Evolutionary Mechanisms and Molecular Regulatory Networks of Plant Breeding Systems

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Crop Breeding and Genetics".

Deadline for manuscript submissions: 31 July 2026 | Viewed by 668

Special Issue Editor


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Guest Editor
Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Interests: evolution, and molecular mechanisms of plant breeding systems; adaptive evolution and molecular mechanisms of key innovations in plants

Special Issue Information

Dear Colleagues,

Plant breeding systems governing sexual reproduction and asexual reproduction are pivotal for plant evolution and crop yields, and their evolutionary and ecological importance has been studied since Darwin. Modern biology now seeks to decode their underlying molecular blueprints, and the field now integrates multi-omics and molecular biology to unravel the mechanisms of plant breeding systems. This Special Issue aims to link evolutionary mechanisms with the genetic regulatory networks controlling reproduction processes such as floral development (morphological traits, patterns, and longevity of various floral parts), flower–pollinator interactions, mating strategies, self-incompatibility, sex determination, and so forth. We seek to highlight cutting-edge studies using multi-omics, molecular technologies, and genetics to decode the evolution and regulations of such processes. We solicit papers, including original research and reviews, on the molecular basis of reproductive traits, the genomic signatures of mating and breeding system evolution, and the evolutionary genomics of plant reproduction and evolutionary dynamics. This Special Issue will provide therefore a platform for interdisciplinary research, advancing both plant fundamental knowledge and applied crop breeding strategies.

Prof. Dr. Xiaokai Ma
Guest Editor

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Keywords

  • plant breeding systems
  • multi-omics
  • evolutionary genomics
  • flower-pollinator interactions
  • floral development
  • mating strategies
  • self-incompatibility
  • sex determination

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Published Papers (1 paper)

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Research

21 pages, 7099 KB  
Article
Pan-Genomic Evolution of R2R3-MYB and bHLH Transcription Factors in Dendrobium
by Tiancai Wang, Mengke Qin, Danni Luo, Runjie Guo, Linxia Bai, Haotian Zhou, Yang Wang, Yufei Liu, Jinpo Su, Yingjie Luo and Xiaokai Ma
Agronomy 2026, 16(5), 521; https://doi.org/10.3390/agronomy16050521 - 27 Feb 2026
Viewed by 414
Abstract
R2R3-MYB and bHLH transcription factors (TFs) are key regulators of floral secondary metabolism and epidermal development in flowering plants. Orchids exhibit remarkable floral diversity, which is critical for pollination success and ornamental value, yet the evolutionary and functional diversification of these TF families [...] Read more.
R2R3-MYB and bHLH transcription factors (TFs) are key regulators of floral secondary metabolism and epidermal development in flowering plants. Orchids exhibit remarkable floral diversity, which is critical for pollination success and ornamental value, yet the evolutionary and functional diversification of these TF families within the genus remains largely unexplored. Here, we conducted a comprehensive pan-genome dissection of R2R3-MYB and bHLH TF families across 18 Dendrobium species, integrating orthologs assignment, phylogenetics, duplication profiling, cis-regulatory annotation, and tissue-specific expression analysis. We identified 3074 R2R3-MYB and 2282 bHLH genes, classified into 69 and 61 orthologous gene groups (OGGs), respectively. Core OGGs accounted for two-thirds of both families, indicating strong evolutionary conservation, whereas variable OGGs reflected lineage-specific diversification. Phylogenetic analyses resolved R2R3-MYBs into 24 canonical subfamilies and revealed conserved heterogeneous expansion patterns in bHLH subfamilies. Promoter architectures of R2R3-MYB genes were enriched in hormone-, stress-, and light-responsive elements, whereas bHLH promoters were dominated by development-related motifs. Tissue-specific expression profiling in Dendrobium ‘Chao Praya Smile’ showed that floral bud-enriched genes were associated with flavonoid/anthocyanin biosynthesis, whereas root-enriched genes were linked to stress and hormone responses. Integration of pan-genomics and transcriptomics highlighted evolutionary trajectory and functional divergence between core and variable gene sets within Dendrobium. Our study establishes a comprehensive, genus-wide framework for understanding the evolutionary and functional characteristics of MYB–bHLH regulatory networks in Dendrobium. These findings provide valuable genetic resources and key candidate targets for functional characterization and molecular breeding, with important implications for genetic improvement of reproductive traits, floral quality, stress resistance, and ornamental and agronomic value in orchids. Full article
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