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Genome Wide Association Mapping in Arabidopsis thaliana Identifies Novel Genes Involved in Linking Allyl Glucosinolate to Altered Biomass and Defense.

Francisco M, Joseph B, Caligagan H, Li B, Corwin JA, Lin C, Kerwin RE, Burow M, Kliebenstein DJ - Front Plant Sci (2016)

Bottom Line: To start developing a deeper understanding of the mechanism(s) that modulate the ability of exogenous allyl GSL to alter growth and defense, we measured changes in plant biomass and defense metabolites in a collection of natural 96 A. thaliana accessions fed with 50 μM of allyl GSL.Exogenous allyl GSL was introduced exclusively to the roots and the compound transported to the leaf leading to a wide range of heritable effects upon plant biomass and endogenous GSL accumulation.This is one of the first instances in which this approach has been successfully utilized to begin dissecting a novel phenotype to the underlying molecular/polygenic basis.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Sciences, University of California, DavisDavis, CA, USA; Group of Genetics, Breeding and Biochemistry of Brassicas, Department of Plant Genetics, Misión Biológica de Galicia, Spanish Council for Scientific ResearchPontevedra, Spain.

ABSTRACT
A key limitation in modern biology is the ability to rapidly identify genes underlying newly identified complex phenotypes. Genome wide association studies (GWAS) have become an increasingly important approach for dissecting natural variation by associating phenotypes with genotypes at a genome wide level. Recent work is showing that the Arabidopsis thaliana defense metabolite, allyl glucosinolate (GSL), may provide direct feedback regulation, linking defense metabolism outputs to the growth, and defense responses of the plant. However, there is still a need to identify genes that underlie this process. To start developing a deeper understanding of the mechanism(s) that modulate the ability of exogenous allyl GSL to alter growth and defense, we measured changes in plant biomass and defense metabolites in a collection of natural 96 A. thaliana accessions fed with 50 μM of allyl GSL. Exogenous allyl GSL was introduced exclusively to the roots and the compound transported to the leaf leading to a wide range of heritable effects upon plant biomass and endogenous GSL accumulation. Using natural variation we conducted GWAS to identify a number of new genes which potentially control allyl responses in various plant processes. This is one of the first instances in which this approach has been successfully utilized to begin dissecting a novel phenotype to the underlying molecular/polygenic basis.

No MeSH data available.


Related in: MedlinePlus

Distribution of the relative difference of individual GSL accumulation in response to allyl GSL treatment across the Arabidopsis accessions. A beanplot is used to show the distribution of the change in GSL accumulation between the treated and untreated samples across the accessions using the abbreviations in Table S1. Relative difference was determined as (GSL treatment − GSL control)/(0.5 × [GSL treatment + GSL control]). The dashed line in the middle of the plot is the overall average of the relative GSL difference between control and allyl treatment across all GSL. The thick black line in the middle of each bean for each compound is the mean response for that specific GSL trait across all the accessions. The black colored curved bean pod surrounding the observations is the theoretical probability density distribution of these observations. The small lines represent individual data points, with the length of the line proportional to the number of observations with that specific value. The relative difference between treatment and control varied across the 96 accessions from −2 to 2 for each GSL compound, depending on whether that GSL was present in the treatment compared with control.
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Figure 2: Distribution of the relative difference of individual GSL accumulation in response to allyl GSL treatment across the Arabidopsis accessions. A beanplot is used to show the distribution of the change in GSL accumulation between the treated and untreated samples across the accessions using the abbreviations in Table S1. Relative difference was determined as (GSL treatment − GSL control)/(0.5 × [GSL treatment + GSL control]). The dashed line in the middle of the plot is the overall average of the relative GSL difference between control and allyl treatment across all GSL. The thick black line in the middle of each bean for each compound is the mean response for that specific GSL trait across all the accessions. The black colored curved bean pod surrounding the observations is the theoretical probability density distribution of these observations. The small lines represent individual data points, with the length of the line proportional to the number of observations with that specific value. The relative difference between treatment and control varied across the 96 accessions from −2 to 2 for each GSL compound, depending on whether that GSL was present in the treatment compared with control.

