ArticlePloS one2013
Genomic DNA enrichment using sequence capture microarrays: a novel approach to discover sequence nucleotide polymorphisms (SNP) in Brassica napus L.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed, 48 citations in OpenAlex.
- Article
- Linkage disequilibrium and population structure in a core collection of Brassica napus (L.).PloS one · 2022Article
- Article
- Genomics Armed With Diversity Leads the Way inFrontiers in genetics · 2021Review
- Article
- Connecting genome structural variation with complex traits in crop plants.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2019Review
- Genetic Diversity and Population Structure of aFrontiers in plant science · 2019Article
- Transcriptome analysis and annotation: SNPs identified from single copy annotated unigenes of three polyploid blueberry crops.PloS one · 2019Article
- Genomic approaches for studying crop evolution.Genome biology · 2018Review
- Development and Applications of a High Throughput Genotyping Tool for Polyploid Crops: Single Nucleotide Polymorphism (SNP) Array.Frontiers in plant science · 2018Review
- Mining sequence variations in representative polyploid sugarcane germplasm accessions.BMC genomics · 2017Article
- Liquid-phase sequence capture and targeted re-sequencing revealed novel polymorphisms in tomato genes belonging to the MEP carotenoid pathway.Scientific reports · 2017Article
- Exploiting the great potential of Sequence Capture data by a new tool, SUPER-CAP.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
- From Genomes to GENE-omes: Exome Sequencing Concept and Applications in Crop Improvement.Frontiers in plant science · 2017Review
- 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.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2016Article
- Sequence capture by hybridization to explore modern and ancient genomic diversity in model and nonmodel organisms.Nucleic acids research · 2016Review
- Understanding and utilizing crop genome diversity via high-resolution genotyping.Plant biotechnology journal · 2016Review
- Microarray experiments and factors which affect their reliability.Biology direct · 2015Review
- Current and new approaches in GMO detection: challenges and solutions.BioMed research international · 2015Review
- Co-localisation of the blackleg resistance genes Rlm2 and LepR3 on Brassica napus chromosome A10.BMC plant biology · 2014Article
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Authors and funding
10 authors at 5 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Targeted genomic selection methodologies, or sequence capture, allow for DNA enrichment and large-scale resequencing and characterization of natural genetic variation in species with complex genomes, such as rapeseed canola (Brassica napus L., AACC, 2n=38). The main goal of this project was to combine sequence capture with next generation sequencing (NGS) to discover single nucleotide polymorphisms (SNPs) in specific areas of the B. napus genome historically associated (via quantitative trait loci -QTL- analysis) to traits of agronomical and nutritional importance. A 2.1 million feature sequence capture platform was designed to interrogate DNA sequence variation across 47 specific genomic regions, representing 51.2 Mb of the Brassica A and C genomes, in ten diverse rapeseed genotypes. All ten genotypes were sequenced using the 454 Life Sciences chemistry and to assess the effect of increased sequence depth, two genotypes were also sequenced using Illumina HiSeq chemistry. As a result, 589,367 potentially useful SNPs were identified. Analysis of sequence coverage indicated a four-fold increased representation of target regions, with 57% of the filtered SNPs falling within these regions. Sixty percent of discovered SNPs corresponded to transitions while 40% were transversions. Interestingly, fifty eight percent of the SNPs were found in genic regions while 42% were found in intergenic regions. Further, a high percentage of genic SNPs was found in exons (65% and 64% for the A and C genomes, respectively). Two different genotyping assays were used to validate the discovered SNPs. Validation rates ranged from 61.5% to 84% of tested SNPs, underpinning the effectiveness of this SNP discovery approach. Most importantly, the discovered SNPs were associated with agronomically important regions of the B. napus genome generating a novel data resource for research and breeding this crop species.
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