Inheritance Patterns of Transcript Levels in F1 Hybrid Mice

Cui, Xiangqin; Affourtit, Jason P.; Shockley, Keith R.; Woo, Yong; Churchill, Gary A.

doi:10.1534/genetics.106.060251

Cited by 35 publications

(45 citation statements)

References 45 publications

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“…The authors found that the F 1 hybrids exhibited additive expression levels much more frequently than nonadditive levels. The few observations of hybrid gene expression outside of the parental range were typically identified in genes with little expression difference between the inbred parents (Cui et al 2006), similar to the results obtained by Swanson-Wagner et al (2006) in maize.…”

Section: Text Box 2 Describing the Gene Expression Levels In Inbredssupporting

confidence: 75%

Allelic variation and heterosis in maize: How do two halves make more than a whole?

Springer¹,

Stupar²

2007

Genome Res.

339

252

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In this review, we discuss the recent research on allelic variation in maize and possible implications of this work toward our understanding of heterosis. Heterosis, or hybrid vigor, is the increased performance of a hybrid relative to the parents, and is a result of the variation that is present within a species. Intraspecific comparisons of sequence and expression levels in maize have documented a surprisingly high level of allelic variation, which includes variation for the content of genic fragments, variation in repetitive elements surrounding genes, and variation in gene expression levels. There is evidence that transposons and repetitive DNA play a major role in the generation of this allelic diversity. The combination of allelic variants provides a more comprehensive suite of alleles in the hybrid that may be involved in novel allelic interactions. A major unresolved question is how the combined allelic variation and interactions in a hybrid give rise to heterotic phenotypes. An understanding of allelic variation present in maize provides an opportunity to speculate on mechanisms that might lead to heterosis. Variation for the presence of genes, the presence of novel beneficial alleles, and modified levels of gene expression in hybrids may all contribute to the heterotic phenotypes.

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Section: Text Box 2 Describing the Gene Expression Levels In Inbredssupporting

confidence: 75%

Allelic variation and heterosis in maize: How do two halves make more than a whole?

Springer¹,

Stupar²

2007

Genome Res.

339

252

View full text Add to dashboard Cite

show abstract

“…Among F1 generations from two inbred mice strains, approximately twothirds of all loci have measurable h 2 with a quarter having an h 2 of >50% (Cui et al, 2006). In both humans and mice, the median h 2 is 34% among loci with measurable h 2 (Cui et al, 2006). The variation in regulatory processes affecting gene expression has been inferred by combining microarray and QTL studies [expressed QTLs (eQTL)].…”

Section: Genetics Of Gene Expressionmentioning

confidence: 99%

The biological importance of measuring individual variation

Crawford¹,

Oleksiak²

2007

Journal of Experimental Biology

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SUMMARY Functional genomics research using Fundulus heteroclitus has focused on variation among individuals because of the evolutionary importance and value of Fundulus in explaining the human condition (why individual humans are different and are affected differently by stress,disease and drugs). Among different populations and species of Fundulus, there are evolutionarily adaptive differences in gene expression. This natural variation in gene expression seems to affect cardiac metabolism because up to 81% of the variation in glucose utilization observed in isolated heart ventricles is related to specific patterns of gene expression. The surprising result from this research is that among different groups of individuals, the expression of mRNA from different metabolic pathways explains substrate-specific metabolism. For example, variation in oxidative phosphorylation mRNAs explains glucose metabolism for one group of individuals but expression of glucose metabolism genes explains this metabolism in a different group of individuals. This variation among individuals has important implications for studies using inbred strains:conclusions based on one individual or one strain will not necessarily reflect a generalized conclusion for a population or species. Finally, there are surprisingly strong positive and negative correlations among metabolic genes,both within and between pathways. These data suggest that measures of mRNA expression are meaningful, yet there is a complexity in how gene expression is related to physiological processes.

