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.
Highlights
Understanding the links between phenotypic variations and their underlying DNA variation is the major challenge facing plant geneticists today
We focus here on the development of a medium to high-throughput multiplexed Single Nucleotide Polymorphisms (SNPs) assay tool based on the Illumina InfiniumH assay for genome-wide evaluation of allelic variation in apple breeding germplasm
A SNP-based strategy for apple genome scanning An international community of apple genomics, genetics, and breeding researchers recently united with the goal of developing high-resolution genome scanning capability for germplasm of cultivated apple
Summary
Understanding the links between phenotypic variations and their underlying DNA variation is the major challenge facing plant geneticists today. Genetic marker-based strategies such as QTL interval mapping, pedigree-based analysis, association mapping, and genomic selection are powerfully enabled by genomics technologies. We focus here on the development of a medium to high-throughput multiplexed SNP assay tool based on the Illumina InfiniumH assay for genome-wide evaluation of allelic variation in apple breeding germplasm. This product of international research community collaboration is intended to benefit apple breeders directly, and growers and consumers who demand better quality pome fruit that is produced more sustainably
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
