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.
Highlights
Within Prunus (Rosaceae), two cherry species, sweet (P. avium) and sour cherry (P. cerasus), are highly valued for their excellent quality fruit
A 9K publicly available single nucleotide polymorphisms (SNPs) array for peach, recently developed by an international consortium, is widely being used for advanced genetic studies of peach [13]. The development of this array was facilitated by release of the peach (Prunus persica) reference genome sequence by the International Peach Genome Initiative [14].The high quality of the peach sequence was reinforced by high congruence between genetic and physical map positions of peach array SNPs
A total of 1,900,695 SNPs anchored to the peach genome were identified, including polymorphism between peach and cherry, approximately a third of which were within-cherry
Summary
Within Prunus (Rosaceae), two cherry species, sweet (P. avium) and sour cherry (P. cerasus), are highly valued for their excellent quality fruit. High-throughput and low-cost generation sequencing (NGS) is a powerful approach to identify single nucleotide polymorphisms (SNPs) which can be used as markers for the development of high-density genome scans. This approach has been successfully used to develop genome scan platforms for diploid crops such as apple [7], maize [8], rice [9] and polyploid crops such as potato [10,11], and wheat [12].
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