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

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

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

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

Conservation implications of the introduction history of meadow fescue (<i>Festuca pratensis</i> Huds.) to the Driftless Area of the Upper Mississippi Valley, USA

<div><p><b><i>Background:</i></b> Meadow fescue (<i>Festuca pratensis</i>) is an important cold climate pasture grass that faces pressures from climate and land use change, competitive pressure and limited genetic diversity at the species level. Naturalised populations in the Driftless Area of the American Midwest may be beneficial for the conservation and agronomic improvement of the species.</p><p><b><i>Aims:</i></b> We explored the population structure and genetic diversity of Driftless Area meadow fescue populations, inferring their introduction histories to evaluate their potential contribution to conservation and breeding.</p><p><b><i>Methods:</i></b> We assigned plants sampled from 71 grasslands throughout the Driftless Area to genetically defined subpopulations based on neutral nuclear (nSSR) markers. Inter-population hybridisation and genetic diversity were combined with chloroplast haplotype scoring to infer introduction history.</p><p><b><i>Results:</i></b> We identified four subpopulations with distinct geographic distributions and haplotype composition, with 28% of sampled individuals representing admixtures of two or more subpopulations. There was moderate differentiation among subpopulations and sampling sites, with nonetheless high within-site diversity. Three chloroplast haplotypes were detected, occurring in different frequencies among subpopulations. Subpopulations appeared to have been derived from separate introductions of heterogeneous genetic material.</p><p><b><i>Conclusions:</i></b> Driftless Area meadow fescue populations are unlikely to contribute to conservation of locally adapted European varieties, but represent a valuable resource for the development of novel varieties and for preserving species-level genetic diversity.</p></div

Sample Metadata

Metadata for the samples. Includes sample name, population, ploidy, phenotype, sequencing read count, and inferred gene pool

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

Barcode Information for Sequencing Libraries

Example of a tab-delimited table containing the information to connect barcodes to samples in different sequencing libraries. This can be used in conjunction with the R functions to de-multiplex the raw data

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