ArticleAnnals of botany2007
Tagging the signatures of domestication in common bean (Phaseolus vulgaris) by means of pooled DNA samples.
Article in Annals of botany, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 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
33 citing papers in PubMed, 89 citations in OpenAlex.
- Sampling strategies for genotyping common bean (Frontiers in plant science · 2024Article
- Limited genetic diversity found among genotypes of the Entada landrace (Frontiers in plant science · 2024Article
- Biocultural diversity and crop improvement.Emerging topics in life sciences · 2023Review
- Genome-wide association study of common resistance to rust species in tetraploid wheat.Frontiers in plant science · 2023Article
- Characterization of fungal pathogens and germplasm screening for disease resistance in the main production area of the common bean in Argentina.Frontiers in plant science · 2022Review
- Consequences of introgression and gene flow on the genetic structure and diversity of Lima bean (PeerJ · 2022Article
- Preserving Biodiversity in Marginal Rural Areas: Assessment of Morphological and Genetic Variability of a Sicilian Common Bean Germplasm Collection.Plants (Basel, Switzerland) · 2020Article
- Current State and Perspectives in Population Genomics of the Common Bean.Plants (Basel, Switzerland) · 2020Review
- Evidence for Strong Kinship Influence on the Extent of Linkage Disequilibrium in Cultivated Common Beans.Genes · 2018Article
- Genetic Mapping of Loci for Resistance to Stem Rust in a Tetraploid Wheat Collection.International journal of molecular sciences · 2018Article
- Genetic markers associated to arbuscular mycorrhizal colonization in durum wheat.Scientific reports · 2018Article
- In-depth genome characterization of a Brazilian common bean core collection using DArTseq high-density SNP genotyping.BMC genomics · 2017Article
- Comparison of Genetic Diversity between Chinese and American Soybean (Frontiers in plant science · 2017Article
- Establishing the Bases for Introducing the Unexplored Portuguese Common Bean Germplasm into the Breeding World.Frontiers in plant science · 2017Article
- Beans (Frontiers in plant science · 2017Review
- High Level of Nonsynonymous Changes in Common Bean Suggests That Selection under Domestication Increased Functional Diversity at Target Traits.Frontiers in plant science · 2016Article
- Identification of New Resistance Loci to African Stem Rust Race TTKSK in Tetraploid Wheats Based on Linkage and Genome-Wide Association Mapping.Frontiers in plant science · 2015Article
- European flint landraces grown in situ reveal adaptive introgression from modern maize.PloS one · 2015Article
- Population Structure, Genetic Variation, and Linkage Disequilibrium in Perennial Ryegrass Populations Divergently Selected for Freezing Tolerance.Frontiers in plant science · 2015Article
- Decreased Nucleotide and Expression Diversity and Modified Coexpression Patterns Characterize Domestication in the Common Bean.The Plant cell · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
BACKGROUND AND
aimsThe main aim of this study was to use an amplified fragment length polymorphism (AFLP)-based, large-scale screening of the whole genome of Phaseolus vulgaris to determine the effects of selection on the structure of the genetic diversity in wild and domesticated populations.
methodsUsing pooled DNA samples, seven each of wild and domesticated populations of P. vulgaris were studied using 2506 AFLP markers (on average, one every 250 kb). About 10 % of the markers were also analysed on individual genotypes and were used to infer allelic frequencies empirically from bulk data. In both data sets, tests were made to determine the departure from neutral expectation for each marker using an F(ST)-based method. KEY
resultsThe most important outcome is that a large fraction of the genome of the common bean (16 %; P < 0.01) appears to have been subjected to effects of selection during domestication. Markers obtained in individual genotypes were also mapped and classified according to their proximities to known genes and quantitative trait loci (QTLs) of the domestication syndrome. Most of the markers that were found to be potentially under the effects of selection were located in the proximity of previously mapped genes and QTLs related to the domestication syndrome.
conclusionsOverall, the results indicate that in P. vulgaris a large portion of the genome appears to have been subjected to the effects of selection, probably because of linkage to the loci selected during domestication. As most of the markers that are under the effects of selection are linked to known loci related to the domestication syndrome, it is concluded that population genomics approaches are very efficient in detecting QTLs. A method based on bulk DNA samples is presented that is effective in pre-screening for a large number of markers to determine selection signatures.
Indexed as
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.