Selection Signatures in Four Lignin Genes from Switchgrass Populations Divergently Selected for <i>In Vitro</i> Dry Matter Digestibility

<div><p>Switchgrass is undergoing development as a dedicated cellulosic bioenergy crop. Fermentation of lignocellulosic biomass to ethanol in a bioenergy system or to volatile fatty acids in a livestock production system is strongly and negatively influenced by lignification of cell walls. This study detects specific loci that exhibit selection signatures across switchgrass breeding populations that differ in <i>in vitro</i> dry matter digestibility (IVDMD), ethanol yield, and lignin concentration. Allele frequency changes in candidate genes were used to detect loci under selection. Out of the 183 polymorphisms identified in the four candidate genes, twenty-five loci in the intron regions and four loci in coding regions were found to display a selection signature. All loci in the coding regions are synonymous substitutions. Selection in both directions were observed on polymorphisms that appeared to be under selection. Genetic diversity and linkage disequilibrium within the candidate genes were low. The recurrent divergent selection caused excessive moderate allele frequencies in the cycle 3 reduced lignin population as compared to the base population. This study provides valuable insight on genetic changes occurring in short-term selection in the polyploid populations, and discovered potential markers for breeding switchgrass with improved biomass quality.</p></div

Distribution of simulated allele frequency change between C-1 and C+3 for an initial allele frequency in C0 of 0.15 at locus 246 of COMT1 gene.

<p>The red arrow indicates the observed change in allele frequency between cycles C-1 and C+3. The lines indicate the Benjamini-Hochberg-adjusted confidence intervals of allele frequency change with one-tailed test with α = 0.05.</p

Genetic diversity and LD in each of the four candidate genes.

<p>Different nucleotide diversity was estimated using SNPs within the whole gene, π, nonsynonymous SNP sites, π(nonsyn), synonymous SNP sites, π(syn), and the silent SNP sites including both synonymous and non-coding sites, π(s). The results of haplotype and LD analysis include number of haplotypes (H), haplotype diversities (Hd), the number of haplotypes with proportions higher than 0.05 (H>0.05), mean of pairwise LD (LD mean) and the half LD decay distance (LD decay).</p

Slope (change in allele frequency per cycle of selection) and fit of the linear regressions (r²) for the polymorphisms with significant allele frequency change across the selection cycles.

<p>Plus signs represent polymorphisms with P≤0.05, and open circles represent polymorphisms with P>0.05.</p

Changes in allele frequency between divergent breeding populations C-1 and C+3 for COMT1, COMT2, CAD2 and 4CL1 in switchgrass.

<p>The data points are observed allele frequency changes plotted on the initial allele frequencies from C0. The dotted lines indicated the Benjamini-Hochberg-adjusted confidence intervals (CI) (α = 0.05) of allele frequency changes using the 10,000-simulation data. Data points inside the CI are deemed due to drift, while those outside the CI (shown in red color) are deemed candidates for selection.</p

The heatmaps of pairwise LD of the polymorphisms in the four candidate genes.

<p>The blue stars indicate the significant loci under selection.</p

Histograms of allele frequency on all 183 polymorphisms undergone statistic tests in C0 and C+3 populations.

<p>Histograms of allele frequency on all 183 polymorphisms undergone statistic tests in C0 and C+3 populations.</p

Total number of polymorphisms for the four candidate genes in switchgrass divergent populations.

<p>Total number of polymorphisms for the four candidate genes in switchgrass divergent populations.</p

Expression of maize glutathione-S-transferase genes (ZmGST) and maize germin-like proteins (ZmGLP) in tissue culture.^a

a<p>Fragments per kilobase of exon per million fragments mapped (FPKM) at 0, 24, 36, 48, and 72 h after placement on tissue culture initiation medium, genes with an 8-fold change in expression or greater as compared to the 0 h time point, and the assigned gene cluster designated by k-means analysis.</p><p>Expression of maize glutathione-S-transferase genes (ZmGST) and maize germin-like proteins (ZmGLP) in tissue culture.^{<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111407#nt102" target="_blank">a</a>}</p

Gene expression changes in early somatic embryogenesis.

<p>Scatter plots of gene expression changes as log2 values of fragments per kilobase of exon model per million fragments mapped (FPKM) in immature zygotic embryo explants of maize inbred line A188 after placement on culture initiation medium for each time point comparison at 0, 24, 36, 48, and 72 h where n is the number of genes differentially expressed greater than 8-fold for each time point comparison. Red dots represent genes that are up-regulated, blue dots represent genes that are down-regulated, the middle green line indicates no fold change in expression, the two outer green lines indicate a 2-fold change in expression, and the solid black line is the best fit linear correlation.</p