Polyploidy, or whole-genome doubling, is one of evolution's most powerful forces in plants, yet its real-world consequences in natural populations remain poorly understood. This study uncovers a rare wild system in which diploid and tetraploid forms coexist within the same species, allowing researchers to trace what happens after genome doubling in nature. By combining population genomics, cytotype mapping, and transcriptome analysis, the team showed that tetraploids arose through autopolyploidy, accumulated a higher load of deleterious mutations, and displayed broad shifts in gene expression. The findings reveal how mutation masking, relaxed purifying selection, and regulatory rewiring together shape the establishment and evolutionary potential of newly formed polyploid lineages.
Polyploidy has repeatedly driven plant diversification, adaptation, and innovation across evolutionary history. But while allopolyploidy has been widely studied, autopolyploidy—genome doubling within a single species—has received much less attention, especially in natural populations. One unresolved question is whether extra chromosome copies help buffer harmful mutations, and if so, whether that short-term advantage comes with long-term costs. Another is how genome doubling alters gene regulation and ecological adaptation in the wild. In the genus Orychophragmus , the mountain endemic O. taibaiensis offers a rare opportunity to answer these questions because both diploid and tetraploid plants occur naturally. Based on these challenges, further in-depth research is needed on the evolutionary history and genomic consequences of autopolyploidization in natural plant populations.
Researchers from Sichuan University, together with a collaborator from the Swedish University of Agricultural Sciences, reported (DOI: 10.1093/hr/uhaf314) on November 8, 2025 in Horticulture Research that natural tetraploid populations of Orychophragmus taibaiensis originated through autopolyploidy and experienced distinct genomic and transcriptional consequences after genome doubling, offering a valuable model for understanding how polyploid plants arise, persist, and evolve in mountainous environments.
The researchers first built a robust phylogenetic framework for all six species in the genus using genomic and transcriptomic data, then compared the demographic histories of the widespread O. violaceus and the mountain endemic O. taibaiensis . They found that O. taibaiensis had undergone stronger population contraction and showed weaker purifying selection, helping explain its heavier burden of deleterious mutations.
The team then examined 94 individuals from natural populations and confirmed two cytotypes in O. taibaiensis : diploids with 2n = 24 and tetraploids with 2n = 48. These cytotypes were largely separated by local mountain barriers. Multiple genomic analyses supported an autopolyploid origin for the tetraploids rather than hybrid formation. Modeling further suggested that diploids and tetraploids diverged about 328 thousand years ago. Tetraploids tended to occupy slightly warmer and drier habitats, hinting at ecological differentiation.
At the molecular level, tetraploids showed relaxed purifying selection and a higher fraction of deleterious mutations. RNA-seq analysis revealed thousands of differentially expressed genes in leaves and roots, many linked to signaling, defense response, regulation of gene expression, and circadian rhythm. Genes such as SNI1 , CERK1 , EXT3 , and RECA2 highlighted how genome doubling was accompanied by major regulatory reprogramming.
The study suggests that genome doubling is not simply an increase in DNA content, but a biological turning point that changes how selection, mutation, and gene regulation interact. In newly formed tetraploids, harmful mutations may be partly masked by extra gene copies, allowing these lineages to establish more easily in the short term. At the same time, that buffering effect may reduce the efficiency of purifying selection, creating long-term evolutionary trade-offs that influence persistence, adaptation, and divergence.
Beyond explaining the history of a little-known mountain plant, the work provides a rare empirical framework for understanding how polyploid lineages emerge and survive in nature. That matters because polyploidy is widespread in crops and wild plants alike, influencing adaptation, stress tolerance, and evolutionary innovation. The results may help researchers better interpret the origins of polyploid germplasm, predict the evolutionary stability of mixed-ploidy populations, and identify gene regulatory changes linked to ecological resilience. In the long run, insights from Orychophragmus could support breeding, germplasm utilization, and broader efforts to understand how plants adapt to environmental stress through genome-scale change.
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References
DOI
Original Source URL
https://doi.org/10.1093/hr/uhaf314
Fundning information
This work was supported by the National Natural Science Foundation of China (32000265) and Fundamental Research Funds for the Central Universities (2023SCUNL105) to J.W.
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.
Horticulture Research
Evolutionary history and genomic consequences of polyploidization in natural populations of Orychophragmus taibaiensis
8-Nov-2025
The authors declare that they have no competing interests.