ArticleMolecular biology and evolution2020
Cis- and Trans-Regulatory Variations in the Domestication of the Chili Pepper Fruit.
Article in Molecular biology and evolution, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 32 citations in OpenAlex.
- Single-Cell CRISPR: An Efficient Strategy for Decoding Plant Cis-Regulatory Complexity.Plant biotechnology journal · 2026Review
- Inheritance of DNA Methylation Patterns and Its Role in Modulating Allelic Expression inPlants (Basel, Switzerland) · 2025Article
- Intraspecific gene regulation in cis- and trans.Evolution; international journal of organic evolution · 2025Review
- Article
- Genetic Regulatory Perturbation of Gene Expression Impacted by Genomic Introgression in Fiber Development of Allotetraploid Cotton.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Decoupling subgenomes within hybrid lavandin provide new insights into speciation and monoterpenoid diversification of Lavandula.Plant biotechnology journal · 2023Article
- Dissecting the genetic basis of heterosis in elite super-hybrid rice.Plant physiology · 2023Article
- Expression inheritance and constraints on cis- and trans-regulatory mutations underlying lotus color variation.Plant physiology · 2023Article
- The role of non-additive gene action on gene expression variation in plant domestication.EvoDevo · 2023Article
- Combined population transcriptomic and genomic analysis reveals cis-regulatory differentiation of non-coding RNAs in maize.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Genetic analysis and QTL mapping of domestication-related traits in chili pepper (Frontiers in genetics · 2023Article
- Existing methods are effective at measuring natural selection on gene expression.Nature ecology & evolution · 2022Article
- Spatiotemporal Regulation of a Single Adaptively Evolving Trans-Regulatory Element Contributes to Spermatogenetic Expression Divergence in Drosophila.Molecular biology and evolution · 2022Article
- Transcriptomic Variations and Network Hubs Controlling Seed Size and Weight During Maize Seed Development.Frontiers in plant science · 2022Article
- Inheritance of gene expression throughout fruit development in chili pepper.Scientific reports · 2021Article
- Review
- Biased allelic expression in tissues of F1 hybrids between tropical and temperate lotus (Nelumbo nuicfera).Plant molecular biology · 2021Article
- Transcriptome Analyses Throughout Chili Pepper Fruit Development Reveal Novel Insights into the Domestication Process.Plants (Basel, Switzerland) · 2021Article
- Genomic, Transcriptomic and Epigenomic Tools to Study the Domestication of Plants and Animals: A Field Guide for Beginners.Frontiers in genetics · 2020Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The process of domestication requires the rapid transformation of the wild morphology into the cultivated forms that humans select for. This process often takes place through changes in the regulation of genes, yet, there is no definite pattern on the role of cis- and trans-acting regulatory variations in the domestication of the fruit among crops. Using allele-specific expression and network analyses, we characterized the regulatory patterns and the inheritance of gene expression in wild and cultivated accessions of chili pepper, a crop with remarkable fruit morphological variation. We propose that gene expression differences associated to the cultivated form are best explained by cis-regulatory hubs acting through trans-regulatory cascades. We show that in cultivated chili, the expression of genes associated with fruit morphology is partially recessive with respect to those in the wild relative, consistent with the hybrid fruit phenotype. Decreased expression of fruit maturation and growth genes in cultivated chili suggest that selection for loss-of-function took place in its domestication. Trans-regulatory changes underlie the majority of the genes showing regulatory divergence and had larger effect sizes on gene expression than cis-regulatory variants. Network analysis of selected cis-regulated genes, including ARP9 and MED25, indicated their interaction with many transcription factors involved in organ growth and fruit ripening. Differentially expressed genes linked to cis-regulatory variants and their interactions with downstream trans-acting genes have the potential to drive the morphological differences observed between wild and cultivated fruits and provide an attractive mechanism of morphological transformation during the domestication of the chili pepper.
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