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“…It has also been hypothesized that the crossing of inbred lines characterized by distinct gene expression levels could lead to advantageous transgressive phenotypic (Birchler et al 2003;Cui et al 2006;Stupar and Springer 2006;Swanson-Wagner et al 2006;Stupar et al 2008). One approach used to study the genetics of phenotypic traits is to measure transcript expression in the hybrids relative to their parents, but such studies have been in the past limited to mouse and Drosophila sp.…”

mentioning

confidence: 99%

“…One approach used to study the genetics of phenotypic traits is to measure transcript expression in the hybrids relative to their parents, but such studies have been in the past limited to mouse and Drosophila sp. (Reiland and Norr 2002;Michalak and Noor 2003;Gibson et al 2004;Ranz et al 2004;Cui et al 2006;Hughes et al 2006;Rottscheidt and Harr 2007). Other studies have also focused on elucidating the genomic basis of heterosis of mollusc production (Hedgecock et al 2007) and plant production (Auger et al 2005;Swanson-Wagner et al 2006;Lippman and Zamir 2007;Ge et al 2008;Stupar et al 2008).…”

mentioning

confidence: 99%

“…Other studies have also focused on elucidating the genomic basis of heterosis of mollusc production (Hedgecock et al 2007) and plant production (Auger et al 2005;Swanson-Wagner et al 2006;Lippman and Zamir 2007;Ge et al 2008;Stupar et al 2008). Comparative studies of genome-wide transcriptomes of parental and hybrid crosses also revealed that hybrids tended to express numerous genes at a level outside the range observed in their parental lines Ranz et al 2004;Auger et al 2005;Cui et al 2006;Hughes et al 2006;Stupar and Springer 2006;Swanson-Wagner et al 2006;Hedgecock et al 2007;Rottscheidt and Harr 2007;Ge et al 2008;Roberge et al 2008;Stupar et al 2008;Normandeau et al 2009;Renaut et al 2009). Thus, divergent lineages can accumulate divergences in gene regulation networks through time and these divergences often result in misexpressed genes (reviewed by Landry et al 2007), which could affect the viability or fitness of individuals.…”

mentioning

confidence: 99%

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The Transcriptional Landscape of Cross-Specific Hybrids and Its Possible Link With Growth in Brook Charr (Salvelinus fontinalis Mitchill)

et al. 2010

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The genetic mechanisms underlying hybridization are poorly understood despite their potentially important roles in speciation processes, adaptative evolution, and agronomical innovation. In this study, transcription profiles were compared among three populations of brook charr and their hybrids using microarrays to assess the influence of hybrid origin on modes of transcription regulation inheritance and on the mechanisms underlying growth. We found that twice as many transcripts were differently expressed between the domestic population and the two wild populations (Rupert and Laval) than between wild ones, despite their deeper genetic distance. This could reflect the consequence of artificial selection during domestication. We detected that hybrids exhibited strikingly different patterns of mode of transcription regulation, being mostly additive (94%) for domestic 3 Rupert, and nonadditive for Laval 3 domestic (45.7%) and Rupert 3 Laval hybrids (37.5%). Both heterosis and outbreeding depression for growth were observed among the crosses. Our results indicated that prevalence of dominance in transcription regulation seems related to growth heterosis, while prevalence of transgressive transcription regulation may be more related to outbreeding depression. Our study clearly shows, for the first time in vertebrates, that the consequences of hybridization on both the transcriptome level and the phenotype are highly dependent on the specific genetic architectures of crossed populations and therefore hardly predictable.

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Inheritance Patterns of Transcript Levels in F1 Hybrid Mice

Cited by 35 publications

References 45 publications

Allelic variation and heterosis in maize: How do two halves make more than a whole?

Allelic variation and heterosis in maize: How do two halves make more than a whole?

The biological importance of measuring individual variation

The Transcriptional Landscape of Cross-Specific Hybrids and Its Possible Link With Growth in Brook Charr (Salvelinus fontinalis Mitchill)

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