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 programmes, and managing wild populations and germplasm collections. Amongst available genotyping tools, SNP 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 SNP markers, exploiting inter-species cross-amplification. In this study, the suitability of a multiplexed plant-animal SNP array, including both closely and distantly related species, was explored. The performance of the SNP 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 SNP array as a technique to further reduce costs was evaluated. SNP performance was generally high, and species-specific SNPs proved suitable for diverse applications. The multi-species SNP-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.

Development of KASP fingerprinting panel for clonal identification in red raspberry (Rubus idaeus L.)

“…A total of 6,884 SNP marker assays were considered high quality with two to three distinct genotype clusters from the multi‐species Affymetrix SNP array (Montanari et al, 2022). The WGS of 210 accessions identified a total of 4,905,377 SNP and indel variants.…”

“…The WGS of 210 accessions identified a total of 4,905,377 SNP and indel variants. Subsequently, 5,886 SNPs from the SNP array (Montanari et al, 2022) were identified that had corresponding biallelic SNP calls with matching alleles in the WGS dataset (File S2). The WGS variant calls were used to assess genotype segregation and missing genotype call rates for the 131 R. idaeus accessions at the 5,886 validated array SNP sites.…”

“…A subset of raspberry SNPs included in the multi-species Affymetrix SNP array designed by Montanari et al (2022) that could be further validated by WGS-based genomic variant calling were selected as candidates for conversion into a low-cost KASP fingerprinting panel. A total of 6,884 SNP marker assays for diploid Rubus were classified as 'PolyHighResolution' (PHR) or 'NoMinorHom' (NMH) (Montanari et al, 2022), indicating support for two or three distinct genotype clusters. SNPs with matching genotyping calls in the multi-species Affymetrix SNP array and WGS were considered for KASP assay development (File S2).…”

A phosphatase gene is linked to nectar dihydroxyacetone accumulation in mānuka (Leptospermum scoparium)

“…The array containing 9002 SNPs for mānuka was described by Montanari et al . (2023), and the genotyping was performed by Labogena (Jouy‐en‐Josas, France) using standard protocols. After genotyping, the SNP data were analysed using the A xiom A nalysis S uite v.5.1.1 software applying a dish QC threshold of 0.82 and a QC Call Rate > 95%.…”

“…In total, 185 individuals from the EC201 9 EC103 segregating population were screened using an Affymetrix Axiom TM (Thermo-Fisher Scientific, Waltham, MA, USA) Single Nucleotide Polymorphism (SNP) array. The array containing 9002 SNPs for m anuka was described by Montanari et al (2023), and the genotyping was performed by Labogena (Jouy-en-Josas, France) using standard protocols. After genotyping, the SNP data were analysed using the AXIOM ANALYSIS SUITE v.5.1.1 software applying a dish QC threshold of 0.82 and a QC Call Rate > 95%.…”