ArticleThe Plant cell2014
Decreased Nucleotide and Expression Diversity and Modified Coexpression Patterns Characterize Domestication in the Common Bean.
Article in The Plant cell, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
59 citing papers in PubMed.
- Evolution of crop phenotypic spaces through domestication.The New phytologist · 2026Article
- Article
- Integration of crop modeling and sensing into molecular breeding for nutritional quality and stress tolerance.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Review
- Differences in the suitability of published honey bee (Apis mellifera) reference genes between the African subspecies Apis mellifera scutellata and European derived Apis mellifera.Molecular ecology · 2025Article
- Genetic and transcriptomic analysis of lentil seed imbibition and dormancy in relation to its domestication.The plant genome · 2025Article
- From the archives: Nitrogen matters in crop domestication, rice nitrogen nutrition, and symbiotic nitrogen fixation.The Plant cell · 2025Article
- Transcriptomic response to nitrogen availability reveals signatures of adaptive plasticity during tetraploid wheat domestication.The Plant cell · 2024Article
- Adaptive gene loss in the common bean pan-genome during range expansion and domestication.Nature communications · 2024Article
- Consistent effects of independent domestication events on the plant microbiota.Current biology : CB · 2024Article
- Article
- Biocultural diversity and crop improvement.Emerging topics in life sciences · 2023Review
- GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes.Genome research · 2023Article
- Domestication of Lima Bean (Phaseolus lunatus) Changes the Microbial Communities in the Rhizosphere.Microbial ecology · 2023Article
- A metabolic perspective of selection for fruit quality related to apple domestication and improvement.Genome biology · 2023Article
- CRISPR/Cas9-Mediated Enrichment Coupled to Nanopore Sequencing Provides a Valuable Tool for the Precise Reconstruction of Large Genomic Target Regions.International journal of molecular sciences · 2023Article
- Evolution of weedy giant ragweed (Ecology and evolution · 2022Article
- The Key to the Future Lies in the Past: Insights from Grain Legume Domestication and Improvement Should Inform Future Breeding Strategies.Plant & cell physiology · 2022Review
- The genomic signature of wild-to-crop introgression during the domestication of scarlet runner bean (Evolution letters · 2022Article
- The INCREASE project: Intelligent Collections of food-legume genetic resources for European agrofood systems.The Plant journal : for cell and molecular biology · 2021Review
- Using precision phenotyping to inform de novo domestication.Plant physiology · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
20 authors.
Funding
Abstract
Using RNA sequencing technology and de novo transcriptome assembly, we compared representative sets of wild and domesticated accessions of common bean (Phaseolus vulgaris) from Mesoamerica. RNA was extracted at the first true-leaf stage, and de novo assembly was used to develop a reference transcriptome; the final data set consists of ∼190,000 single nucleotide polymorphisms from 27,243 contigs in expressed genomic regions. A drastic reduction in nucleotide diversity (∼60%) is evident for the domesticated form, compared with the wild form, and almost 50% of the contigs that are polymorphic were brought to fixation by domestication. In parallel, the effects of domestication decreased the diversity of gene expression (18%). While the coexpression networks for the wild and domesticated accessions demonstrate similar seminal network properties, they show distinct community structures that are enriched for different molecular functions. After simulating the demographic dynamics during domestication, we found that 9% of the genes were actively selected during domestication. We also show that selection induced a further reduction in the diversity of gene expression (26%) and was associated with 5-fold enrichment of differentially expressed genes. While there is substantial evidence of positive selection associated with domestication, in a few cases, this selection has increased the nucleotide diversity in the domesticated pool at target loci associated with abiotic stress responses, flowering time, and morphology.
Identifiers
What OpenQuestion holds
Registered trials
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.