Mentions: To measure the genetic variation in how endogenous GSL accumulation responds to exogenous allyl GSL application, we measured GSL from the 96 Arabidopsis accessions seedlings fed with allyl GSL and from the control samples (Francisco et al., 2016). These were from the same individual seedlings measured for biomass and all values are adjusted to the seedlings' biomass. This analysis detected 14 aliphatic GSL compounds and three indolic GSL compounds from which we could define an additional 15 descriptive variables to isolate specific biosynthetic processes and generate a total of 32 traits (Wentzell et al., 2007; Chan et al., 2010a). The GSL traits significantly varied between the accessions with 29 of the 32 aliphatic and indolic GSL traits showing a significant interaction of accession by allyl GSL treatment, suggesting that the accessions have differential responses to the treatment as measured by GSL accumulation (Table 3; Figure 2). In general, aliphatic GSL accumulation across the accessions tended to increase after the application of allyl GSL (Figure 1). However, like biomass accumulation, these changes in endogenous aliphatic GSL accumulation showed a wide range of both positive and negative responses across the accessions (Figure 2). Further, the positive effects were larger than could be accounted for by the additive effect of exogenous allyl GSL application. Moreover, other GSL that cannot be synthesized from the allyl GSL, such as but-3-enyl GSL were also affected by the allyl treatment showing that this is not caused by the uptake and conversion of allyl GSL to other structures (Figure 2). In contrast to the aliphatic GSL, total indolic GSL content and specific indolic GSL compounds, tended to be reduced in most accessions while a few specific accessions showed an increase (Figures 1, 2). Again, the presence of accessions showing both positive and negative responses suggests that the response to allyl GSL likely involves a number of pathways.


Genome Wide Association Mapping in Arabidopsis thaliana Identifies Novel Genes Involved in Linking Allyl Glucosinolate to Altered Biomass and Defense.

Francisco M, Joseph B, Caligagan H, Li B, Corwin JA, Lin C, Kerwin RE, Burow M, Kliebenstein DJ - Front Plant Sci (2016)

Distribution of the relative difference of individual GSL accumulation in response to allyl GSL treatment across the Arabidopsis accessions. A beanplot is used to show the distribution of the change in GSL accumulation between the treated and untreated samples across the accessions using the abbreviations in Table S1. Relative difference was determined as (GSL treatment − GSL control)/(0.5 × [GSL treatment + GSL control]). The dashed line in the middle of the plot is the overall average of the relative GSL difference between control and allyl treatment across all GSL. The thick black line in the middle of each bean for each compound is the mean response for that specific GSL trait across all the accessions. The black colored curved bean pod surrounding the observations is the theoretical probability density distribution of these observations. The small lines represent individual data points, with the length of the line proportional to the number of observations with that specific value. The relative difference between treatment and control varied across the 96 accessions from −2 to 2 for each GSL compound, depending on whether that GSL was present in the treatment compared with control.
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Related In: Results  -  Collection

