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Single nucleotide polymorphisms for assessing genetic diversity in castor bean (Ricinus communis)

Foster, Jeffrey T. and Allan, Gerard J. and Chan, Agnes P. and Rabinowicz, Pablo D. and Ravel, Jacques and Jackson, Paul J. and Keim, Paul (2010) Single nucleotide polymorphisms for assessing genetic diversity in castor bean (Ricinus communis). BMC Plant Biology, 10 (13). ISSN 1471-2229

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Publisher’s or external URL: http://dx.doi.org/10.1186/1471-2229-10-13


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 ϕPT values, p < 0.01). Conclusion: 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.

Item Type: Article
ID number or DOI: 10.1186/1471-2229-10-13
Keywords: America; angiosperms; APEC countries; Bayes Theorem; Biological Resources; Botany; Castor Bean; Castor beans; cluster analysis; Comparative Genomic Hybridization; cultivars; cultivated varieties; Developed Countries; dicotyledons; DNA, Plant; eukaryotes; Euphorbiaceae; Euphorbiales; Field Crops; Florida; General Molecular Biology; Genes; genetic analysis; genetic diversity; genetic polymorphisms; Genetics, Population; genetic variability; genetic variance; Genetic variation; genome; Genome, Plant; genomes; genotype; genotypic variability; genotypic variation; Geography; germplasm; Gulf States of USA; individuals; inferences; invasive plant; loci; North America; number; OECD Countries; oilseeds; Plant Breeding and Genetics ; plants; Polymorphism, Single Nucleotide; Population genetics; population-structure; program; Ricinus; Ricinus communis; Sequence Analysis, DNA; single nucleotide polymorphism; South Atlantic States of USA; Southeastern States of USA; Southern States of USA; Spermatophyta; United States of America; USA
Subjects: Q Science > QH Natural history > QH301 Biology
Q Science > QH Natural history > QH426 Genetics
NAU Depositing Author Academic Status: Faculty/Staff
Department/Unit: College of Engineering, Forestry, and Natural Science > Biological Sciences
Research Centers > Center for Microbial Genetics and Genomics
Date Deposited: 30 Sep 2015 19:36
URI: http://openknowledge.nau.edu/id/eprint/468

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