title: Genome-wide SNP detection, validation, and development of an 8K SNP array for apple.
abstract: 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.
authors.affiliation: Plant and Food Research, Palmerston North Research Centre, Palmerston North, New Zealand.
authors.forename: David
authors.initials: D
authors.lastname: Chagné
authors.forename: Ross N
authors.initials: RN
authors.lastname: Crowhurst
authors.forename: Michela
authors.initials: M
authors.lastname: Troggio
authors.forename: Mark W
authors.initials: MW
authors.lastname: Davey
authors.forename: Barbara
authors.initials: B
authors.lastname: Gilmore
authors.forename: Cindy
authors.initials: C
authors.lastname: Lawley
authors.forename: Stijn
authors.initials: S
authors.lastname: Vanderzande
authors.forename: Roger P
authors.initials: RP
authors.lastname: Hellens
authors.forename: Satish
authors.initials: S
authors.lastname: Kumar
authors.forename: Alessandro
authors.initials: A
authors.lastname: Cestaro
authors.forename: Riccardo
authors.initials: R
authors.lastname: Velasco
authors.forename: Dorrie
authors.initials: D
authors.lastname: Main
authors.forename: Jasper D
authors.initials: JD
authors.lastname: Rees
authors.forename: Amy
authors.initials: A
authors.lastname: Iezzoni
authors.forename: Todd
authors.initials: T
authors.lastname: Mockler
authors.forename: Larry
authors.initials: L
authors.lastname: Wilhelm
authors.forename: Eric
authors.initials: E
authors.lastname: Van de Weg
authors.forename: Susan E
authors.initials: SE
authors.lastname: Gardiner
authors.forename: Nahla
authors.initials: N
authors.lastname: Bassil
authors.forename: Cameron
authors.initials: C
authors.lastname: Peace
mesh_terms: D001947:Breeding; D020090:Chromosome Segregation / Q000235:genetics; D008040:Genetic Linkage; D018745:Genome, Plant / Q000235:genetics*; D006239:Haplotypes / Q000235:genetics; D007391:International Cooperation; D027845:Malus / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D057188:Workflow