学会抄録

Genetic map file of consensus genotypes for each contig

Genotyping data from 246 loci

The file contains the SNP genotyping data for all loci used in McAssey et al., 2016 BMC Plant Biology. The first tab contains the data where rows contain individuals and every two columns represent the diploid genotype. The second tab contains the identity of the polymorphic nucleotides at each locus. The third tab contains the marker names as described in Bachlava et al., 2012 PLoS ONE

Connectivity in gene coexpression networks negatively correlates with rates of molecular evolution in flowering plants

<div><p>Gene coexpression networks are a useful tool for summarizing transcriptomic data and providing insight into patterns of gene regulation in a variety of species. Though there has been considerable interest in studying the evolution of network topology across species, less attention has been paid to the relationship between network position and patterns of molecular evolution. Here, we generated coexpression networks from publicly available expression data for seven flowering plant taxa (<i>Arabidopsis thaliana</i>, <i>Glycine max</i>, <i>Oryza sativa</i>, <i>Populus</i> spp., <i>Solanum lycopersicum</i>, <i>Vitis</i> spp., and <i>Zea mays</i>) to investigate the relationship between network position and rates of molecular evolution. We found a significant negative correlation between network connectivity and rates of molecular evolution, with more highly connected (i.e., “hub”) genes having significantly lower nonsynonymous substitution rates and <i>dN</i>/<i>dS</i> ratios compared to less highly connected (i.e., “peripheral”) genes across the taxa surveyed. These findings suggest that more centrally located hub genes are, on average, subject to higher levels of evolutionary constraint than are genes located on the periphery of gene coexpression networks. The consistency of this result across disparate taxa suggests that it holds for flowering plants in general, as opposed to being a species-specific phenomenon.</p></div

Simplified representation of a hypothetical coexpression network.

<p>Node A represents a hub gene while node B represents a peripheral gene. Lines connecting nodes represent network edges, and reflect correlations in expression.</p

Genetic diversity (Watterson's θ [37]) in wild (blue), landrace (red), and improved (green) sunflower for 7 presumptively neutral genes (averaged), 13 putative domestication genes, and 14 putative improvement genes.

<p>Genetic diversity (Watterson's θ <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071941#pone.0071941-Watterson1" target="_blank">[37]</a>) in wild (blue), landrace (red), and improved (green) sunflower for 7 presumptively neutral genes (averaged), 13 putative domestication genes, and 14 putative improvement genes.</p

Genetic diversity (Watterson's θ [37]) for seven neutral genes (N), 13 putative domestication genes (D), and 14 putative improvement genes (I) sampled from wild (Wild), landrace (Land) and improved (Imp) sunflower populations.

<p>Six previously analysed genes are indicated by ¶. <i>P</i>-values are given for the results of the ML-HKA test for each candidate gene in each of the three populations. * Significant at <i>P</i>≤0.1,**<i>P</i>≤0.05. Comparisons that remained significant after false discovery rate correction are indicated in bold (FDR <0.05) and underlined (0.05< FDR <0.1).</p

Average (± SE) genetic diversity (Watterson's θ [37]) in wild, landrace, and improved sunflower based on the sequencing of presumptively neutral genes as well as the candidates for selectively-important genes.

<p>Average (± SE) genetic diversity (Watterson's θ <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071941#pone.0071941-Watterson1" target="_blank">[37]</a>) in wild, landrace, and improved sunflower based on the sequencing of presumptively neutral genes as well as the candidates for selectively-important genes.</p

Linear regression of gene connectivity of seven taxa analyzed.

<p>Taxa: <i>A</i>. <i>thaliana</i>, <i>G</i>. <i>max</i>, <i>Populus spp</i>., <i>S</i>. <i>lycopersicum</i>, <i>Vitis spp</i>., <i>O</i>. <i>sativa</i>, and <i>Z</i>. <i>mays</i>, against (a): non-synonymous substitutions (<i>dN</i>), (b): synonymous substitutions (<i>dS</i>), (c): estimates of adaptive evolution (ω = <i>dN</i>/<i>dS</i>) and (d): number of connections in ortholog comparison. Circles represent genes, while the regression coefficient, represented as Kendall's tau (τ) coefficient, is the dashed line. Significance is indicated by bold text. Note that all significant results except the two marked with an asterisk (*) remained significant after correcting for multiple comparisons (see text for details).</p

Phenotypic selection analyses.

<p>Results summary of aster model comparisons and 95% selection gradient (β) confidence intervals for morphological, reproductive, and physiological characteristics in sunflower recombinant inbred line (RIL) cultivar (cmsHA89) x wild (ann1238) hybrids grown under control (CW) and low (LW) water treatments. Sub-models (d.f. = 12), each omitting one trait, were compared to the full model (d.f. = 13). Likelihood ratio test deviance and χ² test <i>P</i>-values are shown.</p

Quantitative trait loci (QTL) mapping results.

<p>Quantitative trait loci (QTL) composite interval mapping results in sunflower recombinant inbred line (RIL) cultivar (cmsHA89) x wild (ann1238) hybrid populations grown under control (CW) and low (LW) water treatments. Columns 2 and 3 list the linkage group (LG) and left-flanking marker for each QTL. Columns 4–6 and 7–9 indicate the logarithm of odds (2-LOD) support thresholds in cM, the standardized additive effect (α) of the crop-derived allele (cmsHA89), and the percent variance (PVE) explained by each QTL in the CW and LW treatments, respectively. If QTL colocalize with those detected in prior studies using the same RIL population, they are coded as B02 (Burke et al. 2002b), B08 (Baack et al. 2008), and D09 (Dechaine et al. 2009); –L indicates that QTL were detected on the same LG but not overlapping and NA specifies that the characteristic was not measured in previous studies.</p