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

doi:10.1186/1471-2229-10-13

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

Journal Article · Sun Jan 17 23:00:00 EST 2010 · BMC Plant Biology

DOI:https://doi.org/10.1186/1471-2229-10-13· OSTI ID:1626501

Foster, Jeffrey T. ^[1]; Allan, Gerard J. ^[2]; Chan, Agnes P. ^[3]; Rabinowicz, Pablo D. ^[4]; Ravel, Jacques ^[5]; Jackson, Paul J. ^[6]; Keim, Paul ^[7]

Northern Arizona Univ., Flagstaff, AZ (United States). Center for Microbial Genetics and Genomics; DOE/OSTI
Northern Arizona Univ., Flagstaff, AZ (United States). Dept. of Biological Sciences. Environmental Genetics and Genomics Lab.
J. Craig Venter Inst., Inc., Rockville, MD (United States)
J. Craig Venter Inst., Inc., Rockville, MD (United States); Univ. of Maryland Baltimore County (UMBC), Baltimore, MD (United States). School of Medicine. Inst. for Genome Sciences; Univ. of Maryland Baltimore County (UMBC), Baltimore, MD (United States). School of Medicine. Dept. of Biochemistry Molecular Biology
J. Craig Venter Inst., Inc., Rockville, MD (United States); Univ. of Maryland Baltimore County (UMBC), Baltimore, MD (United States). School of Medicine. Inst. for Genome Sciences; Univ. of Maryland Baltimore County (UMBC), Baltimore, MD (United States). School of Medicine. Dept. of Microbiology Immunology
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Defense Biology Division
Northern Arizona Univ., Flagstaff, AZ (United States). Center for Microbial Genetics and Genomics

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_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.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC52-07NA27344

OSTI ID:: 1626501

Journal Information:: BMC Plant Biology, Journal Name: BMC Plant Biology Journal Issue: 1 Vol. 10; ISSN 1471-2229

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

References (40)

