Development and Evaluation of a Genome-Wide 6K SNP Array for Diploid Sweet Cherry and Tetraploid Sour Cherry

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.

高通量基因组扫描是遗传学研究与育种应用的重要工具。本研究针对二倍体甜樱桃（Prunus avium）与异源四倍体酸樱桃（P. cerasus），开发了一款适配Illumina Infinium®检测系统的6K单核苷酸多态性（Single Nucleotide Polymorphism, SNP）阵列。该开发工作由RosBREED牵头，这是一项旨在推动蔷薇科作物标记辅助育种的社区倡议。研究团队对多样化的育种种质资源开展下一代测序，共获得250亿碱基对（Gb）的樱桃DNA序列数据，从中分别鉴定出甜樱桃的全基因组SNP，以及源自甜樱桃（avium亚基因组）和P. fruticosa（fruticosa亚基因组）的两个酸樱桃亚基因组的全基因组SNP。依托国际桃基因组计划（International Peach Genome Initiative）最新发布的桃基因组序列，对检测到的190万个推定SNP进行锚定以确定其相对物理位置，并初步筛选至368,943个SNP。后续筛选以144个SNP的子集为参考依据，该子集通过Illumina GoldenGate®检测试剂盒对160份种质材料进行了分型验证。研究团队设计了一款6K Infinium® II阵列，其SNP在甜樱桃与酸樱桃基因组上呈均匀的遗传间隔分布。针对酸樱桃的两个亚基因组，研究团队通过分析酸樱桃检测群体中的次要等位基因频率，富集亚基因组特异性SNP，再结合甜樱桃中检测到的等位基因，将SNP靶向对应亚基因组。该阵列通过甜樱桃（n=269）与酸樱桃（n=330）的育种种质资源群体进行了性能评估。两款作物分别有约三分之一的阵列SNP具有分型信息价值。在甜樱桃中共验证得到1825个多态性SNP，其中13%的SNP最初是为酸樱桃开发的。在酸樱桃中成功解析了2058个多态性SNP的等位基因剂量，其中三分之一的SNP最初是为甜樱桃开发的。这一公开可得的基因组学资源，显著提升了樱桃的基因组扫描能力，将加速该二倍体-四倍体作物类群中标记-位点-性状关联发掘、基因组结构解析以及遗传多样性评估工作。