ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2010
Deleterious amino acid polymorphisms in Arabidopsis thaliana and rice.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 48 citations in OpenAlex.
- Genomic insights into deleterious mutations and their impact on agronomic traits during pear domestication.Horticulture research · 2025Article
- Elevated Mutation Burdens in Canadian Oat and Wheat Cultivars Released over the Past Century.Cells · 2025Article
- Incorporating genetic load contributes to predicting Arabidopsis thaliana's response to climate change.Nature communications · 2025Article
- Patterns of the Predicted Mutation Burden in 19,778 Domesticated Barley Accessions Conserved Ex Situ.International journal of molecular sciences · 2024Article
- Deleterious and Adaptive Mutations in Plant Germplasm Conserved Ex Situ.Molecular biology and evolution · 2023Article
- Genetic structure and first genome-wide insights into the adaptation of a wild relative of grapevine,Evolutionary applications · 2023Article
- PPVED: A machine learning tool for predicting the effect of single amino acid substitution on protein function in plants.Plant biotechnology journal · 2022Article
- Non-CG DNA methylation-deficiency mutations enhance mutagenesis rates during salt adaptation in cultured Arabidopsis cells.Stress biology · 2021Article
- Evolutionary Genomics of Structural Variation in Asian Rice (Oryza sativa) Domestication.Molecular biology and evolution · 2020Article
- Allelic Variation in the Chloroplast Division GenePlant physiology · 2019Article
- Article
- Comparative Genomics Approaches Accurately Predict Deleterious Variants in Plants.G3 (Bethesda, Md.) · 2018Article
- A Pipeline for Classifying Deleterious Coding Mutations in Agricultural Plants.Frontiers in plant science · 2018Article
- Bioinformatically predicted deleterious mutations reveal complementation in the interior spruce hybrid complex.BMC genomics · 2017Article
- The interplay of demography and selection during maize domestication and expansion.Genome biology · 2017Article
- The Role of Deleterious Substitutions in Crop Genomes.Molecular biology and evolution · 2016Article
- Genetic shift in local rice populations during rice breeding programs in the northern limit of rice cultivation in the world.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2015Article
- The pattern and distribution of deleterious mutations in maize.G3 (Bethesda, Md.) · 2014Article
- SIFT web server: predicting effects of amino acid substitutions on proteins.Nucleic acids research · 2012Article
- Crop genomics: advances and applications.Nature reviews. Genetics · 2011Review
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Plant genetic diversity has been mainly investigated with neutral markers, but large-scale DNA sequencing projects now enable the identification and analysis of different classes of genetic polymorphisms, such as non-synonymous single nucleotide polymorphisms (nsSNPs) in protein coding sequences. Using the SIFT and MAPP programs to predict whether nsSNPs are tolerated (i.e., effectively neutral) or deleterious for protein function, genome-wide nsSNP data from Arabidopsis thaliana and rice were analyzed. In both species, about 20% of polymorphic sites with nsSNPs were classified as deleterious; they segregate at lower allele frequencies than tolerated nsSNPs due to purifying selection. Furthermore, A. thaliana accessions from marginal populations show a higher relative proportion of deleterious nsSNPs, which likely reflects differential selection or demographic effects in subpopulations. To evaluate the sensitivity of predictions, genes from model and crop plants with known functional effects of nsSNPs were inferred with the algorithms. The programs predicted about 70% of nsSNPs correctly as tolerated or deleterious, i.e., as having a functional effect. Forward-in-time simulations of bottleneck and domestication models indicated a high power to detect demographic effects on nsSNP frequencies in sufficiently large datasets. The results indicate that nsSNPs are useful markers for analyzing genetic diversity in plant genetic resources and breeding populations to infer natural/artificial selection and genetic drift.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.