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

Jeffrey T Foster, Gerard J Allan, Agnes P. Chan, Pablo D. Rabinowicz, Jacques Ravel, Paul J. Jackson, Paul S Keim

Research output: Contribution to journalArticle

61 Citations (Scopus)

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 φ{symbol}PT 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.

Original languageEnglish (US)
Article number13
JournalBMC Plant Biology
Volume10
DOIs
StatePublished - Jan 18 2010

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castor beans
Ricinus communis
single nucleotide polymorphism
genetic variation
population genetics
population structure
cultivars
plant collections
genome assembly
genome
genotype
ornamental plants
germplasm
sampling
loci

ASJC Scopus subject areas

  • Plant Science

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Single nucleotide polymorphisms for assessing genetic diversity in castor bean (Ricinus communis). / Foster, Jeffrey T; Allan, Gerard J; Chan, Agnes P.; Rabinowicz, Pablo D.; Ravel, Jacques; Jackson, Paul J.; Keim, Paul S.

In: BMC Plant Biology, Vol. 10, 13, 18.01.2010.

Research output: Contribution to journalArticle

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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 φ{symbol}PT 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.",
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