Identification of candidate genes associated with cell wall digestibility and eQTL (expression quantitative trait loci) analysis in a Flint × Flint maize recombinant inbred line population

Shi, Chun; Użarowska, Anna; Ouzunova, Milena; Landbeck, Matthias; Wenzel, G.; Lübberstedt, Thomas

doi:10.1186/1471-2164-8-22

Cited by 67 publications

(44 citation statements)

References 29 publications

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“…S3), consistent with reports from other species (15,(18)(19)(20)(21)(22)(23) and of trans-regulation of diverse biological processes in maize (24)(25)(26)(27)(28). Previous studies may have overestimated the number or proportion of cis-regulated genes (3,29) due to ascertainment bias because they only analyzed genes containing single nucleotide polymorphisms between B73 and Mo17 and/or had limited statistical power to detect the more subtle effects of trans-eQTL (15).…”

supporting

confidence: 84%

Paternal Dominance of Trans-eQTL Influences Gene Expression Patterns in Maize Hybrids

Swanson-Wagner

DeCook

Jia

et al. 2009

Science

130

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Heterosis refers to the superior performance of hybrid progeny relative to their inbred parents, but the mechanisms responsible are unknown. Hybrids between the maize inbred lines B73 and Mo17 exhibit heterosis regardless of cross direction. These reciprocal hybrids differ from each other phenotypically, and 30 to 50% of their genes are differentially expressed. We identified approximately 4000 expression quantitative trait loci (eQTL) that allowed us to identify markers linked to variation in expression. We found that over three-quarters of these eQTL act in trans (78%) and that 86% of these differentially regulate transcript accumulation in a manner consistent with gene expression in the hybrid being regulated exclusively by the paternally transmitted allele. This result suggests that widespread imprinting contributes to the regulation of gene expression in maize hybrids.

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supporting

confidence: 84%

Paternal Dominance of Trans-eQTL Influences Gene Expression Patterns in Maize Hybrids

Swanson-Wagner

DeCook

Jia

et al. 2009

Science

130

View full text Add to dashboard Cite

show abstract

“…Knowledge on regulation of gene expression and pathways has recently been combined with genetic linkage analysis, allowing localisation of eQTLs in linkage maps for further MAS breeding (Shi et al, 2007).…”

Section: Molecular Histology: a Brief View Into The Futurementioning

confidence: 99%

Host plant resistance against broomrapes (Orobanche spp.): defence reactions and mechanisms of resistance

Pérez‐de‐Luque

Moreno

Rubiales

2008

Annals of Applied Biology

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Over 4000 species of angiosperms are able to directly invade and parasitise other plants, but only very few are weedy and parasitise cultivated plants. Together with the witchweeds (Striga spp.) and dodders (Cuscuta spp.), the broomrapes (Orobanche spp.) affect important crops causing complete yield loses with severe infestations. Genetic resistance to parasitisation remains as one of the most desirable components in an integrated control strategy. However, breeding for resistance is a difficult task and many aspects of the host/parasite interaction remain unknown. In the present work, we review the cytological and cytochemical studies investigating the mechanisms of resistance involved in the process leading to an incompatible host-parasite interaction. We have attempted to identify the main gaps and problems related to such studies with parasitic plants and present an in-depth review of histochemical techniques used to assess mechanisms of resistance against these parasitic plants. Furthermore, we discuss future research directions and novel techniques and finally, how such techniques can be applied and incorporated within a breeding programme.

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“…It is now well established that natural genetic variation contributes significantly to variation in gene expression, and the loci of regulatory variation for individual transcripts have been mapped in yeast (Brem and Kruglyak 2005), mice (Schadt et al 2003), rats (Hubner et al 2005), humans (Morley et al 2004), maize (Shi et al 2007), Eucalyptus (Kirst et al 2005), and Arabidopsis (West et al 2007). These studies show that variation in transcript abundance arises from expression quantitative trait loci (eQTL) that can be classified as either local (cis-eQTLs) or distant (trans-eQTLs) regulatory variants (Rockman and Kruglyak 2006).…”

mentioning

confidence: 99%

High resolution mapping of expression QTLs in heterogeneous stock mice in multiple tissues

Huang

Shifman

Valdar³

et al. 2009

Genome Res.

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A proportion of the genetic variants underlying complex phenotypes do so through their effects on gene expression, so an important challenge in complex trait analysis is to discover the genetic basis for the variation in transcript abundance. So far, the potential of mapping both quantitative trait loci (QTLs) and expression quantitative trait loci (eQTLs) in rodents has been limited by the low mapping resolution inherent in crosses between inbred strains. We provide a megabase resolution map of thousands of eQTLs in hippocampus, lung, and liver samples from heterogeneous stock (HS) mice in which 843 QTLs have also been mapped at megabase resolution. We exploit dense mouse SNP data to show that artifacts due to allele-specific hybridization occur in ;30% of the cis-acting eQTLs and, by comparison with exon expression data, we show that alternative splicing of the 39 end of the genes accounts for <1% of cis-acting eQTLs. Approximately one third of cis-acting eQTLs and one half of trans-acting eQTLs are tissue specific. We have created an important systems biology resource for the genetic analysis of complex traits in a key model organism.

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Identification of candidate genes associated with cell wall digestibility and eQTL (expression quantitative trait loci) analysis in a Flint × Flint maize recombinant inbred line population

Abstract: Background: Cell-wall digestibility is the major target for improving the feeding value of forage maize. An understanding of the molecular basis for cell-wall digestibility is crucial towards breeding of highly digestible maize.

Cited by 67 publications

References 29 publications

Paternal Dominance of Trans-eQTL Influences Gene Expression Patterns in Maize Hybrids

Paternal Dominance of Trans-eQTL Influences Gene Expression Patterns in Maize Hybrids

Host plant resistance against broomrapes (Orobanche spp.): defence reactions and mechanisms of resistance

High resolution mapping of expression QTLs in heterogeneous stock mice in multiple tissues

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