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

Authors: MONTANARI, SARA - New Zealand Institute Of Plant & Food Research; DENG, CECILIA - New Zealand Institute Of Plant & Food Research; KOOT, EMILY - New Zealand Institute Of Plant & Food Research; Bassil, Nahla; ZURN, JASON - Kansas State University; MORRISON-WHITTLE, PETER - New Zealand Institute Of Plant & Food Research; WORTHINGTON, MARGARET - University Of Arkansas; ARYAL, RISHI - North Carolina State University; ASHRAFI, HAMID - North Carolina State University; PRADELLES, JULIEN - Laboratoire D'Analyses Genetiques Pour Les Especes Animales(LABOGENA); WELLENREUTHER, MAREN - New Zealand Institute Of Plant & Food Research; CHAGNE, DAVID - New Zealand Institute Of Plant & Food Research

Submitted to: bioRxiv
Publication Type: Pre-print Publication
Publication Acceptance Date: 9/11/2022
Publication Date: 9/11/2022
Citation: Montanari, S., Deng, C., Koot, E., Bassil, N.V., Zurn, J.D., Morrison-Whittle, P., Worthington, M., Aryal, R., Ashrafi, H., Pradelles, J., Wellenreuther, M., Chagne, D. 2022. A multiplexed plant-animal SNP array for selective breeding and species conservation applications. bioRxiv. https://doi.org/10.1101/2022.09.07.507051.
DOI: https://doi.org/10.1101/2022.09.07.507051

Interpretive Summary: Reliable and high-throughput genotyping platforms are important tool that can assist selection processes in breeding programs, manage wild populations and germplasm collections, and dissect genomic regions controlling important traits. Amongst all genotyping tools available, array technology interrogates thousands of DNA variants at the same time and have been shown to be comparatively easy to use and generate highly accurate 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 DNA markers. The objective of this study was to develop a multiplexed plant-animal DNA array, including both closely and distantly related species and assess its usefulness for diverse applications and its cost effectiveness. DNA marker performance was generally high, and species-specific markers proved suitable for different applications such as distinguishing unique blackberry, raspberry, manuka, snapper and trevally genotypes and clustering them mostly based on breeding program or origin. The multi-species SNP-array approach reported here could be transferred to other species to achieve cost savings resulting from the increasing throughput when several projects use the same array, and the pooling technique adds another highly promising advancement to additionally decrease genotyping costs by half.

Technical Abstract: Reliable and high-throughput genotyping platforms are of immense importance to support selection processes in breeding programmes, manage wild populations and germplasm collections, and dissect genomic regions controlling important phenotypes. Amongst all genotyping tools available, SNP arrays have been shown to be comparatively easy to use and to 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 increasing throughput when several projects use the same array, and the pooling technique adds another highly promising advancement to additionally decrease genotyping costs by half.