Additional file 1: of Natural variation in genes potentially involved in plant architecture and adaptation in switchgrass (Panicum virgatum L.)
Creators: name: Bochra Bahri
name: Daverdin, Guillaume
name: Xiangyang Xu
name: Jan-Fang Cheng
name: Barry, Kerrie
name: E. Brummer
name: Devos, Katrien
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: FOS: Health sciences
subject: Plant Biology

description: Table S1. List of switchgrass accessions used in the study with their ID and name, number of genotypes, ecotype identification, ploidy level, state of origin, and GPS coordinates [114–116]. Table S2. Sequences and annealing temperatures of the 33 primer pairs used for PCR amplification of the selected 12 genes. Conserved regions in orthologous exons in Oryza sativa (rice), Sorghum bicolor (sorghum), Zea mays (maize) and Setaria italica (foxtail millet) were used for primer design. Table S3. Sequences of 56 regions of AP13 extracted from the Phytozome database ( http://www.phytozome.net/ ), and used as reference for read mapping and SNP identification. Table S4. Number of amplicon reads mapped to each of the 56 reference switchgrass contigs. Table S5. Summary statistics for the non-synonymous SNPs analyzed in 12 biomass genes. Table S6. Genic regions for which the SNP distribution is different in the K and N subgenomes. The percentage of SNPs and the region in which they are located are given for each subgenome. Table S7. Tajima’s, and Fu and Li’s tests on a per gene basis within each subpopulation. Figure S1. Distance between SNPs. Figure S2. Log probability of data as a function of K. STRUCTURE was run for K ranging from 1 to 10, and 10 repetitions were performed with 100,000 burn-ins and 100,000 runs. K = 3 clusters were retained as the most likely number of genetic clusters in the switchgrass panel analyzed. Figure S3. UPGMA tree performed on the 251 SNPs across the 372 genotypes with a 500 replicates bootstrap test using Mega 6 [60] based on the maximum composite likelihood method. C1, C2 and C3 clusters are colored in blue, green and red respectively; admixed individuals are in gray. Figure S4. Local Indicator of Spatial Autocorrelation Analysis (2D-LSA) on 372 genotypes. Individuals that are consistently significantly more related to their 7 to 14 nearest neighbors than to random individuals are represented as plain blue dots. The number of genotypes is given in parenthesis. Accessions with significant P values for more than 90% of the genotypes are listed; their subpopulation and number of genotypes are indicated. USA Map source: https://upload.wikimedia.org/wikipedia/commons/c/ca/Blank_US_map_borders.svg . Figure S5. Regression analysis of the percentage of polymorphic loci and latitude bins across the switchgrass accessions. Figure S6. Protein structure modeling of an amino acid substitution in the PAS domain of 1D06, a protein with similar PAS domain as PHYB (A) Original structure of protein 1D06; (B) modified structure after two amino-acid changes in the PAS domain (in yellow): one conservative substitution (Val - &gt; Ile; in green) and one non-conservative substitution (Asp - &gt; Tyr; in pink). Swiss-Pdb Viewer 4.1.0 [70] was used to visualize the crystal structure. (PDF 1034 kb)