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Organ specificity and transcriptional control of metabolic routes revealed by expression QTL profiling of source--sink tissues in a segregating potato population.

ABSTRACT: BACKGROUND: With the completion of genome sequences belonging to some of the major crop plants, new challenges arise to utilize this data for crop improvement and increased food security. The field of genetical genomics has the potential to identify genes displaying heritable differential expression associated to important phenotypic traits. Here we describe the identification of expression QTLs (eQTLs) in two different potato tissues of a segregating potato population and query the potato genome sequence to differentiate between cis- and trans-acting eQTLs in relation to gene subfunctionalization. RESULTS: Leaf and tuber samples were analysed and screened for the presence of conserved and tissue dependent eQTLs. Expression QTLs present in both tissues are predominantly cis-acting whilst for tissue specific QTLs, the percentage of trans-acting QTLs increases. Tissue dependent eQTLs were assigned to functional classes and visualized in metabolic pathways. We identified a potential regulatory network on chromosome 10 involving genes crucial for maintaining circadian rhythms and controlling clock output genes. In addition, we show that the type of genetic material screened and sampling strategy applied, can have a high impact on the output of genetical genomics studies. CONCLUSIONS: Identification of tissue dependent regulatory networks based on mapped differential expression not only gives us insight in tissue dependent gene subfunctionalization but brings new insights into key biological processes and delivers targets for future haplotyping and genetic marker development.

SUBMITTER: Kloosterman B

PROVIDER: S-EPMC3546430 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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Organ specificity and transcriptional control of metabolic routes revealed by expression QTL profiling of source--sink tissues in a segregating potato population.

Kloosterman Bjorn B Anithakumari A M AM Chibon Pierre-Yves PY Oortwijn Marian M van der Linden Gerard C GC Visser Richard G F RG Bachem Christian W B CW

BMC plant biology 20120207

<h4>Background</h4>With the completion of genome sequences belonging to some of the major crop plants, new challenges arise to utilize this data for crop improvement and increased food security. The field of genetical genomics has the potential to identify genes displaying heritable differential expression associated to important phenotypic traits. Here we describe the identification of expression QTLs (eQTLs) in two different potato tissues of a segregating potato population and query the potat ...[more]

PMID: 22313736

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Project description:Background and aimsPlant growth depends on carbon availability and allocation among organs. QualiTree has been designed to simulate carbon allocation and partitioning in the peach tree (Prunus persica), whereas MappleT is dedicated to the simulation of apple tree (Malus × domestica) architecture. The objective of this study was to couple both models and adapt QualiTree to apple trees to simulate organ growth traits and their within-tree variability.MethodsMappleT was used to generate architectures corresponding to the 'Fuji' cultivar, accounting for the variability within and among individuals. These architectures were input into QualiTree to simulate shoot and fruit growth during a growth cycle. We modified QualiTree to account for the observed shoot polymorphism in apple trees, i.e. different classes (long, medium and short) that were characterized by different growth function parameters. Model outputs were compared with observed 3D tree geometries, considering shoot and final fruit size and growth dynamics.Key resultsThe modelling approach connecting MappleT and QualiTree was appropriate to the simulation of growth and architectural characteristics at the tree scale (plant leaf area, shoot number and types, fruit weight at harvest). At the shoot scale, mean fruit weight and its variability within trees was accurately simulated, whereas the model tended to overestimate individual shoot leaf area and underestimate its variability for each shoot type. Varying the parameter related to the intensity of carbon exchange between shoots revealed that behaviour intermediate between shoot autonomy and a common assimilate pool was required to properly simulate within-tree fruit growth variability. Moreover, the model correctly dealt with the crop load effect on organ growth.ConclusionsThis study provides understanding of the integration of shoot ontogenetic properties, carbon supply and transport between entities for simulating organ growth in trees. Further improvements regarding the integration of retroaction loops between carbon allocation and the resulting plant architecture are expected to allow multi-year simulations.

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Dataset Information

Organ specificity and transcriptional control of metabolic routes revealed by expression QTL profiling of source--sink tissues in a segregating potato population.

Publications

Organ specificity and transcriptional control of metabolic routes revealed by expression QTL profiling of source--sink tissues in a segregating potato population.

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