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A high-density SNP genotyping array for Brassica napus and its ancestral diploid species based on optimised selection of single-locus markers in the allotetraploid genome
- Source :
- TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik, Theoretical and Applied Genetics
- Publication Year :
- 2016
- Publisher :
- Springer Science and Business Media LLC, 2016.
-
Abstract
- A high-density single nucleotide polymorphism (SNP) Illumina Infinium array, containing 52,157 markers, was developed for the allotetraploid Brassica napus. A stringent selection process employing the short probe sequence for each SNP assay was used to limit the majority of the selected markers to those represented a minimum number of times across the highly replicated genome. As a result approximately 60 % of the SNP assays display genome-specificity, resolving as three clearly separated clusters (AA, AB, and BB) when tested with a diverse range of B. napus material. This genome specificity was supported by the analysis of the diploid ancestors of B. napus, whereby 26,504 and 29,720 markers were scorable in B. oleracea and B. rapa, respectively. Forty-four percent of the assayed loci on the array were genetically mapped in a single doubled-haploid B. napus population allowing alignment of their physical and genetic coordinates. Although strong conservation of the two positions was shown, at least 3 % of the loci were genetically mapped to a homoeologous position compared to their presumed physical position in the respective genome, underlying the importance of genetic corroboration of locus identity. In addition, the alignments identified multiple rearrangements between the diploid and tetraploid Brassica genomes. Although mostly attributed to genome assembly errors, some are likely evidence of rearrangements that occurred since the hybridisation of the progenitor genomes in the B. napus nucleus. Based on estimates for linkage disequilibrium decay, the array is a valuable tool for genetic fine mapping and genome-wide association studies in B. napus and its progenitor genomes.<br />yes
- Subjects :
- Genetic Markers
0106 biological sciences
0301 basic medicine
DNA, Plant
Genotyping Techniques
Brassica
Polymorphism, Single Nucleotide
01 natural sciences
Genome
03 medical and health sciences
Genetics
Selection (genetic algorithm)
Whole genome sequencing
biology
Brassica napus
Chromosome Mapping
food and beverages
Sequence Analysis, DNA
General Medicine
biology.organism_classification
Diploidy
SNP genotyping
Tetraploidy
030104 developmental biology
Genetic marker
Original Article
Ploidy
Agronomy and Crop Science
Genome, Plant
010606 plant biology & botany
Biotechnology
Subjects
Details
- ISSN :
- 14322242 and 00405752
- Volume :
- 129
- Database :
- OpenAIRE
- Journal :
- Theoretical and Applied Genetics
- Accession number :
- edsair.doi.dedup.....c4ed188e0ea148afed9b52b0e304252c