A footprint of past climate change on the diversity and population structure of Miscanthus sinensis

Abstract

Population structure of Msi was driven by patterns of warming since the LGM, and secondarily by geographical barriers. This study will facilitate germplasm conservation, association analyses and identification of potential heterotic groups for the improvement of Miscanthus as a bioenergy crop.

Ecological characteristics andin situgenetic associations for yield-component traits of wildMiscanthusfrom eastern Russia

“…Filtering for SNPs with a minimum call rate of 0Á5 and a minimum minor allele frequency of 0Á01 produced 29 260 SNPs (Supplementary Data Dataset S2). To obtain SNP genotypes for M. sinensis, we ran the UNEAK pipeline under the same conditions on the 14 Russian M. sinensis individuals and 595 individuals from a previous study (576 M. sinensis individuals plus 19 M. sacchariflorus and hybrid individuals; Clark et al, 2014), and removed SNPs that appeared heterozygous in double haploid lines, yielding 24 132 SNPs.…”

“…Geographic distances between collection sites were calculated using the R (R Core Team, 2014) package geosphere (Hijmans, 2014). SNP data were imported in numeric (0 or 2 for homozygotes, 1 for heterozygotes) format, with individuals as rows and markers as columns ('hapMap2genlight' function;Clark et al, 2014), and genetic distances between individuals were calculated as Euclidian distances between rows using the 'dist' function in R. Correlation between the geographic and genetic distance matrices was then tested using the 'mantel.rtest' function in the R package ade4 (Chessel et al, 2004) with 999 permutations. To make a matrix of genetic distances based on plastid haplotypes, plastid microsatellite data were imported into the R package polysat (Clark and Jasieniuk, 2011) and dissimilarities were calculated with the 'meandistance.matrix' and 'Lynch.distance' functions.…”

“…Nuclear SNPs were obtained by RAD-seq (Poland et al, 2012a). Entries were also screened with ten plastid microsatellites (de Cesare et al, 2010;Jiang et al, 2012) using previously described protocols (Clark et al, 2014). Additional details are provided in Supplementary Data Materials and Methods.…”

“…Thus, a major goal of Miscanthus breeding is the production of biomass cultivars with improved cold hardiness and chillingtolerant photosynthesis. A large public gene bank for Miscanthus does not yet exist, but several academic research groups have recently imported germplasm to Europe and North America from the native range, characterized those collections with genotyping by sequencing (GBS) or restriction siteassociated DNA sequencing (RAD-seq) approaches (Slavov et al, 2013;Barth et al, 2014;Clark et al, 2014Clark et al, , 2015 and performed genome-wide association studies (GWAS) using phenotypic data from replicated field trials (Slavov et al, 2014).…”

Miscanthus: a case study for the utilization of natural genetic variation

“…Some species such as M. floridulus generally grow at sea level or in warm tropical climates, but others such as M. paniculatus can tolerate high altitudes of up to 3100 m on dry mountain slopes of Guizhou, Sichuan and Yunnan in China (Chen and Renvoize, 2006). Given such a wide native distribution, it is not surprising that Miscanthus has also become naturalized following human introduction in many regions of the world including Eurasia, North and South America, and New Zealand (Meyer et al, 2010;Quinn et al, 2010Quinn et al, , 2011Quinn et al, , 2012Barney et al, 2012;Matlaga et al, 2012;Clark et al, 2014). Clark et al (2014) used high-density single-nucleotide polymorphism (SNP) markers to show that naturalized populations of M. sinensis were derived from a subset of ornamental cultivars that were themselves derived from Southern Japan.…”