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.

Features
This publication contains information about 315 features:
Feature NameUniquenameType
WriPdK249WriPdK249genetic_marker
WriPdK250WriPdK250genetic_marker
WriPdK251WriPdK251genetic_marker
WriPdK252WriPdK252genetic_marker
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WriPdK259WriPdK259genetic_marker
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WriPdK267WriPdK267genetic_marker
WriPdK268WriPdK268genetic_marker
WriPdK269WriPdK269genetic_marker
WriPdK270WriPdK270genetic_marker
WriPdK271WriPdK271genetic_marker
WriPdK272WriPdK272genetic_marker
WriPdK273WriPdK273genetic_marker

Pages

Projects
This publication contains information about 1 projects:
Project NameDescription
Almond-shell_hardness-Goonetilleke-2018
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
NonpareilNonpareilaccession
LauranneLauranneaccession
ConstantiConstantiaccession
TarracoTarracoaccession
VairoVairoaccession