Genome-wide SNP detection, validation, and development of an 8K SNP array for apple

Chagné, D., Crowhurst, R.N., Troggio, M., Davey, M.W., Gilmore, B., Lawley, C., Vanderzande, S., Hellens, R.P., Kumar, S., Cestaro, A., Velasco, R., Main, D., Rees, J.D., Iezzoni, A., Mockler, T., Wilhelm, L., van de Weg, E., Gardiner, S.E., Bassil, N., & Peace, C. (2012) Genome-wide SNP detection, validation, and development of an 8K SNP array for apple. PLoS ONE, 7(2), e31745.

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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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ID Code: 71425
Item Type: Journal Article
Refereed: Yes
Additional Information: Cited By (since 1996):34
Export Date: 6 May 2014
Source: Scopus
Art. No.: e31745
PubMed ID: 22363718
Additional URLs:
DOI: 10.1371/journal.pone.0031745
ISSN: 1932-6203
Divisions: Current > QUT Faculties and Divisions > Science & Engineering Faculty
Copyright Owner: Copyright 2012 Chagne et al.
Copyright Statement: This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Deposited On: 12 May 2014 05:45
Last Modified: 13 May 2014 05:38

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