hybrid crosses, and allelic imbalance could be analyzed for 69 of them. Among these 69 genes, 36 genes exhibited cis-acting regulatory effects in both of the two crosses, thus confirming the prevalent role of cis-acting regulatory elements in the regulation of differentially expressed genes among intraspecific hybrids. In addition, we detected a significant association between SNP genotypes of three genes and length at age. Our study is thus one of the few that have highlighted some of the molecular mechanisms potentially involved in the differential phenotypic expression in intraspecific hybrids for nonmodel species.

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Segregating Variation in the Transcriptome:CisRegulation and Additivity of Effects

Cited by 66 publications

References 40 publications

Global eQTL Mapping Reveals the Complex Genetic Architecture of Transcript-Level Variation in Arabidopsis

Global eQTL Mapping Reveals the Complex Genetic Architecture of Transcript-Level Variation in Arabidopsis

QUANTITATIVE TRAIT LOCUS ANALYSIS OF MALE MATING SUCCESS AND SPERM COMPETITION INDROSOPHILA MELANOGASTER

Linking transcriptomic and genomic variation to growth in brook charr hybrids (Salvelinus fontinalis, Mitchill)

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