Development and evaluation of a genome-wide 6K SNP array for diploid sweet cherry and tetraploid sour cherry

Authors: PEACE, CAMERON - Washington State University; Bassil, Nahla; MAIN, DORRIE - Washington State University; FICKLIN, STEPHEN - Washington State University; ROSYARA, UMESH - Michigan State University; STEGMEIR, TRAVIS - Michigan State University; SEBOLT, AUDREY - Michigan State University; Gilmore, Barbara; LAWLEY, CINDY - Illumina, Inc; MOCKLER, TODD - Danforth Plant Science Center; BRYANT, DOUGLAS - Danforth Plant Science Center; WILHELM, LARRY - Oregon Health & Science University; IEZZONI, AMY - Michigan State University

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/16/2012
Publication Date: N/A
Citation: N/A

Interpretive Summary: We have identified thousands of important markers that are located throughout all chromosomes in cherry using peach DNA sequences. These markers have application to sweet and tart cherry. Up to now only a limited number of molecular markers were developed in cherry. Our goal was to develop and characterize a collection of many markers that can be simultaneously examined for each cherry DNA sample. We determined the DNA code information for 16 cherry individuals. Approximately 1.9 million single base marker changes were detected. Markers were validated. Up to 6,000 markers were then encoded on a microcomputer chip. These markers were located throughout all eight cherry chromosomes. Evaluation of this chip on 269 sweet and 330 tart cherry plants identified 1,825 and 2,058 useful markers in sweet and tart cehrry, respectively. The publically available cherry chip version 1 will be used worldwide for genetic studies and genetic diversity analyses in sweet and tart cherry.

Technical Abstract: High-throughput genome scans are important tools for genetic studies and breeding applications. Here, a 6K SNP array for use with the Illumina Infinium® system was developed for diploid sweet cherry (Prunus avium) and allotetraploid sour cherry (P. cerasus). This effort was led by RosBREED, a community initiative to enable marker-assisted breeding for rosaceous crops. Next-generation sequencing in diverse breeding germplasm provided 25 billion basepairs (Gb) of cherry DNA sequence from which were identified genome-wide SNPs for sweet cherry and for the two sour cherry subgenomes derived from sweet cherry (avium subgenome) and P. fruticosa(fruticosa subgenome). Anchoring to the peach genome sequence, recently released by the International Peach Genome Initiative, predicted relative physical locations of the 1.9 million putative SNPs detected, preliminarily filtered to 368,943 SNPs. Further filtering was guided by results of a 144-SNP subset examined with the Illumina GoldenGate® assay on 160 accessions. A 6K Infinium® II array was designed with SNPs evenly spaced genetically across the sweet and sour cherry genomes. SNPs were developed for each sour cherry subgenome by using minor allele frequency in the sour cherry detection panel to enrich for subgenome-specific SNPs followed by targeting to either subgenome according to alleles observed in sweet cherry. The array was evaluated using panels of sweet (n=269) and sour (n=330) cherry breeding germplasm. Approximately one third of array SNPs were informative for each crop. A total of 1825 polymorphic SNPs were verified in sweet cherry, 13% of these originally developed for sour cherry. Allele dosage was resolved for 2058 polymorphic SNPs in sour cherry, one third of these being originally developed for sweet cherry. This publicly available genomics resource represents a significant advance in cherry genome-scanning capability that will accelerate marker-locus-trait association discovery, genome structure investigation, and genetic diversity assessment in this diploid-tetraploid crop group.