Genotyping by Sequencing for SNP-Based Linkage Map Construction and QTL Analysis of Chilling Requirement and Bloom Date in Peach [Prunus persica (L.) Batsch]

PLoS One. 2015 Oct 2;10(10):e0139406. doi: 10.1371/journal.pone.0139406. eCollection 2015.

Abstract

Low-cost, high throughput genotyping methods are crucial to marker discovery and marker-assisted breeding efforts, but have not been available for many 'specialty crops' such as fruit and nut trees. Here we apply the Genotyping-By-Sequencing (GBS) method developed for cereals to the discovery of single nucleotide polymorphisms (SNPs) in a peach F2 mapping population. Peach is a genetic and genomic model within the Rosaceae and will provide a template for the use of this method with other members of this family. Our F2 mapping population of 57 genotypes segregates for bloom time (BD) and chilling requirement (CR) and we have extensively phenotyped this population. The population derives from a selfed F1 progeny of a cross between 'Hakuho' (high CR) and 'UFGold' (low CR). We were able to successfully employ GBS and the TASSEL GBS pipeline without modification of the original methodology using the ApeKI restriction enzyme and multiplexing at an equivalent of 96 samples per Illumina HiSeq 2000 lane. We obtained hundreds of SNP markers which were then used to construct a genetic linkage map and identify quantitative trait loci (QTL) for BD and CR.

Publication types

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

MeSH terms

  • Agriculture / methods*
  • Archaeal Proteins
  • Chromosome Mapping / methods*
  • Chromosomes, Plant / genetics
  • Cold Temperature
  • Crosses, Genetic
  • DNA, Plant / genetics*
  • Deoxyribonucleases, Type II Site-Specific
  • Flowers / growth & development
  • Gene Library
  • Genes, Plant*
  • Genetic Linkage
  • Genotype
  • Genotyping Techniques*
  • High-Throughput Nucleotide Sequencing / methods*
  • Polymorphism, Single Nucleotide*
  • Prunus persica / genetics*
  • Prunus persica / growth & development
  • Prunus persica / physiology
  • Quantitative Trait Loci*
  • Time Factors

Substances

  • Archaeal Proteins
  • DNA, Plant
  • Deoxyribonucleases, Type II Site-Specific
  • endodeoxyribonuclease ApeKI, Aeropyrum pernix

Grants and funding

This research was supported by the Israel United States Binational Agricultural Research and Development program project US-3746-05R to AGA, GLR and DGB and USDA-NRI CSREES grant 2007-35304-17896 to DGB. The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.