ArticleGenome biology2015
A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes.
Article in Genome biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 131 papers.
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Who cites it
131 citing papers in PubMed.
- Integration of the D-Genome Reshapes Gene Transcription, Chromatin Architecture, and Metabolome of Allohexaploid Wheat, Leading to Enhanced Environmental Adaptability.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Wheat's war against stripe rust: Integrating host immunity, genomics and breeding for durable resistance.The plant genome · 2026Review
- Dissecting adult plant resistance to stripe and leaf rust in advanced Indian wheat breeding lines through a genome-wide association study.BMC plant biology · 2026Article
- A whole-genome assembly of St. Augustinegrass and visualizing diversity within the species.The plant genome · 2026Article
- Uncover the genetic basis of processing quality related traits in common wheat (Frontiers in plant science · 2026Article
- Whole-genome sequencing of 1,060 Brettanomyces bruxellensis isolates reveals significant phenotypic impact of acquired subgenomes in allopolyploids.Nature communications · 2025Article
- A novel quantitative trait locus for barley yellow dwarf virus resistance and kernel traits on chromosome 2D of a wheat cultivar Jagger.The plant genome · 2025Article
- Using cross-country datasets for association mapping in Arachis hypogaea L.The plant genome · 2024Article
- Analysis of a global wheat panel reveals a highly diverse introgression landscape and provides evidence for inter-homoeologue chromosomal recombination.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- GWAS elucidated grain yield genetics in Indian spring wheat under diverse water conditions.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Genomic wide association study and selective sweep analysis identify genes associated with improved yield under drought in Turkish winter wheat germplasm.Scientific reports · 2024Article
- Skim exome capture genotyping in wheat.The plant genome · 2023Article
- Whole-genome sequencing of diverse wheat accessions uncovers genetic changes during modern breeding in China and the United States.The Plant cell · 2023Article
- Wheat bZIPC1 interacts with FT2 and contributes to the regulation of spikelet number per spike.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Duplicate Genes Contribute to Variability in Abiotic Stress Resistance in Allopolyploid Wheat.Plants (Basel, Switzerland) · 2023Review
- Polygenic influences on the behavioral effects of alcohol withdrawal in a mixed-ancestry population from the collaborative study on the genetics of alcoholism (COGA).Molecular and cellular neurosciences · 2023Article
- Wheat EARLY FLOWERING 3 affects heading date without disrupting circadian oscillations.Plant physiology · 2023Article
- Triticeae crop genome biology: an endless frontier.Frontiers in plant science · 2023Review
- Genome-wide association mapping for wheat morphometric seed traits in Iranian landraces and cultivars under rain-fed and well-watered conditions.Scientific reports · 2022Article
- InDels Identification and Association Analysis with Spike and Awn Length in Chinese Wheat Mini-Core Collection.International journal of molecular sciences · 2022Article
71 more citing papers are in PubMed but not listed here.
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Authors and funding
25 authors.
Funding
Abstract
backgroundBread wheat is an allopolyploid species with a large, highly repetitive genome. To investigate the impact of selection on variants distributed among homoeologous wheat genomes and to build a foundation for understanding genotype-phenotype relationships, we performed population-scale re-sequencing of a diverse panel of wheat lines.
resultsA sample of 62 diverse lines was re-sequenced using the whole exome capture and genotyping-by-sequencing approaches. We describe the allele frequency, functional significance, and chromosomal distribution of 1.57 million single nucleotide polymorphisms and 161,719 small indels. Our results suggest that duplicated homoeologous genes are under purifying selection. We find contrasting patterns of variation and inter-variant associations among wheat genomes; this, in addition to demographic factors, could be explained by differences in the effect of directional selection on duplicated homoeologs. Only a small fraction of the homoeologous regions harboring selected variants overlapped among the wheat genomes in any given wheat line. These selected regions are enriched for loci associated with agronomic traits detected in genome-wide association studies.
conclusionsEvidence suggests that directional selection in allopolyploids rarely acted on multiple parallel advantageous mutations across homoeologous regions, likely indicating that a fitness benefit could be obtained by a mutation at any one of the homoeologs. Additional advantageous variants in other homoelogs probably either contributed little benefit, or were unavailable in populations subjected to directional selection. We hypothesize that allopolyploidy may have increased the likelihood of beneficial allele recovery by broadening the set of possible selection targets.
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