ArticleGenome biology2011
Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome.
Article in Genome biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.
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79 citing papers in PubMed.
- Wheat improvement through advances in single nucleotide polymorphism (SNP) detection and genotyping with a special emphasis on rust resistance.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Review
- mosGraphGen: a novel tool to generate multi-omics signaling graphs to facilitate integrative and interpretable graph AI model development.bioRxiv : the preprint server for biology · 2024Article
- Distinct structural variants and repeat landscape shape the genomes of the ancient grapes Aglianico and Falanghina.BMC plant biology · 2024Article
- mosGraphGen: a novel tool to generate multi-omics signaling graphs to facilitate integrative and interpretable graph AI model development.Bioinformatics advances · 2024Article
- Phenotypic and transcriptional characterization ofFrontiers in microbiology · 2024Article
- Genetic approaches to exploit landraces for improvement ofFrontiers in plant science · 2023Review
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- Pharmacologically induced weight loss is associated with distinct gut microbiome changes in obese rats.BMC microbiology · 2022Article
- Early Changes in Immune Cell Count, Metabolism, and Function Following Sleeve Gastrectomy: A Prospective Human Study.The Journal of clinical endocrinology and metabolism · 2022Article
- Comprehensive evaluation of mapping complex traits in wheat using genome-wide association studies.Molecular breeding : new strategies in plant improvement · 2022Review
- The Use and Limitations of Exome Capture to Detect Novel Variation in the Hexaploid Wheat Genome.Frontiers in plant science · 2022Article
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- Early changes in immune cell metabolism and function are a hallmark of sleeve gastrectomy: a prospective human study.medRxiv : the preprint server for health sciences · 2020Article
- Next Generation Sequencing Based Forward Genetic Approaches for Identification and Mapping of Causal Mutations in Crop Plants: A Comprehensive Review.Plants (Basel, Switzerland) · 2020Review
- Genomic Patterns of Introgression in Interspecific Populations Created by Crossing Wheat with Its Wild Relative.G3 (Bethesda, Md.) · 2020Article
- Development and deployment of KASP markers for multiple alleles of Lr34 in wheat.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Article
- A genome-wide survey of copy number variations reveals an asymmetric evolution of duplicated genes in rice.BMC biology · 2020Article
- AthCNV: A Map of DNA Copy Number Variations in the Arabidopsis Genome.The Plant cell · 2020Article
- An Integrated Strategy for Identifying Targets of Ubiquitin-Mediated Degradation in CD4+ T Cells.Methods in molecular biology (Clifton, N.J.) · 2020Article
- Structural Variations Affecting Genes and Transposable Elements of Chromosome 3B in Wheats.Frontiers in genetics · 2020Article
19 more citing papers are in PubMed but not listed here.
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3 authors.
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Abstract
backgroundThe ability of grass species to adapt to various habitats is attributed to the dynamic nature of their genomes, which have been shaped by multiple rounds of ancient and recent polyploidization. To gain a better understanding of the nature and extent of variation in functionally relevant regions of a polyploid genome, we developed a sequence capture assay to compare exonic sequences of allotetraploid wheat accessions.
resultsA sequence capture assay was designed for the targeted re-sequencing of 3.5 Mb exon regions that surveyed a total of 3,497 genes from allotetraploid wheat. These data were used to describe SNPs, copy number variation and homoeologous sequence divergence in coding regions. A procedure for variant discovery in the polyploid genome was developed and experimentally validated. About 1% and 24% of discovered SNPs were loss-of-function and non-synonymous mutations, respectively. Under-representation of replacement mutations was identified in several groups of genes involved in translation and metabolism. Gene duplications were predominant in a cultivated wheat accession, while more gene deletions than duplications were identified in wild wheat.
conclusionsWe demonstrate that, even though the level of sequence similarity between targeted polyploid genomes and capture baits can bias enrichment efficiency, exon capture is a powerful approach for variant discovery in polyploids. Our results suggest that allopolyploid wheat can accumulate new variation in coding regions at a high rate. This process has the potential to broaden functional diversity and generate new phenotypic variation that eventually can play a critical role in the origin of new adaptations and important agronomic traits.
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