Abstract
Cherry breeding and genetic studies can benefit from genome-wide genetic marker assays. Currently, a 6K SNP array enables genome scans in cherry; however, only a third of these SNPs are informative, with low coverage in many genomic regions. Adding previously detected SNPs to this array could provide a cost-efficient upgrade with increased genomic coverage across the 670 cM/352.9 Mb cherry whole genome sequence. For sweet cherry, new SNPs were chosen following a focal point strategy, grouping six to eight SNPs within 10-kb windows with an average of 0.6 cM (627 kb) between focal points. Additional SNPs were chosen to represent important regions. Sweet cherry, the fruticosa subgenome of sour cherry, and cherry organellar genomes were targeted with 6942, 2020, and 38 new SNPs, respectively. The +9K add-on provided 2128, 1091, and 70 new reliable, polymorphic SNPs for sweet cherry and the avium and the fruticosa subgenomes of sour cherry, respectively. For sweet cherry, 1241 reliable polymorphic SNPs formed 237 informative focal points, with another 2504 SNPs in-between. The +9K SNPs increased genetic resolution and genome coverage of the original cherry SNP array and will help increase understanding of the genetic control of key traits and relationships among individuals in cherry.
Highlights
Cherry breeding and genetic studies can benefit from genome-wide genetic marker assays
For the fruticosa subgenome of sour cherry, 190,770 single nucleotide polymorphism (SNP) were initially available: 48,025 intragenic SNPs identified during development of the original SNP array and 142,745 SNPs identified through GBS on P. fruticosa individuals (Fig. 1, Table 1)
The new, improved genetic map provided by this study enables improved precision of determining genomic positions of recombination events, in turn improving haploblock informativeness for sweet cherry germplasm and fine-mapping of quantitative trait loci (QTL) and candidate genes
Summary
Cherry breeding and genetic studies can benefit from genome-wide genetic marker assays. The +9K add-on provided 2128, 1091, and 70 new reliable, polymorphic SNPs for sweet cherry and the avium and the fruticosa subgenomes of sour cherry, respectively. The cherry 6K SNP array has been used in sweet cherry to deduce pedigree and parentage[3], create high-density linkage maps[4,5], identify quantitative trait loci (QTL) and candidate genes controlling important horticultural traits[6,7], dissect the genetic structure and inheritance of alleles at a QTL hotspot[8], estimate heritability and genomic breeding values of industry-prioritized traits[9,10], determine genetic diversity, linkage disequilibrium, and population structure of a germplasm collection and inform development of a core colleciton[11], and identify patterns of domestication[12].
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