High-quality, genome-wide SNP genotypic data for pedigreed germplasm of the diploid outbreeding species apple, peach, and sweet cherry through a common workflow

• DOI: 10.1371/journal.pone.0210928
• Publication Date: 2019-06-27T17:29:46Z
• Authors: Stijn Vanderzande; Nicholas P. Howard; Lichun Cai; Cassia Da Silva L...; Laima Antanaviciute; Marco C. A. M. Bink; Johannes W. Kruis...; Nahla Bassil; Ksenija Gasic; Amy Iezzoni; Eric Van de Weg; Cameron Peace
• Keywords: Germ plasm; SNP genotyping

High-quality genotypic data is a requirement for many genetic analyses. For any crop, errors in genotype calls, phasing of markers, linkage maps, pedigree records, and unnoticed variation ploidy levels can lead to spurious marker-locus-trait associations incorrect origin assignment alleles individuals. High-throughput genotyping requires automated scoring, as manual inspection thousands scored loci too time-consuming. However, SNP scoring result that should be corrected ensure recorded are accurate thereby confidence downstream To enable quick identification large set, we have developed comprehensive workflow. This multiple-step workflow based on inheritance principles removal markers individuals do not follow these principles, demonstrated here apple, peach, sweet cherry. Genotypic was obtained pedigreed germplasm using 6-9K arrays each crop subset well-performing SNPs created ASSIsT. Use correct (and corrected) records readily identified violations simple the data, streamlined with FlexQTL software. Retained were grouped into haploblocks increase information content single reduce computational power needed Haploblock borders defined by recombination locations detected ancestral generations cultivars selections. Another round inheritance-checking conducted, haploblock (i.e., haplotypes). sets this collections representing U.S. breeding cherry evaluated within RosBREED project. These contain 3855, 4005, 1617 spread over 932, 103, 196 cherry, respectively. The highly curated phased haplotype sets, well raw iScan Crop Reference Sets available through Genome Database Rosaceae.