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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

Overlap of significant GWA candidate genes between control (MS) and treated samples with 50 μM of allyl GSL (MS + Allyl GSL). VENN diagram showing common candidate genes identified among the plant biomass, short-chain GSLs, long-chain GSLs, total aliphatic GSLs, total incolic GSLs, and total GSLs traits.
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Figure 4: Overlap of significant GWA candidate genes between control (MS) and treated samples with 50 μM of allyl GSL (MS + Allyl GSL). VENN diagram showing common candidate genes identified among the plant biomass, short-chain GSLs, long-chain GSLs, total aliphatic GSLs, total incolic GSLs, and total GSLs traits.

Mentions: To map genes that influence the variation in endogenous GSL responses to exogenous allyl GSL, we focused on five GSL phenotypes that are present in all accessions, the total amount of long-chain GSLs, total short-chain GSLs, total aliphatic GSLs, total indolic GSLs and the sum of all GSLs (Kliebenstein et al., 2001b,c, 2002; Wentzell et al., 2007; Chan et al., 2010a, 2011). The accumulation of individual GSLs is heavily dependent on presence/absence variation of known GSL enzyme loci leading to presence/absence variation in these compounds and confounds the GWAS mapping. In contrast, these summation based traits are measurable in all accessions and are largely independent of the known major effect GSL polymorphisms as shown by previous GWAS analysis (Kliebenstein et al., 2001b,c, 2002; Wentzell et al., 2007; Chan et al., 2010a, 2011). This increases our power to identify causal genes both by having data for all accessions and by eliminating major effect polymorphisms that can otherwise hinder the power to identify smaller effect loci (Nordborg and Weigel, 2008). Given the quantitative distribution of GSL responses to exogenous allyl treatment, we expected mainly small to moderate effect loci (Figure 3). GWAS with these traits identified on average 2750 genes significantly associated with any given trait (Tables S2, S3). Of these candidate genes, 36% were typically found with the treated samples, 43% with the control treatment and 21% under both conditions (Figure 4). Interestingly, this contrasts with biomass accumulation where only 5% of the genes were found under both conditions. A survey of these genes by either GO analysis or by co-expression network clustering did not identify any obvious mechanistic patterns.


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)

Overlap of significant GWA candidate genes between control (MS) and treated samples with 50 μM of allyl GSL (MS + Allyl GSL). VENN diagram showing common candidate genes identified among the plant biomass, short-chain GSLs, long-chain GSLs, total aliphatic GSLs, total incolic GSLs, and total GSLs traits.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4940622&req=5

Figure 4: Overlap of significant GWA candidate genes between control (MS) and treated samples with 50 μM of allyl GSL (MS + Allyl GSL). VENN diagram showing common candidate genes identified among the plant biomass, short-chain GSLs, long-chain GSLs, total aliphatic GSLs, total incolic GSLs, and total GSLs traits.
Mentions: To map genes that influence the variation in endogenous GSL responses to exogenous allyl GSL, we focused on five GSL phenotypes that are present in all accessions, the total amount of long-chain GSLs, total short-chain GSLs, total aliphatic GSLs, total indolic GSLs and the sum of all GSLs (Kliebenstein et al., 2001b,c, 2002; Wentzell et al., 2007; Chan et al., 2010a, 2011). The accumulation of individual GSLs is heavily dependent on presence/absence variation of known GSL enzyme loci leading to presence/absence variation in these compounds and confounds the GWAS mapping. In contrast, these summation based traits are measurable in all accessions and are largely independent of the known major effect GSL polymorphisms as shown by previous GWAS analysis (Kliebenstein et al., 2001b,c, 2002; Wentzell et al., 2007; Chan et al., 2010a, 2011). This increases our power to identify causal genes both by having data for all accessions and by eliminating major effect polymorphisms that can otherwise hinder the power to identify smaller effect loci (Nordborg and Weigel, 2008). Given the quantitative distribution of GSL responses to exogenous allyl treatment, we expected mainly small to moderate effect loci (Figure 3). GWAS with these traits identified on average 2750 genes significantly associated with any given trait (Tables S2, S3). Of these candidate genes, 36% were typically found with the treated samples, 43% with the control treatment and 21% under both conditions (Figure 4). Interestingly, this contrasts with biomass accumulation where only 5% of the genes were found under both conditions. A survey of these genes by either GO analysis or by co-expression network clustering did not identify any obvious mechanistic patterns.

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