Genetic Variation in Lathyrus Latifolius (Leguminosae) Godt, Mary Jo W.; Hamrick, J. L. American Journal of Botany, Vol. 78, Issue 9 https://doi.org/10.1002/j.1537-2197.1991.tb11409.x	journal	September 1991
Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome Rabinowicz, Pablo D.; Schutz, Kristin; Dedhia, Neilay Nature Genetics, Vol. 23, Issue 3 https://doi.org/10.1038/15479	journal	November 1999
Genetic variation in Bromus tectorum (Poaceae): comparison between native and introduced populations Novak, Stephen J.; Mack, Richard N. Heredity, Vol. 71, Issue 2 https://doi.org/10.1038/hdy.1993.121	journal	August 1993
Comparison of allozyme variability in a native and an introduced species of Lonicera Schierenbeck, Kristina A.; Hamrick, J. L.; Mack, Richard N. Heredity, Vol. 75, Issue 1 https://doi.org/10.1038/hdy.1995.97	journal	July 1995
SSR individual identification system construction and population genetics analysis for Chamaecyparis formosensis Huang, Chiun-Jr; Chu, Fang-Hua; Huang, Yi-Shiang Scientific Reports, Vol. 12, Issue 1 https://doi.org/10.1038/s41598-022-07870-5	journal	March 2022
Progress in high throughput SNP genotyping methods Tsuchihashi, Z.; Dracopoli, N. C. The Pharmacogenomics Journal, Vol. 2, Issue 2 https://doi.org/10.1038/sj.tpj.6500094	journal	February 2002
distruct: a program for the graphical display of population structure: PROGRAM NOTE Rosenberg, Noah A. Molecular Ecology Notes, Vol. 4, Issue 1 https://doi.org/10.1046/j.1471-8286.2003.00566.x	journal	December 2003
Impacts of genetic bottlenecks on soybean genome diversity Hyten, D. L.; Song, Q.; Zhu, Y. Proceedings of the National Academy of Sciences, Vol. 103, Issue 45 https://doi.org/10.1073/pnas.0604379103	journal	October 2006
Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.) Tenaillon, M. I.; Sawkins, M. C.; Long, A. D. Proceedings of the National Academy of Sciences, Vol. 98, Issue 16 https://doi.org/10.1073/pnas.151244298	journal	July 2001
Genetic Variation and Molecular Biogeography of a North American Invasive Plant Species (Alliaria petiolata, Brassicaceae) Meekins, J. F.; Ballard, Jr., H. E.; McCarthy, B. C. International Journal of Plant Sciences, Vol. 162, Issue 1 https://doi.org/10.1086/317903	journal	January 2001
The Discovery of Single-Nucleotide Polymorphisms—and Inferences about Human Demographic History Wakeley, John; Nielsen, Rasmus; Liu-Cordero, Shau Neen The American Journal of Human Genetics, Vol. 69, Issue 6 https://doi.org/10.1086/324521	journal	December 2001
Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Excoffier, L.; Smouse, P. E.; Quattro, J. M. Genetics, Vol. 131, Issue 2 https://doi.org/10.1093/genetics/131.2.479	journal	June 1992
Estimation of Population Parameters and Recombination Rates From Single Nucleotide Polymorphisms Nielsen, Rasmus Genetics, Vol. 154, Issue 2 https://doi.org/10.1093/genetics/154.2.931	journal	February 2000
Inference of Population Structure Using Multilocus Genotype Data Pritchard, Jonathan K.; Stephens, Matthew; Donnelly, Peter Genetics, Vol. 155, Issue 2 https://doi.org/10.1093/genetics/155.2.945	journal	June 2000
Fast algorithms for large-scale genome alignment and comparison Delcher, A. L. Nucleic Acids Research, Vol. 30, Issue 11 https://doi.org/10.1093/nar/30.11.2478	journal	June 2002
The Origin, Variation, Immunity and Breeding of Cultivated Plants Vavilov, N. I. Soil Science, Vol. 72, Issue 6 https://doi.org/10.1097/00010694-195112000-00018	journal	December 1951
Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy Assessment Ewing, Brent; Hillier, LaDeana; Wendl, Michael C. Genome Research, Vol. 8, Issue 3 https://doi.org/10.1101/gr.8.3.175	journal	March 1998
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities Ewing, Brent; Green, Phil Genome Research, Vol. 8, Issue 3 https://doi.org/10.1101/gr.8.3.186	journal	March 1998
Detecting the number of clusters of individuals using the software structure: a simulation study Evanno, G.; Regnaut, S.; Goudet, J. Molecular Ecology, Vol. 14, Issue 8 https://doi.org/10.1111/j.1365-294x.2005.02553.x	journal	July 2005
genalex 6: genetic analysis in Excel. Population genetic software for teaching and research Peakall, Rod; Smouse, Peter E. Molecular Ecology Notes, Vol. 6, Issue 1 https://doi.org/10.1111/j.1471-8286.2005.01155.x	journal	March 2006
Number of SNPS Loci Needed to Detect Population Structure Turakulov, Rust; Easteal, Simon Human Heredity, Vol. 55, Issue 1 https://doi.org/10.1159/000071808	journal	January 2003
Biodiversity of 20 chicken breeds assessed by SNPs located in gene regions Twito, T.; Weigend, S.; Blum, S. Cytogenetic and Genome Research, Vol. 117, Issue 1-4 https://doi.org/10.1159/000103194	journal	January 2007
Pollen Shedding and Dispersal in the Castor Plant Ricinus communis L. ¹ Meinders, Hadley C.; Jones, Melvin D. Agronomy Journal, Vol. 42, Issue 4 https://doi.org/10.2134/agronj1950.00021962004200040009x	journal	April 1950
Natural Outcrossing in Dwarf‐Internode Castor, Ricinus communis L. ¹ Brigham, Raymond D. Crop Science, Vol. 7, Issue 4 https://doi.org/10.2135/cropsci1967.0011183x000700040022x	journal	July 1967
Latitudinal population differentiation in two species of Solidago (Asteraceae) introduced into Europe Weber, Ewald; Schmid, Bernhard American Journal of Botany, Vol. 85, Issue 8 https://doi.org/10.2307/2446344	journal	August 1998
Genetic variation inPueraria lobata(Fabaceae), an introduced, clonal, invasive plant of the southeastern United States Pappert, Rebecca A.; Hamrick, J. L.; Donovan, Lisa A. American Journal of Botany, Vol. 87, Issue 9 https://doi.org/10.2307/2656716	journal	September 2000
Worldwide genotyping of castor bean germplasm (Ricinus communis L.) using AFLPs and SSRs Allan, Gerard; Williams, Amber; Rabinowicz, Pablo D. Genetic Resources and Crop Evolution, Vol. 55, Issue 3 https://doi.org/10.1007/s10722-007-9244-3	journal	July 2007
The utility of single nucleotide polymorphisms in inferences of population history Brumfield, Robb T.; Beerli, Peter; Nickerson, Deborah A. Trends in Ecology & Evolution, Vol. 18, Issue 5 https://doi.org/10.1016/S0169-5347(03)00018-1	journal	May 2003
Determining the source of individuals: multilocus genotyping in nonequilibrium population genetics Davies, Neil; Villablanca, Francis X.; Roderick, George K. Trends in Ecology & Evolution, Vol. 14, Issue 1 https://doi.org/10.1016/S0169-5347(98)01530-4	journal	January 1999
Evaluation of genetic relationships among botanical varieties of cultivated peanut (Arachis hypogaea L.) using AFLP markers He, Guohao; Prakash, Channapatna Genetic Resources and Crop Evolution, Vol. 48, Issue 4, p. 347-352 https://doi.org/10.1023/A:1012019600318	journal	January 2001
Genetic diversity among watermelon (Citrullus lanatus and Citrullus colocynthis) accessions Levi, Amnon; Thomas, Claude E.; Keinath, Anthony P. Genetic Resources and Crop Evolution, Vol. 48, Issue 6, p. 559-566 https://doi.org/10.1023/A:1013888418442	journal	January 2001
Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis Estoup, Arnaud; Jarne, Philippe; Cornuet, Jean-Marie Molecular Ecology, Vol. 11, Issue 9 https://doi.org/10.1046/j.1365-294X.2002.01576.x	journal	September 2002
Cryptic invasion by a non-native genotype of the common reed, Phragmites australis , into North America Saltonstall, Kristin Proceedings of the National Academy of Sciences, Vol. 99, Issue 4 https://doi.org/10.1073/pnas.032477999	journal	February 2002
CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure Jakobsson, M.; Rosenberg, N. A. Bioinformatics, Vol. 23, Issue 14 https://doi.org/10.1093/bioinformatics/btm233	journal	May 2007
Detecting the number of clusters of individuals using the software structure: a simulation study Evanno, G.; Regnaut, S.; Goudet, J. Molecular Ecology, Vol. 14, Issue 8 https://doi.org/10.1111/j.1365-294X.2005.02553.x	journal	July 2005
Distribution of genetic variation within and among local populations of Arabidopsis thaliana over its species range Bakker, E. G.; Stahl, E. A.; Toomajian, C. Molecular Ecology, Vol. 15, Issue 5 https://doi.org/10.1111/j.1365-294X.2006.02884.x	journal	April 2006
Zusammensetzung von Populationen und Korrelationserscheinungen vom Standpunkt der Vererbungslehre aus Betrachtet Wahlund, Sten Hereditas, Vol. 11, Issue 1 https://doi.org/10.1111/j.1601-5223.1928.tb02483.x	journal	May 1928
Secondary seed dispersal of Ricinus communis Linnaeus (Euphorbiaceae) by ants in secondary growth vegetation in Minas Gerais Santo, Mário Marcos do Espírito Revista Árvore, Vol. 31, Issue 6 https://doi.org/10.1590/S0100-67622007000600005	journal	December 2007
Natural Outcrossing in Dwarf‐Internode Castor, Ricinus communis L. ¹ Brigham, Raymond D. Crop Science, Vol. 7, Issue 4 https://doi.org/10.2135/cropsci1967.0011183X000700040022x	journal	July 1967
Genetic variation in Lathyrus latifolius (Leguminosae) Godt, Mary Jo W.; Hamrick, J. L. American Journal of Botany, Vol. 78, Issue 9, 1163-1171 https://doi.org/10.2307/2444920	journal	September 1991

