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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

Manhattan plots of GWAS results. Genome wide distribution of the absolute value of the heteroscedastic SNP effects. Shades of gray represent nonsignificant SNP effects. Blue points represent significant SNP effects under control (MS) and allyl treatment (MS + Allyl). (A) Plant Biomass, (B) Short-Chain GSLs, (C) Long-Chain GSLs, (D) Aliphatic GSLs, (E) Indolic GSLs.
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Figure 3: Manhattan plots of GWAS results. Genome wide distribution of the absolute value of the heteroscedastic SNP effects. Shades of gray represent nonsignificant SNP effects. Blue points represent significant SNP effects under control (MS) and allyl treatment (MS + Allyl). (A) Plant Biomass, (B) Short-Chain GSLs, (C) Long-Chain GSLs, (D) Aliphatic GSLs, (E) Indolic GSLs.

Mentions: To identify genes within Arabidopsis that may control the biomass or GSL accumulation responses to exogenous allyl GSL treatment, we utilized the mean biomass and GSL accumulation in each accession grown with or without allyl GSL to conduct GWA mapping (Figure 3). For these analysis we employed a ridge-regression model that treats all SNPs as random effects (Shen et al., 2013). Using this ridge-regression model we tested all traits for significance associations across 115,301 SNPs with a MAF > 0.2 that covered 19,352 unique genes. Significance thresholds were determined by measuring the 95th percentile of the randomly generated effects of 1000 permutations of the means among the accessions (Chan et al., 2011; Corwin et al., 2016). This permutation threshold, while conservative, allows us to utilize an empirically derived threshold for significance based on the specific phenotypes distribution. We then applied a filter to these SNP lists to find candidate genes by requiring a gene to be considered as a potential GWA candidate only if it has two or more significant SNPs. This approach has previously been shown to identify genes with a high validation success rate for an array of traits (Chan et al., 2011; Corwin et al., 2016). Using this approach we identified 671 genes significantly associated with biomass accumulation with the majority found uniquely in either the control (203) or allyl treated accessions (435) (Tables S2, S3). Only 33 genes were significant GWA candidates using biomass in the presence and absence of allyl GSL. A survey of these genes by either GO analysis or by co-expression network clustering using ATTED-II (Obayashi et al., 2009), did not identify any obvious enrichment 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)

Manhattan plots of GWAS results. Genome wide distribution of the absolute value of the heteroscedastic SNP effects. Shades of gray represent nonsignificant SNP effects. Blue points represent significant SNP effects under control (MS) and allyl treatment (MS + Allyl). (A) Plant Biomass, (B) Short-Chain GSLs, (C) Long-Chain GSLs, (D) Aliphatic GSLs, (E) Indolic GSLs.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 3: Manhattan plots of GWAS results. Genome wide distribution of the absolute value of the heteroscedastic SNP effects. Shades of gray represent nonsignificant SNP effects. Blue points represent significant SNP effects under control (MS) and allyl treatment (MS + Allyl). (A) Plant Biomass, (B) Short-Chain GSLs, (C) Long-Chain GSLs, (D) Aliphatic GSLs, (E) Indolic GSLs.
Mentions: To identify genes within Arabidopsis that may control the biomass or GSL accumulation responses to exogenous allyl GSL treatment, we utilized the mean biomass and GSL accumulation in each accession grown with or without allyl GSL to conduct GWA mapping (Figure 3). For these analysis we employed a ridge-regression model that treats all SNPs as random effects (Shen et al., 2013). Using this ridge-regression model we tested all traits for significance associations across 115,301 SNPs with a MAF > 0.2 that covered 19,352 unique genes. Significance thresholds were determined by measuring the 95th percentile of the randomly generated effects of 1000 permutations of the means among the accessions (Chan et al., 2011; Corwin et al., 2016). This permutation threshold, while conservative, allows us to utilize an empirically derived threshold for significance based on the specific phenotypes distribution. We then applied a filter to these SNP lists to find candidate genes by requiring a gene to be considered as a potential GWA candidate only if it has two or more significant SNPs. This approach has previously been shown to identify genes with a high validation success rate for an array of traits (Chan et al., 2011; Corwin et al., 2016). Using this approach we identified 671 genes significantly associated with biomass accumulation with the majority found uniquely in either the control (203) or allyl treated accessions (435) (Tables S2, S3). Only 33 genes were significant GWA candidates using biomass in the presence and absence of allyl GSL. A survey of these genes by either GO analysis or by co-expression network clustering using ATTED-II (Obayashi et al., 2009), did not identify any obvious enrichment 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