ArticlePloS one2013
Characterization of Capsicum annuum genetic diversity and population structure based on parallel polymorphism discovery with a 30K unigene Pepper GeneChip.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 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
37 citing papers in PubMed.
- Elucidating the callus-to-shoot-forming mechanism in Capsicum annuum 'Dempsey' through comparative transcriptome analyses.BMC plant biology · 2024Article
- Article
- Development of a 45K pepper GBTS liquid-phase gene chip and its application in genome-wide association studies.Frontiers in plant science · 2024Article
- Article
- Genomic regions and candidate genes linked with Phytophthora capsici root rot resistance in chile pepper (Capsicum annuum L.).BMC plant biology · 2021Article
- Antibacterial and Therapeutic Potentials of theBioMed research international · 2021Article
- Whole genome resequencing of four Italian sweet pepper landraces provides insights on sequence variation in genes of agronomic value.Scientific reports · 2020Article
- Cis- and Trans-Regulatory Variations in the Domestication of the Chili Pepper Fruit.Molecular biology and evolution · 2020Article
- Target sequencing reveals genetic diversity, population structure, core-SNP markers, and fruit shape-associated loci in pepper varieties.BMC plant biology · 2019Article
- Genome-wide variation patterns between landraces and cultivars uncover divergent selection during modern wheat breeding.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2019Article
- Translation initiation codon (ATG) or SCoT markers-based polymorphism study within and across variousJournal of genetics · 2019Article
- Mitotypes Based on Structural Variation of Mitochondrial Genomes Imply Relationships With Morphological Phenotypes and Cytoplasmic Male Sterility in Peppers.Frontiers in plant science · 2019Article
- Whole-Genome Resequencing of Seven Eggplant (Frontiers in plant science · 2019Article
- Genetic diversity and structure ofHereditas · 2019Article
- Genome-wide genotyping of a novel Mexican Chile Pepper collection illuminates the history of landrace differentiation afterEvolutionary applications · 2019Article
- Article
- The Complete Plastome Sequences of ElevenGenes · 2018Article
- Article
- Quantitative Trait Loci Controlling Fruit Size and Other Horticultural Traits in Bell Pepper (The plant genome · 2018Article
- Response to organic cultivation of heirloom Capsicum peppers: Variation in the level of bioactive compounds and effect of ripening.PloS one · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The widely cultivated pepper, Capsicum spp., important as a vegetable and spice crop world-wide, is one of the most diverse crops. To enhance breeding programs, a detailed characterization of Capsicum diversity including morphological, geographical and molecular data is required. Currently, molecular data characterizing Capsicum genetic diversity is limited. The development and application of high-throughput genome-wide markers in Capsicum will facilitate more detailed molecular characterization of germplasm collections, genetic relationships, and the generation of ultra-high density maps. We have developed the Pepper GeneChip® array from Affymetrix for polymorphism detection and expression analysis in Capsicum. Probes on the array were designed from 30,815 unigenes assembled from expressed sequence tags (ESTs). Our array design provides a maximum redundancy of 13 probes per base pair position allowing integration of multiple hybridization values per position to detect single position polymorphism (SPP). Hybridization of genomic DNA from 40 diverse C. annuum lines, used in breeding and research programs, and a representative from three additional cultivated species (C. frutescens, C. chinense and C. pubescens) detected 33,401 SPP markers within 13,323 unigenes. Among the C. annuum lines, 6,426 SPPs covering 3,818 unigenes were identified. An estimated three-fold reduction in diversity was detected in non-pungent compared with pungent lines, however, we were able to detect 251 highly informative markers across these C. annuum lines. In addition, an 8.7 cM region without polymorphism was detected around Pun1 in non-pungent C. annuum. An analysis of genetic relatedness and diversity using the software Structure revealed clustering of the germplasm which was confirmed with statistical support by principle components analysis (PCA) and phylogenetic analysis. This research demonstrates the effectiveness of parallel high-throughput discovery and application of genome-wide transcript-based markers to assess genetic and genomic features among Capsicum annuum.
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.