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).

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.

Figure 1

Clustering of samples (n = 488) from program Structure where samples are displayed based on country of origin. Values of K (number of clusters) ranged from 2 to 5. The most supported model was K = 5; models with lower K values are shown to demonstrate progression of groupings.

Figure 2

Genotypes of Ricinus communis from nuclear SNPs were best described by five genetic clusters in a worldwide collection of 488 germplasm samples. Group colors correspond to Fig. 1 and circle sizes represent relative number of samples. Samples were only considered in a particular group if they meet a 60% threshold of group assignment. Thus, not all samples were assigned to a group because they shared affiliation with several different groups.

Figure 3

Genotypes of Ricinus communis from nuclear SNPs in a collection (n = 188) from 13 sites in 12 counties of Florida were best described by two genetic clusters. Inset is a Structure diagram on which map is based. Populations correspond to those from Table 2.