Genotyping by Sequencing Using Specific Allelic Capture to Build a High-Density Genetic Map of Durum Wheat

Targeted sequence capture is a promising technology which helps reduce costs for sequencing and genotyping numerous genomic regions in large sets of individuals. Bait sequences are designed to capture specific alleles previously discovered in parents or reference populations. We studied a set of 135...

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Bibliographic Details
Published in:PloS one 2016-05, Vol.11 (5), p.e0154609-e0154609
Main Authors: Holtz, Yan, Ardisson, Morgane, Ranwez, Vincent, Besnard, Alban, Leroy, Philippe, Poux, Gérard, Roumet, Pierre, Viader, Véronique, Santoni, Sylvain, David, Jacques
Format: Article
Language:English
Subjects:
Agricultural sciences
Alleles
Baits
Bioinformatics
Biology and Life Sciences
Cereals
Chromosome Mapping
Chromosomes
Contig Mapping
Deoxyribonucleic acid
DNA
Domestication
Gene mapping
Gene sequencing
Genetic aspects
Genetics
Genomes
Genotyping
Genotyping Techniques - methods
Influence
Life Sciences
Medicine and Health Sciences
Parents
Physical mapping
Polymorphism, Genetic
Polymorphism, Single Nucleotide - genetics
Population genetics
Population studies
Research and Analysis Methods
Sequence Analysis, DNA - methods
Single nucleotide polymorphisms
Single-nucleotide polymorphism
Triticum
Triticum - genetics
Triticum aestivum
Triticum durum
Triticum turgidum
Vegetal Biology
Wheat
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Summary:Targeted sequence capture is a promising technology which helps reduce costs for sequencing and genotyping numerous genomic regions in large sets of individuals. Bait sequences are designed to capture specific alleles previously discovered in parents or reference populations. We studied a set of 135 RILs originating from a cross between an emmer cultivar (Dic2) and a recent durum elite cultivar (Silur). Six thousand sequence baits were designed to target Dic2 vs. Silur polymorphisms discovered in a previous RNAseq study. These baits were exposed to genomic DNA of the RIL population. Eighty percent of the targeted SNPs were recovered, 65% of which were of high quality and coverage. The final high density genetic map consisted of more than 3,000 markers, whose genetic and physical mapping were consistent with those obtained with large arrays.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0154609