A multiplexed plant-animal SNP array for selective breeding and species conservation applications

Abstract

Reliable and high-throughput genotyping platforms are of immense importance for identifying and dissecting genomic regions controlling important phenotypes, supporting selection processes in breeding programs, and managing wild populations and germplasm collections. Amongst available genotyping tools, single nucleotide polymorphism arrays have been shown to be comparatively easy to use and generate highly accurate genotypic data. Single-species arrays are the most commonly used type so far; however, some multi-species arrays have been developed for closely related species that share single nucleotide polymorphism markers, exploiting inter-species cross-amplification. In this study, the suitability of a multiplexed plant-animal single nucleotide polymorphism array, including both closely and distantly related species, was explored. The performance of the single nucleotide polymorphism array across species for diverse applications, ranging from intra-species diversity assessments to parentage analysis, was assessed. Moreover, the value of genotyping pooled DNA of distantly related species on the single nucleotide polymorphism array as a technique to further reduce costs was evaluated. Single nucleotide polymorphism performance was generally high, and species-specific single nucleotide polymorphisms proved suitable for diverse applications. The multi-species single nucleotide polymorphism array approach reported here could be transferred to other species to achieve cost savings resulting from the increased throughput when several projects use the same array, and the pooling technique adds another highly promising advancement to additionally decrease genotyping costs by half.

Keywords: Chrysophrys auratus; Leptospermum scoparium; Pseudocaranx georgianus; Rubus spp; DNA pooling; SNP markers.

Fig. 1.

Genetic diversity of diploid Rubus samples. PCA with samples colored by repository a) and assigned species b). DAPC plot with samples colored according to repository c) and DAPC clustering d). Circles and arrows in plots a and c show correspondence between PCA and DAPC clustering. NCGR = USDA-ARS National Clonal Germplasm Repository; PFR = The New Zealand Institute for Plant and Food Research Ltd.

Fig. 2.

Genetic diversity of tetraploid Rubus samples. PCA with samples colored by repository. UArk = University of Arkansas System Division of Agriculture; NCGR = USDA-ARS National Clonal Germplasm Repository; PFR = The New Zealand Institute for Plant and Food Research Ltd.

Fig. 3.

Population genetics analysis of mānuka samples from Aotearoa-NZ. a) DAPC plot with samples colored according to provenance. b) F_ST analysis. NNI: Northern North Island; Central and Southern North Island (CSNI); East Cape North Island (ECNI); SI = South Island.

Fig. 4.

Population genetic analysis and pedigree reconstruction of Australasian snapper and Japanese red seabream. PCA colored by species and population: a) PC1 vs PC2 and b) PC3 vs PC4. c) Pedigree networks: parent-offspring relationships are indicated by a line connecting the adult snapper (square points) and juvenile snapper (circular points) of the three broodstock lines.

Fig. 5.

PCA of trevally samples caught in Australia and Aotearoa-NZ.

Fig. 6.

Comparison of genotyping quality parameters among species. Boxplots for DQC a), QC call rate b), and call rate values c) grouped by species.

Fig. 7.

Comparison of genotyping quality parameters between pooled and non-pooled DNA samples. Boxplots for DQC a), QC call rate, b) and call rate values c) grouped by species and pooling, with corresponding values for sample count, mean, SDs, and median, and the T-test P-value. Scatter plots for DQC d), QC call rate e), and call rate values f) of pooled plant vs fish samples.