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Figure 2: Distribution of the relative difference of individual GSL accumulation in response to allyl GSL treatment across the Arabidopsis accessions. A beanplot is used to show the distribution of the change in GSL accumulation between the treated and untreated samples across the accessions using the abbreviations in Table S1. Relative difference was determined as (GSL treatment − GSL control)/(0.5 × [GSL treatment + GSL control]). The dashed line in the middle of the plot is the overall average of the relative GSL difference between control and allyl treatment across all GSL. The thick black line in the middle of each bean for each compound is the mean response for that specific GSL trait across all the accessions. The black colored curved bean pod surrounding the observations is the theoretical probability density distribution of these observations. The small lines represent individual data points, with the length of the line proportional to the number of observations with that specific value. The relative difference between treatment and control varied across the 96 accessions from −2 to 2 for each GSL compound, depending on whether that GSL was present in the treatment compared with control.
Mentions: To measure the genetic variation in how endogenous GSL accumulation responds to exogenous allyl GSL application, we measured GSL from the 96 Arabidopsis accessions seedlings fed with allyl GSL and from the control samples (Francisco et al., 2016). These were from the same individual seedlings measured for biomass and all values are adjusted to the seedlings' biomass. This analysis detected 14 aliphatic GSL compounds and three indolic GSL compounds from which we could define an additional 15 descriptive variables to isolate specific biosynthetic processes and generate a total of 32 traits (Wentzell et al., 2007; Chan et al., 2010a). The GSL traits significantly varied between the accessions with 29 of the 32 aliphatic and indolic GSL traits showing a significant interaction of accession by allyl GSL treatment, suggesting that the accessions have differential responses to the treatment as measured by GSL accumulation (Table 3; Figure 2). In general, aliphatic GSL accumulation across the accessions tended to increase after the application of allyl GSL (Figure 1). However, like biomass accumulation, these changes in endogenous aliphatic GSL accumulation showed a wide range of both positive and negative responses across the accessions (Figure 2). Further, the positive effects were larger than could be accounted for by the additive effect of exogenous allyl GSL application. Moreover, other GSL that cannot be synthesized from the allyl GSL, such as but-3-enyl GSL were also affected by the allyl treatment showing that this is not caused by the uptake and conversion of allyl GSL to other structures (Figure 2). In contrast to the aliphatic GSL, total indolic GSL content and specific indolic GSL compounds, tended to be reduced in most accessions while a few specific accessions showed an increase (Figures 1, 2). Again, the presence of accessions showing both positive and negative responses suggests that the response to allyl GSL likely involves a number of pathways.

Bottom Line: To start developing a deeper understanding of the mechanism(s) that modulate the ability of exogenous allyl GSL to alter growth and defense, we measured changes in plant biomass and defense metabolites in a collection of natural 96 A. thaliana accessions fed with 50 μM of allyl GSL.Exogenous allyl GSL was introduced exclusively to the roots and the compound transported to the leaf leading to a wide range of heritable effects upon plant biomass and endogenous GSL accumulation.This is one of the first instances in which this approach has been successfully utilized to begin dissecting a novel phenotype to the underlying molecular/polygenic basis.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Sciences, University of California, DavisDavis, CA, USA; Group of Genetics, Breeding and Biochemistry of Brassicas, Department of Plant Genetics, Misión Biológica de Galicia, Spanish Council for Scientific ResearchPontevedra, Spain.

ABSTRACT
A key limitation in modern biology is the ability to rapidly identify genes underlying newly identified complex phenotypes. Genome wide association studies (GWAS) have become an increasingly important approach for dissecting natural variation by associating phenotypes with genotypes at a genome wide level. Recent work is showing that the Arabidopsis thaliana defense metabolite, allyl glucosinolate (GSL), may provide direct feedback regulation, linking defense metabolism outputs to the growth, and defense responses of the plant. However, there is still a need to identify genes that underlie this process. To start developing a deeper understanding of the mechanism(s) that modulate the ability of exogenous allyl GSL to alter growth and defense, we measured changes in plant biomass and defense metabolites in a collection of natural 96 A. thaliana accessions fed with 50 μM of allyl GSL. Exogenous allyl GSL was introduced exclusively to the roots and the compound transported to the leaf leading to a wide range of heritable effects upon plant biomass and endogenous GSL accumulation. Using natural variation we conducted GWAS to identify a number of new genes which potentially control allyl responses in various plant processes. This is one of the first instances in which this approach has been successfully utilized to begin dissecting a novel phenotype to the underlying molecular/polygenic basis.

No MeSH data available.


Related in: MedlinePlus