Genetic description of the sorghum accession panel
To visualize the global origin of various sorghum genotypes andStriga range, we utilized the Geographical Positioning System
(GPS) coordinates available at https://www.genesys-pgr.org/ and
https://www.pnas.org/content/117/8/4243/tab-figure-data
(Dataset_S03) and Dataset_S1 to construct distribution maps using the
MapTool (Lemmond 1994) version 2 package in R. We then obtained Single
Nucleotide Polymorphism (SNP) data (Morris et al. 2013) from the
repository of Colorado State University available at
https://www.morislab.org/data. These polymorphisms were used to
determine the genetic structure of the SAP using phylogenetic
relationships, Bayesian-based clustering, and discriminant analysis of
principle components (DAPC). To infer phylogenetic relationships of
sorghum accessions, we first converted the SNP Hapmap file to a Variant
Calling File (VCF) using Trait Analysis by aSSociation, Evolution and
Linkage (TASSEL) version 5.0 (Bradbury et al. 2007). The
resulting file was subsequently used to construct a neighbor-joining
(NJ) tree using the Analyses of Phylogenetics and Evolution (APE)
package in R (Paradis, Claude & Strimmer 2004). For Bayesian
clustering, we used ADMIXTURE in plink (Alexander, Novembre & Lange
2009) by first converting the SNP data in Hapmap format into plink
format TASSEL. The resulting file was used to determine clusters of the
population through analysis of K values from 1 to 10 with a burn-in
period of 50,000 iterations and 500,000 Markov Chain Monte Carlo (MCMC)
iterations by assuming the admixture model. The most likely number of
clusters were determined from the K value with the least cross
validation error. Admixture plots were then visualized using the ggplot2
function in R (Villanueva & Chen 2019). Calculation of principal
components was done using Adegenet R package (Jombart 2008) and
factoextra in R.