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Genotype to phenotype maps: multiple input abiotic signals combine to produce growth effects via attenuating signaling interactions in maize.

Makumburage GB, Richbourg HL, LaTorre KD, Capps A, Chen C, Stapleton AE - G3 (Bethesda) (2013)

Bottom Line: Additive allele effects are the foundation for selection in animal and plant breeding, and complex genetic and environmental interactions contribute to inefficient detection of desirable loci.Comparisons of single and combined stress effects on growth and biomass traits exhibit patterns of allele effects that suggest attenuating interactions among physiological signaling steps in drought and ultraviolet radiation stress responses.The presence of attenuating interactions implies that shared QTL found in sets of environments could be used to group environment types and identify underlying environmental similarities, and that patterns of stress-dependent genetic architecture should be studied as a way to prioritize prebreeding populations.

View Article: PubMed Central - PubMed

Affiliation: Department of Mathematics and Statistics, University of North Carolina Wilmington, Wilmington, North Carolina 28401.

ABSTRACT
The complexity of allele interactions constrains crop improvement and the prediction of disease susceptibility. Additive allele effects are the foundation for selection in animal and plant breeding, and complex genetic and environmental interactions contribute to inefficient detection of desirable loci. Manipulation and modeling of other sources of variation, such as environmental variables, have the potential to improve our prediction of phenotype from genotype. As an example of our approach to analysis of the network linking environmental input to alleles, we mapped the genetic architecture of single and combined abiotic stress responses in two maize mapping populations and compared the observed genetic architecture patterns to simple theoretical predictions. Comparisons of single and combined stress effects on growth and biomass traits exhibit patterns of allele effects that suggest attenuating interactions among physiological signaling steps in drought and ultraviolet radiation stress responses. The presence of attenuating interactions implies that shared QTL found in sets of environments could be used to group environment types and identify underlying environmental similarities, and that patterns of stress-dependent genetic architecture should be studied as a way to prioritize prebreeding populations. A better understanding of whole-plant interactor pathways and genetic architecture of multiple-input environmental signaling has the potential to improve the prediction of genomic value in plant breeding and crop modeling.

Show MeSH
Signaling pathways with constitutive sensors drought and ultraviolet radiation are perceived by sensors that negatively regulate (reduce the effect of) signals from the other environmental input. This mutually negative and attenuating effect is drawn as a direct interaction for simplicity.
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fig5: Signaling pathways with constitutive sensors drought and ultraviolet radiation are perceived by sensors that negatively regulate (reduce the effect of) signals from the other environmental input. This mutually negative and attenuating effect is drawn as a direct interaction for simplicity.

Mentions: Our modified explanation for the prevalence of combined stress–lost loci in our results incorporated a modifier with a blocking effect (Figure 5). Any allelic difference in the UV signaling step would be “invisible” under drought alone, and any allelic effect for the drought signaling step would be undetectable under UV alone. This symbolized the classic modifier locus (Hamilton and Yu 2012) with the additional specification of an attenuating, negative effect on signaling. Signals characterized as blocking, negative, or repressive are often experimentally observed in physiological or regulatory networks. For example, negative edges are prevalent in immune system networks (Campbell et al. 2011) and in rice complex trait epistasic networks (Zhang et al. 2011). Theoretical analysis of stable network structures also suggested that negative regulation should be favored (Mittenthal and Zou 2011). Recent work regarding metabolic pathways showed that inhibitory pathway interactions are difficult to detect (Blair et al. 2012); our approach of manipulating environments provided an alternative detection scheme.


Genotype to phenotype maps: multiple input abiotic signals combine to produce growth effects via attenuating signaling interactions in maize.

Makumburage GB, Richbourg HL, LaTorre KD, Capps A, Chen C, Stapleton AE - G3 (Bethesda) (2013)

Signaling pathways with constitutive sensors drought and ultraviolet radiation are perceived by sensors that negatively regulate (reduce the effect of) signals from the other environmental input. This mutually negative and attenuating effect is drawn as a direct interaction for simplicity.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3852382&req=5

fig5: Signaling pathways with constitutive sensors drought and ultraviolet radiation are perceived by sensors that negatively regulate (reduce the effect of) signals from the other environmental input. This mutually negative and attenuating effect is drawn as a direct interaction for simplicity.
Mentions: Our modified explanation for the prevalence of combined stress–lost loci in our results incorporated a modifier with a blocking effect (Figure 5). Any allelic difference in the UV signaling step would be “invisible” under drought alone, and any allelic effect for the drought signaling step would be undetectable under UV alone. This symbolized the classic modifier locus (Hamilton and Yu 2012) with the additional specification of an attenuating, negative effect on signaling. Signals characterized as blocking, negative, or repressive are often experimentally observed in physiological or regulatory networks. For example, negative edges are prevalent in immune system networks (Campbell et al. 2011) and in rice complex trait epistasic networks (Zhang et al. 2011). Theoretical analysis of stable network structures also suggested that negative regulation should be favored (Mittenthal and Zou 2011). Recent work regarding metabolic pathways showed that inhibitory pathway interactions are difficult to detect (Blair et al. 2012); our approach of manipulating environments provided an alternative detection scheme.

Bottom Line: Additive allele effects are the foundation for selection in animal and plant breeding, and complex genetic and environmental interactions contribute to inefficient detection of desirable loci.Comparisons of single and combined stress effects on growth and biomass traits exhibit patterns of allele effects that suggest attenuating interactions among physiological signaling steps in drought and ultraviolet radiation stress responses.The presence of attenuating interactions implies that shared QTL found in sets of environments could be used to group environment types and identify underlying environmental similarities, and that patterns of stress-dependent genetic architecture should be studied as a way to prioritize prebreeding populations.

View Article: PubMed Central - PubMed

Affiliation: Department of Mathematics and Statistics, University of North Carolina Wilmington, Wilmington, North Carolina 28401.

ABSTRACT
The complexity of allele interactions constrains crop improvement and the prediction of disease susceptibility. Additive allele effects are the foundation for selection in animal and plant breeding, and complex genetic and environmental interactions contribute to inefficient detection of desirable loci. Manipulation and modeling of other sources of variation, such as environmental variables, have the potential to improve our prediction of phenotype from genotype. As an example of our approach to analysis of the network linking environmental input to alleles, we mapped the genetic architecture of single and combined abiotic stress responses in two maize mapping populations and compared the observed genetic architecture patterns to simple theoretical predictions. Comparisons of single and combined stress effects on growth and biomass traits exhibit patterns of allele effects that suggest attenuating interactions among physiological signaling steps in drought and ultraviolet radiation stress responses. The presence of attenuating interactions implies that shared QTL found in sets of environments could be used to group environment types and identify underlying environmental similarities, and that patterns of stress-dependent genetic architecture should be studied as a way to prioritize prebreeding populations. A better understanding of whole-plant interactor pathways and genetic architecture of multiple-input environmental signaling has the potential to improve the prediction of genomic value in plant breeding and crop modeling.

Show MeSH