Assessing Genetic Diversity and Population Differentiation of Colored Calla Lily (Zantedeschia Hybrid) for an Efficient Breeding Program

Abstract

Plastome-genome incompatibility (PGI) is prevalent in several plants including the Zantedeschia species, a worldwide commercial flower crop native to South Africa. Generally, hybrids suffering from PGI appear less vigorous and more susceptible than normal plants. Previous reports revealed that the PGI level in interspecific hybrids is correlated with the relatedness of the parental species in the genus Zantedeschia. To provide a basis for utilizing and improving resources in breeding programs, a total of 117 accessions of colored calla lily (Zantedeschia hybrid), collected from New Zealand, the Netherlands and the United States, were genotyped using 31 transferable expressed sequence tags-simple sequence repeats (EST-SSR) markers from the white calla lily (Zantedeschia aethiopica). A moderately high level of genetic diversity was observed, with 111 alleles in total, an observed/expected heterozygosity (Ho/He) of 0.453/0.478, and polymorphism information content (PIC) of 0.26. Genetic distance and STRUCTURE-based analysis further clustered all accessions into four subgroups (G-Ia, G-Ib, G-IIa and G-IIb), which mostly consisted of Zantedeschia pentlandii, Zantedeschia elliotiana, Zantedeschia albomaculata and Zantedeschia rehmannii, respectively. Significant genetic differentiation was observed between all inferred subgroup pairs, with the Fst ranging from 0.142 to 0.281. Finally, the accessions assigned into G-IIb (Z. rehmannii) were recommended as top priority parents in efficient Zantedeschia breeding program designs.

Keywords: EST-SSRs; Zantedeschia species; colored calla lily; genetic diversity; population differentiation; white calla lily.

Figure 1

Summary of the simple sequence repeats (SSRs) distribution (a), the main motif types of dinucleotide repeats (b) and trinucleotide repeats (c) in assembled unigenes of white calla lily.

Figure 2

Characteristics of homology search of white calla lily 182 unigenes against the Nr (non-redundant) and GO (Gene Ontology) database. (a) The E-value, similarity and species distribution of BLAST (basic local alignment search tool) hits for each unique sequence with a cut-off E-value of 1 × 10⁻³. (b) The GO assignment into biological process, molecular function and cellular component at the third level.

Figure 3

Phylogenic tree aligned with the structure analysis for 117 colored calla lily accessions from New Zealand, the Netherlands and the USA. (a) neighbor-joining (NJ) dendrogram based on Nei’s distance of 31 EST-SSR markers showing two major clusters, Group I (54 accessions) and Group II (63 accessions). Each cluster was further separated into two sub-clusters (Group I-a and Group I-b, Group II-a and Group II-b). (b) Clustering based on multilocus analysis using the STRUCTURE package. The two best fitting models (K = 2 and K = 4) according to Evanno’s ΔK are shown. Each individual accession is represented by a vertical line divided into K colored bars. The length of each colored bar refers to the estimated membership coefficient (Q) in different K subpopulations for each accession.