Abstract
BackgroundCastor 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.ResultsBayesian 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).ConclusionLow 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.
Highlights
Castor bean (Ricinus communis) is an agricultural crop and garden ornamental that is widely cultivated and has been introduced worldwide
That this still represents a small fraction of the genome, as reads of 98% identity and 98% read coverage in the Hale genome revealed 15.2 Mb of total sequence before filtering the data set for Single nucleotide polymorphism (SNP) discovery
Given that reads with 100% identity among all 8 cultivars were excluded from this analysis, it is likely that the number of SNPs per base is overestimated and true nucleotide diversity across the genome is much lower
Summary
Castor bean (Ricinus communis) is an agricultural crop and garden ornamental that is widely cultivated and has been introduced worldwide. We determined the population genetic structure of 676 samples using single nucleotide polymorphisms (SNPs) at 48 loci. Assessing genetic diversity in plants has involved increasingly sophisticated approaches, from early allozyme work, to amplified fragment length polymorphisms (AFLPs), and microsatellites. Due to their multi-allelic states, development of simple sequence repeats (SSR) or microsatellites is often the best option for investigating population differentiation, but development and genotyping of large numbers of samples can be costly and size homoplasy is often a concern [1]. As binary, codominant markers, heterozygosity can be directly measured Unlike microsatellites their power comes not from the number of alleles, but from the large number of loci that can be assessed. Methylation filtration is not a new method but it is not commonly used to target polymorphic sites in low diversity species and should serve as a useful tool for other plant species with limited genetic diversity
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