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Genetic Diversity of Castor Bean (Ricinus communis L.) Revealed by ISSR and RAPD Markers Kim, HyokChol; Lei, Pei; Wang, Aizhi Agronomy, Vol. 11, Issue 3 https://doi.org/10.3390/agronomy11030457	journal	March 2021
A Brief Review of Molecular Techniques to Assess Plant Diversity Arif, Ibrahim A.; Bakir, Mohammad A.; Khan, Haseeb A. International Journal of Molecular Sciences, Vol. 11, Issue 5 https://doi.org/10.3390/ijms11052079	journal	May 2010
Diversity and path coefficient analysis of Southern African maize hybrids Mhoswa, Lorraine; Derera, John; Qwabe, Fikile N. P. Chilean journal of agricultural research, Vol. 76, Issue 2 https://doi.org/10.4067/s0718-58392016000200002	journal	June 2016
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Additional file 2 of Genomic insights into the origin, domestication and genetic basis of agronomic traits of castor bean Xu, Wei; Wu, Di; Yang, Tianquan figshare https://doi.org/10.6084/m9.figshare.14450691.v1	dataset	January 2021
Draft genome sequence of the oilseed species Ricinus communis Chan, Agnes P.; Crabtree, Jonathan; Zhao, Qi Nature Biotechnology, Vol. 28, Issue 9 https://doi.org/10.1038/nbt.1674	journal	August 2010
Nuclear DNA content in Sinningia (Gesneriaceae); intraspecific genome size variation and genome characterization in S. speciosa Zaitlin, David; Pierce, Andrew J. Genome, Vol. 53, Issue 12 https://doi.org/10.1139/g10-077	journal	December 2010
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