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

PLoS One. 2019 Jun 27;14(6):e0210928. doi: 10.1371/journal.pone.0210928. eCollection 2019.

Abstract

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

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Breeding
  • Databases, Genetic
  • Diploidy
  • Genome, Plant / genetics*
  • Genotype*
  • Haplotypes
  • Malus / genetics
  • Pedigree
  • Polymorphism, Single Nucleotide / genetics*
  • Prunus avium / genetics
  • Prunus persica / genetics
  • Rosaceae / genetics*
  • Seed Bank
  • Sequence Analysis, DNA / methods
  • Workflow*

Grants and funding

This project was co-funded by the USDA-NIFA-Specialty Crop Research Initiative projects, “RosBREED: Enabling marker-assisted breeding in Rosaceae” (2009-51181-05808), “RosBREED: Combining disease resistance with horticultural quality in new rosaceous cultivars” (2014-51181-22378), USDA NIFA Hatch projects 0211277 and 1014919, and the FruitBreedomics project No 265582: “Integrated approach for increasing breeding efficiency in fruit tree crops” that was co-funded by the EU seventh Framework Programme. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.