title: Genotyping by Sequencing for SNP-Based Linkage Map Construction and QTL Analysis of Chilling Requirement and Bloom Date in Peach [Prunus persica (L.) Batsch].
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.
authors.affiliation: Department of Biological Sciences, College of Agriculture, Forestry & Life Sciences, Clemson University, Clemson, South Carolina, 29634-0314, United States of America.
authors.forename: Douglas Gary
authors.initials: DG
authors.lastname: Bielenberg
authors.affiliation: Advanced Plant Technology Program, Clemson University, Clemson, South Carolina, 29634, United States of America.
authors.forename: Bradley
authors.initials: B
authors.lastname: Rauh
authors.affiliation: Department of Genetics & Biochemistry, College of Agriculture, Forestry & Life Sciences, Clemson University, Clemson, South Carolina, 29634, United States of America.
authors.forename: Shenghua
authors.initials: S
authors.lastname: Fan
authors.affiliation: Department of Agricultural and Environmental Sciences, College of Agriculture, Forestry & Life Sciences, Clemson University, Clemson, South Carolina, 29634, United States of America.
authors.forename: Ksenija
authors.initials: K
authors.lastname: Gasic
authors.affiliation: Department of Genetics & Biochemistry, College of Agriculture, Forestry & Life Sciences, Clemson University, Clemson, South Carolina, 29634, United States of America.
authors.forename: Albert Glenn
authors.initials: AG
authors.lastname: Abbott
authors.affiliation: Department of Agricultural and Environmental Sciences, College of Agriculture, Forestry & Life Sciences, Clemson University, Clemson, South Carolina, 29634, United States of America.
authors.forename: Gregory Lynn
authors.initials: GL
authors.lastname: Reighard
authors.affiliation: Southeastern Fruit and Tree Nut Research Laboratory (retired), USDA-ARS, Byron, Georgia, 31008, United States of America.
authors.forename: William R
authors.initials: WR
authors.lastname: Okie
authors.affiliation: Department of Biological Sciences, College of Agriculture, Forestry & Life Sciences, Clemson University, Clemson, South Carolina, 29634-0314, United States of America.
authors.forename: Christina Elizabeth
authors.initials: CE
authors.lastname: Wells
mesh_terms: D000383:Agriculture / Q000379:methods*; D019843:Archaeal Proteins; D002874:Chromosome Mapping / Q000379:methods*; D032461:Chromosomes, Plant / Q000235:genetics; D003080:Cold Temperature; D003433:Crosses, Genetic; D018744:DNA, Plant / Q000235:genetics*; D015252:Deoxyribonucleases, Type II Site-Specific; D035264:Flowers / Q000254:growth & development; D015723:Gene Library; D017343:Genes, Plant; D008040:Genetic Linkage; D005838:Genotype; D060005:Genotyping Techniques; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D000068239:Prunus persica / Q000235:genetics* / Q000254:growth & development / Q000502:physiology; D040641:Quantitative Trait Loci; D013997:Time Factors
chemical_list: D019843:Archaeal Proteins; D018744:DNA, Plant; D015252:Deoxyribonucleases, Type II Site-Specific; C000608138:endodeoxyribonuclease ApeKI, Aeropyrum pernix