Genome-Wide SNP Detection, Validation, and Development of an 8K SNP Array for Apple

• Published in: PloS one Vol. 7; no. 2; p. e31745
• Main Authors: Chagné, David, Crowhurst, Ross N, Troggio, Michela, Davey, Mark W, Gilmore, Barbara, Lawley, Cindy, Vanderzande, Stijn, Hellens, Roger P, Kumar, Satish, Cestaro, Alessandro, Velasco, Riccardo, Main, Dorrie, Rees, Jasper D, Iezzoni, Amy, Mockler, Todd, Wilhelm, Larry, Van de Weg, Eric, Gardiner, Susan E, Bassil, Nahla, Peace, Cameron, Bendahmane, Mohammed
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 21-02-2012; Public Library of Science (PLoS)
• Subjects: apples; Biology; Breeding; Chromosome Segregation - genetics; Cloning; Consortia; Cultivars; discovery; diversity; Evaluation; exons; Filtration; Food; fruit; Fruits; Gene frequency; Gene sequencing; Genetic diversity; Genetic Linkage; Genetic markers; genetic variation; Genetics; genome; Genome, Plant - genetics; Genomes; Genomics; Genotyping; genus vitis; Germplasm; Haplotypes; Haplotypes - genetics; Horticulture; International Cooperation; Laboratories; Landscape architecture; Malus - genetics; Malus domestica; marker-assisted selection; markers; Mutation; Nucleotide sequence; Oligonucleotide Array Sequence Analysis - methods; Oryza; Pinus taeda; Plant biology; Plant breeding; Plant genetics; Polymorphism; Polymorphism, Single Nucleotide - genetics; quantitative traits; Reproducibility of Results; Screening; Sequence Analysis, DNA; shelf-life; Single-nucleotide polymorphism; single-nucleotide polymorphisms; transcription factor; Transcription factors; Vitis vinifera; Workflow; x-domestica borkh; Yang, Cindy; New Zealand; Oregon; Italy; Belgium; United States > US; Michigan
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0031745

As high-throughput genetic marker screening systems are essential for a range of genetics studies and plant breeding applications, the International RosBREED SNP Consortium (IRSC) has utilized the Illumina Infinium® II system to develop a medium- to high-throughput SNP screening tool for genome-wide evaluation of allelic variation in apple (Malus × domestica) breeding germplasm. For genome-wide SNP discovery, 27 apple cultivars were chosen to represent worldwide breeding germplasm and re-sequenced at low coverage with the Illumina Genome Analyzer II. Following alignment of these sequences to the whole genome sequence of ‘Golden Delicious’, SNPs were identified using SoapSNP . A total of 2,113,120 SNPs were detected, corresponding to one SNP to every 288 bp of the genome. The Illumina GoldenGate® assay was then used to validate a subset of 144 SNPs with a range of characteristics, using a set of 160 apple accessions. This validation assay enabled fine-tuning of the final subset of SNPs for the Illumina Infinium® II system. The set of stringent filtering criteria developed allowed choice of a set of SNPs that not only exhibited an even distribution across the apple genome and a range of minor allele frequencies to ensure utility across germplasm, but also were located in putative exonic regions to maximize genotyping success rate. A total of 7867 apple SNPs was established for the IRSC apple 8K SNP array v1, of which 5554 were polymorphic after evaluation in segregating families and a germplasm collection. This publicly available genomics resource will provide an unprecedented resolution of SNP haplotypes, which will enable marker-locus-trait association discovery, description of the genetic architecture of quantitative traits, investigation of genetic variation (neutral and functional), and genomic selection in apple.