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"Missing" G x E Variation Controls Flowering Time in Arabidopsis thaliana.

Sasaki E, Zhang P, Atwell S, Meng D, Nordborg M - PLoS Genet. (2015)

Bottom Line: The SNP-based scan identified several variants that had common effects in both environments, but found no trace of G x E effects, whereas the scan using local variance components found both.Furthermore, the G x E effects appears to be concentrated in a small fraction of the genome (0.5%).Our conclusion is that G x E effects in this study are mostly due to large numbers of allele or haplotypes at a small number of loci, many of which correspond to previously identified flowering time genes.

View Article: PubMed Central - PubMed

Affiliation: Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.

ABSTRACT
Understanding how genetic variation interacts with the environment is essential for understanding adaptation. In particular, the life cycle of plants is tightly coordinated with local environmental signals through complex interactions with the genetic variation (G x E). The mechanistic basis for G x E is almost completely unknown. We collected flowering time data for 173 natural inbred lines of Arabidopsis thaliana from Sweden under two growth temperatures (10°C and 16°C), and observed massive G x E variation. To identify the genetic polymorphisms underlying this variation, we conducted genome-wide scans using both SNPs and local variance components. The SNP-based scan identified several variants that had common effects in both environments, but found no trace of G x E effects, whereas the scan using local variance components found both. Furthermore, the G x E effects appears to be concentrated in a small fraction of the genome (0.5%). Our conclusion is that G x E effects in this study are mostly due to large numbers of allele or haplotypes at a small number of loci, many of which correspond to previously identified flowering time genes.

No MeSH data available.


Manhattan plots of GWAS results for flowering time at 10°C and 16°C using MTMM.A. From top to bottom, results for full SNP, common SNP effect, and GSNP x E effect tests. B. Zoom-in on chromosome 5 peak from full SNP test. C. Zoom-in on chromosome 2 peak from common effect by SNP markers, and D. by indel markers. Orange arrows show position of the strongest association in the peak. Horizontal dashed lines show 5% genome-wide significance thresholds after Bonferroni-correction.
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pgen.1005597.g002: Manhattan plots of GWAS results for flowering time at 10°C and 16°C using MTMM.A. From top to bottom, results for full SNP, common SNP effect, and GSNP x E effect tests. B. Zoom-in on chromosome 5 peak from full SNP test. C. Zoom-in on chromosome 2 peak from common effect by SNP markers, and D. by indel markers. Orange arrows show position of the strongest association in the peak. Horizontal dashed lines show 5% genome-wide significance thresholds after Bonferroni-correction.

Mentions: The full SNP test identified two peaks with genome-wide significance (Fig 2A). The strongest association was centered around position 3,180,721 on chromosome 5, in the promoter region of the well-known flowering regulator FLOWERING LOCUS C (FLC) (Fig 2B), which has previously been shown to play a major role in natural variation for flowering time, but has generally been difficult to map using GWAS [5, 12, 13], presumably because of extensive genetic heterogeneity [18, 19]. Interestingly, the FLC peak can be seen using both the common SNP and the GSNP x E effect tests, but was significant in neither, suggest that it has a weak GSNP x E effect as well as a weak common SNP effect.


"Missing" G x E Variation Controls Flowering Time in Arabidopsis thaliana.

Sasaki E, Zhang P, Atwell S, Meng D, Nordborg M - PLoS Genet. (2015)

Manhattan plots of GWAS results for flowering time at 10°C and 16°C using MTMM.A. From top to bottom, results for full SNP, common SNP effect, and GSNP x E effect tests. B. Zoom-in on chromosome 5 peak from full SNP test. C. Zoom-in on chromosome 2 peak from common effect by SNP markers, and D. by indel markers. Orange arrows show position of the strongest association in the peak. Horizontal dashed lines show 5% genome-wide significance thresholds after Bonferroni-correction.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4608753&req=5

pgen.1005597.g002: Manhattan plots of GWAS results for flowering time at 10°C and 16°C using MTMM.A. From top to bottom, results for full SNP, common SNP effect, and GSNP x E effect tests. B. Zoom-in on chromosome 5 peak from full SNP test. C. Zoom-in on chromosome 2 peak from common effect by SNP markers, and D. by indel markers. Orange arrows show position of the strongest association in the peak. Horizontal dashed lines show 5% genome-wide significance thresholds after Bonferroni-correction.
Mentions: The full SNP test identified two peaks with genome-wide significance (Fig 2A). The strongest association was centered around position 3,180,721 on chromosome 5, in the promoter region of the well-known flowering regulator FLOWERING LOCUS C (FLC) (Fig 2B), which has previously been shown to play a major role in natural variation for flowering time, but has generally been difficult to map using GWAS [5, 12, 13], presumably because of extensive genetic heterogeneity [18, 19]. Interestingly, the FLC peak can be seen using both the common SNP and the GSNP x E effect tests, but was significant in neither, suggest that it has a weak GSNP x E effect as well as a weak common SNP effect.

Bottom Line: The SNP-based scan identified several variants that had common effects in both environments, but found no trace of G x E effects, whereas the scan using local variance components found both.Furthermore, the G x E effects appears to be concentrated in a small fraction of the genome (0.5%).Our conclusion is that G x E effects in this study are mostly due to large numbers of allele or haplotypes at a small number of loci, many of which correspond to previously identified flowering time genes.

View Article: PubMed Central - PubMed

Affiliation: Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.

ABSTRACT
Understanding how genetic variation interacts with the environment is essential for understanding adaptation. In particular, the life cycle of plants is tightly coordinated with local environmental signals through complex interactions with the genetic variation (G x E). The mechanistic basis for G x E is almost completely unknown. We collected flowering time data for 173 natural inbred lines of Arabidopsis thaliana from Sweden under two growth temperatures (10°C and 16°C), and observed massive G x E variation. To identify the genetic polymorphisms underlying this variation, we conducted genome-wide scans using both SNPs and local variance components. The SNP-based scan identified several variants that had common effects in both environments, but found no trace of G x E effects, whereas the scan using local variance components found both. Furthermore, the G x E effects appears to be concentrated in a small fraction of the genome (0.5%). Our conclusion is that G x E effects in this study are mostly due to large numbers of allele or haplotypes at a small number of loci, many of which correspond to previously identified flowering time genes.

No MeSH data available.