Genotyping-by-Sequencing in Almond: SNP Discovery, Linkage Mapping and Marker Design

Publication Overview
TitleGenotyping-by-Sequencing in Almond: SNP Discovery, Linkage Mapping and Marker Design
AuthorsGoonetilleke SN, March TJ, Wirthensohn MG, Arús P, Walker AR, Mather DE
TypeJournal Article
Journal NameG3: GENES, GENOMES, GENETICS
Volume8
Issue1
Year2017
Page(s)161-172
CitationGoonetilleke SN, March TJ, Wirthensohn MG, Arús P, Walker AR, Mather DE. Genotyping-by-Sequencing in Almond: SNP Discovery, Linkage Mapping and Marker Design. G3. 2017 Nov 15; 8(1):161-172.

Abstract

In crop plant genetics, linkage maps provide the basis for the mapping of loci that affect important traits and for the selection of markers to be applied in crop improvement. In outcrossing species such as almond [Prunus dulcis (Mill.) D.A. Webb], application of a double pseudo-testcross mapping approach to the F1 progeny of a bi-parental cross leads to the construction of a linkage map for each parent. Here, we report on the application of genotyping-by-sequencing to discover and map single-nucleotide polymorphisms in the almond cultivars 'Nonpareil' and 'Lauranne'. Allele-specific marker assays were developed for 309 tag pairs. Application of these assays to 231 'Nonpareil' × 'Lauranne' F1 progeny provided robust linkage maps for each parent. Analysis of phenotypic data for shell hardness demonstrated the utility of these maps for quantitative trait locus mapping. Comparison of these maps to the peach genome assembly confirmed high synteny and collinearity between the peach and almond genomes. The marker assays were applied to progeny from several other 'Nonpareil' crosses, providing the basis for a composite linkage map of 'Nonpareil'. Applications of the assays to a panel of almond clones and a panel of rootstocks used for almond production demonstrated the broad applicability of the markers and providing subsets of markers that could be used to discriminate among accessions. The sequence-based linkage maps and single nucleotide polymorphism assays presented here could be useful resources for the genetic analysis and genetic improvement of almond.

Stocks
This publication contains information about 9 stocks:
Stock NameUniquenameType
Nonpareil_x_LauranneNonpareil_x_Laurannepopulation
Nonpareil_x_ConstantiNonpareil_x_Constantipopulation
Nonpareil_x_TarracoNonpareil_x_Tarracopopulation
Nonpareil_x_VairoNonpareil_x_Vairopopulation
NonpareilNonpareilcultivar
LauranneLaurannecultivar
ConstantiConstanticultivar
TarracoTarracocultivar
VairoVairocultivar
Projects
This publication contains information about 1 projects:
Project NameDescription
Almond-shell_hardness-Goonetilleke-2018
Features
This publication contains information about 315 features:
Feature NameUniquenameType
shell hardnessqSH.NL-2018-Lauranne-LG5.2QTL
shell hardnessqSH.NL-2018-Lauranne-LG8QTL
WriPdK1WriPdK1genetic_marker
WriPdK2WriPdK2genetic_marker
WriPdK3WriPdK3genetic_marker
WriPdK4WriPdK4genetic_marker
WriPdK5WriPdK5genetic_marker
WriPdK6WriPdK6genetic_marker
WriPdK7WriPdK7genetic_marker
WriPdK8WriPdK8genetic_marker
WriPdK9WriPdK9genetic_marker
WriPdK10WriPdK10genetic_marker
WriPdK11WriPdK11genetic_marker
WriPdK12WriPdK12genetic_marker
WriPdK13WriPdK13genetic_marker
WriPdK14WriPdK14genetic_marker
WriPdK15WriPdK15genetic_marker
WriPdK16WriPdK16genetic_marker
WriPdK17WriPdK17genetic_marker
WriPdK18WriPdK18genetic_marker
WriPdK19WriPdK19genetic_marker
WriPdK20WriPdK20genetic_marker
WriPdK21WriPdK21genetic_marker
WriPdK22WriPdK22genetic_marker
WriPdK23WriPdK23genetic_marker

Pages

Properties
Additional details for this publication include:
Property NameValue
CopyrightCopyright © 2017, G3: Genes, Genomes, Genetics.
DOI10.1534/g3.117.300376
eISSN2160-1836
ISSN2160-1836
Journal AliasG3 (Bethesda)
Journal CountryUnited States
LanguageEnglish
Language Abbreng
PIIg3.300376.2017
Publication Date2017 Nov 15
Publication ModelPrint-Electronic
Publication TypeJournal Article
URLhttp://www.g3journal.org/content/8/1/161.long
Published Location161-172
Journal AliasG3 (Bethesda, Md.)
Cross References
This publication is also available in the following databases:
DatabaseAccession
PMID: PubMedPMID:29141988