title: Single nucleotide polymorphisms for assessing genetic diversity in castor bean (Ricinus communis).
abstract: BACKGROUND
  Castor bean (Ricinus communis) is an agricultural crop and garden ornamental that is widely cultivated and has been introduced worldwide. Understanding population structure and the distribution of castor bean cultivars has been challenging because of limited genetic variability. We analyzed the population genetics of R. communis in a worldwide collection of plants from germplasm and from naturalized populations in Florida, U.S. To assess genetic diversity we conducted survey sequencing of the genomes of seven diverse cultivars and compared the data to a reference genome assembly of a widespread cultivar (Hale). We determined the population genetic structure of 676 samples using single nucleotide polymorphisms (SNPs) at 48 loci.
  
  
  RESULTS
  Bayesian clustering indicated five main groups worldwide and a repeated pattern of mixed genotypes in most countries. High levels of population differentiation occurred between most populations but this structure was not geographically based. Most molecular variance occurred within populations (74%) followed by 22% among populations, and 4% among continents. Samples from naturalized populations in Florida indicated significant population structuring consistent with local demes. There was significant population differentiation for 56 of 78 comparisons in Florida (pairwise population phiPT values, p < 0.01).
  
  
  CONCLUSIONS
  Low levels of genetic diversity and mixing of genotypes have led to minimal geographic structuring of castor bean populations worldwide. Relatively few lineages occur and these are widely distributed. Our approach of determining population genetic structure using SNPs from genome-wide comparisons constitutes a framework for high-throughput analyses of genetic diversity in plants, particularly in species with limited genetic diversity.
authors.affiliation: Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA.
authors.forename: Jeffrey T
authors.initials: JT
authors.lastname: Foster
authors.forename: Gerard J
authors.initials: GJ
authors.lastname: Allan
authors.forename: Agnes P
authors.initials: AP
authors.lastname: Chan
authors.forename: Pablo D
authors.initials: PD
authors.lastname: Rabinowicz
authors.forename: Jacques
authors.initials: J
authors.lastname: Ravel
authors.forename: Paul J
authors.initials: PJ
authors.lastname: Jackson
authors.forename: Paul
authors.initials: P
authors.lastname: Keim
mesh_terms: D001499:Bayes Theorem; D002367:Ricinus communis / Q000235:genetics*; D016000:Cluster Analysis; D055028:Comparative Genomic Hybridization; D018744:DNA, Plant / Q000235:genetics; D005828:Genetics, Population; D018745:Genome, Plant; D005838:Genotype; D005843:Geography; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant