Genome-wide analysis of genetic diversity in a germplasm collection including wild relatives and interspecific clones of garden asparagus

Abstract

The Asparagus genus includes approximately 240 species, the most important of which is garden asparagus (Asparagus officinalis L.), as this is a vegetable crop cultivated worldwide for its edible spear. Along with garden asparagus, other species are also cultivated (e.g., Asparagus maritimus L.) or have been proposed as untapped sources of variability in breeding programs (e.g., Asparagus acutifolius L.). In the present work, we applied reduced-representation sequencing to examine a panel of 378 diverse asparagus genotypes, including commercial hybrids, interspecific lines, wild relatives of garden asparagus, and doubled haploids currently used in breeding programs, which enabled the identification of more than 200K single-nucleotide polymorphisms (SNPs). These SNPs were used to assess the extent of linkage disequilibrium in the diploid gene pool of asparagus and combined with preliminary phenotypic information to conduct genome-wide association studies for sex and traits tied to spear quality and production. Moreover, using the same phenotypic and genotypic information, we fitted and cross-validated genome-enabled prediction models for the same set of traits. Overall, our analyses demonstrated that, unlike the diversity detected in wild species related to garden asparagus and in interspecific crosses, cultivated and wild genotypes of A. officinalis L. show a narrow genetic basis, which is a contributing factor hampering the genetic improvement of this crop. Estimating the extent of linkage disequilibrium and providing the first example of genome-wide association study and genome-enabled prediction in this species, we concluded that the asparagus panel examined in the present study can lay the foundation for determination of the genetic bases of agronomically important traits and for the implementation of predictive breeding tools to sustain breeding.

Keywords: GWAS; asparagus; breeding; genetic diversity; genomic prediction; germplasm collection.

Figure 1

Diversity analysis of 15 groups of different asparagus genotypes. (A) Principal component analysis of the entire collection of 378 asparagus genotypes examined in this study. (B) Principal component plots in which different classes of asparagus examined in this study are highlighted in red. BC, back-cross; CH, commercial hybrid; DH, double haploid; DI, dihaploid; EH, experimental hybrid; HE, hermaphrodite; HF, heterozygous female; HM, heterozygous male; IC, interspecific cross; IH, interspecific hybrid; IL, interspecific line; IS, interspecific individual; LI, line obtained by anther culture; MS, maritimus selected; MW, maritimus wild-type.

Figure 2

Diversity analysis of Asparagus maritimus, Asparagus officinalis, and ‘Violetto d’Albenga’ genotypes. Principal component analysis carried out on a reduced set of 74 asparagus genotypes, including plants belonging to the ‘Violetto d’Albenga’ population along with accessions of A. maritimus and A. officinalis.

Figure 3

Decay of linkage disequilibrium in diploid asparagus genotypes. The 10 plots show the average r² values computed between pairs of loci in 100-kb bins across the asparagus chromosomes.

Figure 4

Frequency distributions of scores measured for quality and seed production traits. Histograms show the frequency distribution of nine agronomic traits, each measured on an ordinal categorical scale from 1 to 9, in 131 genotypes of asparagus.

Figure 5

Heatmap of pairwise correlations computed among nine asparagus traits. Numbers reported within the heatmap represent polychoric pairwise coefficients between the ordinal categorical traits measured. Positive correlations are displayed in red and negative correlations in blue; correlations with associated p-values greater than 0.05 are marked with crosses.

Figure 6

Genome-wide association analyses for sex and intensity of anthocyanic coloration in spears. The top and bottom panels show Manhattan plots of genome-wide association analyses carried out for sex and intensity of anthocyanic coloration in spears, respectively. The red line on each plot indicates the threshold for significance, which was fixed at $-{\text{log}}_{10}(p \text{value})=6$ .

Figure 7

Genome-wide association analyses for asparagus quality traits. Each panel shows a Manhattan plot of a genome-wide association analysis carried out for a single trait (density of phylloclades, number of stems, spear diameter, spear head firmness, opening of spear bracts), stem length, flowering time, and spear emergence). The red line on each plot indicates the significance threshold of $-{\text{log}}_{10}(p \text{value})=6$ .

Figure 8

Predictive ability of genome-enabled prediction models for asparagus quality traits. Each bar shows Brier Scores obtained using leave-one-out cross-validations carried out for a single trait (phylloclade density, number of stems, spear diameter, spear head firmness, opening of spear bracts, stem length, flowering time, and spear emergence). Lower Brier scores correspond to greater predictive ability of the model.