Validation of SNP markers for fruit quality and disease resistance loci in apple (Malus x domestica Borkh.) using the OpenArray® platform

Authors: CHAGNE, DAVID - New Zealand Institute Of Plant & Food Research; VANDERZANDE, STIJN - Washington State University; KIRK, CHRIS - New Zealand Institute Of Plant & Food Research; PROFITT, NATALIE - New Zealand Institute Of Plant & Food Research; WESKETT, ROSEMARY - New Zealand Institute Of Plant & Food Research; GARDINER, SUSAN - New Zealand Institute Of Plant & Food Research; PEACE, CAMERON - Washington State University; VOLZ, RICHARD - New Zealand Institute Of Plant & Food Research; Bassil, Nahla

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/12/2018
Publication Date: 3/1/2019
Citation: Chagne, D., Vanderzande, S., Kirk, C., Profitt, N., Weskett, R., Gardiner, S., Peace, C., Volz, R., Bassil, N.V. 2019. Validation of SNP markers for fruit quality and disease resistance loci in apple (Malus x domestica Borkh.) using the OpenArray® platform. Horticulture Research. 6. Article 30. https://doi.org/10.1038/s41438-018-0114-2.
DOI: https://doi.org/10.1038/s41438-018-0114-2

Interpretive Summary: The objective of this study was to develop validated and easy to use single nucleotide polymorphism (SNP) markers for many traits in apple. We first designed an assay with Thermo Fischer that enables multiplexing a set of 128 SNPs linked to fruit quality and pest and disease resistance traits. Up to 240 apple individuals with know phenotypes for these traits were screened with this assay. This set of individuals comprised commercial and heritage cultivars, elite selections, and families segregating for traits of importance to breeders. In total, 33 SNP markers of this assay were validated for use in marker-assisted selection (MAS) for the scab resistances, fire blight resistance, powdery mildew resistance, fruit firmness, skin colour, flavour intensity, and acidity. The availability of this set of validated trait-associated SNP markers, which can be used individually on multiple genotyping platforms available to various apple breeding programmes, represents a large translational genetics step from genomics to crop improvement of apple.

Technical Abstract: Genome mapping has promised much to tree fruit breeding during the last 10 years. Nevertheless, one of the greatest challenges remaining to tree fruit geneticists is the translation of trait loci and whole genome sequences into diagnostic genetic markers that are efficient and cost-effective for use by breeders, who must select genetically optimal parents and subsequently select genetically superior individuals among their progeny. To take this translational step, we designed the apple International RosBREED SNP Consortium OpenArray v1.0 (IRSCOA v1.0) assay using a set of 128 apple single nucleotide polymorphisms (SNPs) linked to fruit quality and pest and disease resistance trait loci. The Thermo Fisher Scientific OpenArray® technology enables multiplexed screening of SNP markers using a real-time PCR instrument with fluorescent probe-based Taqman® assays. We validated the apple IRSCOA v1.0 multi-trait assay by screening 240 phenotyped individuals from the Plant & Food Research apple cultivar breeding programme. This set of individuals comprised commercial and heritage cultivars, elite selections, and families segregating for traits of importance to breeders. In total, 33 SNP markers of the IRSCOA v1.0 were validated for use in marker-assisted selection (MAS) for the scab resistances Rvi2/Vh2, Rvi4/Vh4, Rvi6/Vf, fire blight resistance MR5/RLP1, powdery mildew resistance Pl2, fruit firmness, skin colour, flavour intensity, and acidity. The availability of this set of validated trait-associated SNP markers, which can be used individually on multiple genotyping platforms available to various apple breeding programmes, represents a large translational genetics step from genomics to crop improvement of apple.