Validation of SNP markers for fruit quality and disease resistance loci in apple (Malus × domestica Borkh.) using the OpenArray® platform. Issue 1 (1st March 2019)

• Record Type: Journal Article
• Authors: Chagné, David; Vanderzande, Stijn; Kirk, Chris; Profitt, Natalie; Weskett, Rosemary; Gardiner, Susan E; Peace, Cameron P; Volz, Richard K; Bassil, Nahla V
• Is Part Of: Horticulture research. Volume 6:Issue 1(2019)
• Publication Date: 2019-03-01
• Subjects: High-throughput screening -- Plant breeding; Horticulture -- Research -- Periodicals; 635.072
• DOI: 10.1038/s41438-018-0114-2
• Languages: English
• ISSNs: 2052-7276

Abstract

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 or re-designed using the flanking sequences, represents a large translational genetics step from genomics to crop improvement of apple. Breeding science: A new way to weed out bad apples: Improving the taste, colour, and disease resistance of apple varieties will now be easier, thanks to a set of genetic markers that can be used to select the best individuals to breed. Although many crop genomes have been sequenced, the information must be translated into inexpensive and easy-to-use tests for particular traits before it is practical to apply it in breeding programs. David Chagné at The New Zealand Institute for Plant & Food Research and co-workers have developed a set of markers for apple trees that indicate fruit quality, and disease and pest resistance. Using these markers, breeders will be able to peer inside the genomes of parent and offspring trees to determine whether or not they possess desirable traits. This approach shows promise to improve breeding programs for apples and other crops.