ArticleMolecular biology and evolution2016
The Role of Deleterious Substitutions in Crop Genomes.
Article in Molecular biology and evolution, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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Who cites it
54 citing papers in PubMed.
- Measuring the change in deleterious mutation burden of barley germplasm conserved over one regeneration cycle.G3 (Bethesda, Md.) · 2026Article
- Prioritization of deleterious mutations informs genomic prediction and increases the rate of gain in common bean (Phaseolus vulgaris L.), a simulation study.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Genomic divergence, adaptation, and the genetic basis of quality traits in ancient walnut landraces and wild relatives.Horticulture research · 2026Article
- Whole-genome resequencing of the wild barley diversity collection: a resource for identifying and exploiting genetic variation for cultivated barley improvement.G3 (Bethesda, Md.) · 2026Article
- The Evolutionary Dynamics of Genetic Mutational Load Throughout Tomato Domestication History.Molecular ecology · 2025Article
- Domestication During Restoration: Unintentional Selection During Eight Generations of Wild Seed Propagation Reduces Herkogamy, Dichogamy and Heterozygosity in Clarkia pulchella.Molecular ecology · 2025Article
- Genomic insights into deleterious mutations and their impact on agronomic traits during pear domestication.Horticulture research · 2025Article
- Accumulating Heterozygous Deleterious Mutations in Conserved Soybean Germplasm over Successive Regenerations.Plants (Basel, Switzerland) · 2025Article
- Elevated Mutation Burdens in Canadian Oat and Wheat Cultivars Released over the Past Century.Cells · 2025Article
- Sodium azide mutagenesis induces a unique pattern of mutations.PLoS genetics · 2025Article
- Incorporating genetic load contributes to predicting Arabidopsis thaliana's response to climate change.Nature communications · 2025Article
- Population Genomics Reveals Elevated Inbreeding and Accumulation of Deleterious Mutations in White Raccoon Dogs.Biology · 2025Article
- Article
- Patterns of the Predicted Mutation Burden in 19,778 Domesticated Barley Accessions Conserved Ex Situ.International journal of molecular sciences · 2024Article
- Conservation genomics provides insights into genetic resilience and adaptation of the endangered Chinese hazelnut,Plant diversity · 2024Article
- Porous borders at the wild-crop interface promote weed adaptation in Southeast Asia.Nature communications · 2024Article
- Deleterious and Adaptive Mutations in Plant Germplasm Conserved Ex Situ.Molecular biology and evolution · 2023Article
- Genomic signatures of bottleneck and founder effects in dingoes.Ecology and evolution · 2023Article
- Unraveling Prevalence and Effects of Deleterious Mutations in Maize Elite Lines across Decades of Modern Breeding.Molecular biology and evolution · 2023Article
- Deleterious Variation in Natural Populations and Implications for Conservation Genetics.Annual review of animal biosciences · 2023Review
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Populations continually incur new mutations with fitness effects ranging from lethal to adaptive. While the distribution of fitness effects of new mutations is not directly observable, many mutations likely either have no effect on organismal fitness or are deleterious. Historically, it has been hypothesized that a population may carry many mildly deleterious variants as segregating variation, which reduces the mean absolute fitness of the population. Recent advances in sequencing technology and sequence conservation-based metrics for inferring the functional effect of a variant permit examination of the persistence of deleterious variants in populations. The issue of segregating deleterious variation is particularly important for crop improvement, because the demographic history of domestication and breeding allows deleterious variants to persist and reach moderate frequency, potentially reducing crop productivity. In this study, we use exome resequencing of 15 barley accessions and genome resequencing of 8 soybean accessions to investigate the prevalence of deleterious single nucleotide polymorphisms (SNPs) in the protein-coding regions of the genomes of two crops. We conclude that individual cultivars carry hundreds of deleterious SNPs on average, and that nonsense variants make up a minority of deleterious SNPs. Our approach identifies known phenotype-altering variants as deleterious more frequently than the genome-wide average, suggesting that putatively deleterious variants are likely to affect phenotypic variation. We also report the implementation of a SNP annotation tool BAD_Mutations that makes use of a likelihood ratio test based on alignment of all currently publicly available Angiosperm genomes.
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