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CC BY V4.0, Open Access
Journal article
Genome-wide SNP detection, validation, and development of an 8K SNP array for apple
PloS one, Vol.7(2), pp.e31745-e31745
2012
Handle:
https://hdl.handle.net/2376/104472
PMCID: PMC3283661
PMID: 22363718
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.
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Details
- Title
- Genome-wide SNP detection, validation, and development of an 8K SNP array for apple
- Creators
- David Chagné - Plant and Food Research, Palmerston North Research Centre, Palmerston North, New ZealandRoss N CrowhurstMichela TroggioMark W DaveyBarbara GilmoreCindy LawleyStijn VanderzandeRoger P HellensSatish KumarAlessandro CestaroRiccardo VelascoDorrie MainJasper D ReesAmy IezzoniTodd MocklerLarry WilhelmEric Van de WegSusan E GardinerNahla BassilCameron Peace
- Publication Details
- PloS one, Vol.7(2), pp.e31745-e31745
- Academic Unit
- Department of Horticulture
- Publisher
- United States
- Identifiers
- 99900546766301842
- Language
- English
- Resource Type
- Journal article