Limits...
"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.


Reaction norms for flowering time at 10°C and 16°C in 173 Swedish lines (plus Col-0).A. Flowering time was significantly accelerated in 51 lines (shown in magenta), significantly decelerated in 28 lines (blue), and not significantly affected in 95 lines (green). B. Histogram of the ratio of flowering times using the same color scheme as in A.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4608753&req=5

pgen.1005597.g001: Reaction norms for flowering time at 10°C and 16°C in 173 Swedish lines (plus Col-0).A. Flowering time was significantly accelerated in 51 lines (shown in magenta), significantly decelerated in 28 lines (blue), and not significantly affected in 95 lines (green). B. Histogram of the ratio of flowering times using the same color scheme as in A.

Mentions: The increase in growing temperature from 10°C to 16°C had a dramatic effect on flowering behavior, significantly accelerating flowering in 29% of the lines, significantly decelerating flowering in 16% of the lines, and generally increasing the variance both within and between lines (t-test, q-value < 0.01; Fig 1; S1–S2 Tables). Broad-sense heritabilities (H2) were extremely high (over 90%) at both temperatures (albeit significantly lower at 16°C, p < 0.01), demonstrating strong genetic effects, in agreement with published results (Table 1) [12, 16, 17]. We partitioned the variance in flowering time using a model with four components: genotype (G, the variance attributable to genome-wide relatedness), environment (E), G x E, and noise (see Methods). This analysis revealed massive G x E effects. The G x E effects are largely due to the differences in the reaction norm between the subsets in Fig 1. For example, 67.9% of the variation among lines with accelerated flowering is due to direct genetic effects (Table 2).


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

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

Reaction norms for flowering time at 10°C and 16°C in 173 Swedish lines (plus Col-0).A. Flowering time was significantly accelerated in 51 lines (shown in magenta), significantly decelerated in 28 lines (blue), and not significantly affected in 95 lines (green). B. Histogram of the ratio of flowering times using the same color scheme as in A.
© Copyright Policy
Related In: Results  -  Collection

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

pgen.1005597.g001: Reaction norms for flowering time at 10°C and 16°C in 173 Swedish lines (plus Col-0).A. Flowering time was significantly accelerated in 51 lines (shown in magenta), significantly decelerated in 28 lines (blue), and not significantly affected in 95 lines (green). B. Histogram of the ratio of flowering times using the same color scheme as in A.
Mentions: The increase in growing temperature from 10°C to 16°C had a dramatic effect on flowering behavior, significantly accelerating flowering in 29% of the lines, significantly decelerating flowering in 16% of the lines, and generally increasing the variance both within and between lines (t-test, q-value < 0.01; Fig 1; S1–S2 Tables). Broad-sense heritabilities (H2) were extremely high (over 90%) at both temperatures (albeit significantly lower at 16°C, p < 0.01), demonstrating strong genetic effects, in agreement with published results (Table 1) [12, 16, 17]. We partitioned the variance in flowering time using a model with four components: genotype (G, the variance attributable to genome-wide relatedness), environment (E), G x E, and noise (see Methods). This analysis revealed massive G x E effects. The G x E effects are largely due to the differences in the reaction norm between the subsets in Fig 1. For example, 67.9% of the variation among lines with accelerated flowering is due to direct genetic effects (Table 2).

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.