Ligulate inflorescence of Helianthus × multiflorus, cv. Soleil d'Or, correlates with a mis-regulation of a CYCLOIDEA gene characterised by insertion of a transposable element

Exploring the patterns of evolution: Core thoughts and focus on the saltational model

The Modern Synthesis, a pillar in biological thought, united Darwin's species origin concepts with Mendel's laws of character heredity, providing a comprehensive understanding of evolution within species. Highlighting phenotypic variation and natural selection, it elucidated the environment's role as a selective force, shaping populations over time. This framework integrated additional mechanisms, including genetic drift, random mutations, and gene flow, predicting their cumulative effects on microevolution and the emergence of new species. Beyond the Modern Synthesis, the Extended Evolutionary Synthesis expands perspectives by recognizing the role of developmental plasticity, non-genetic inheritance, and epigenetics. We suggest that these aspects coexist in the plant evolutionary process; in this context, we focus on the saltational model, emphasizing how saltation events, such as dichotomous saltation, chromosomal mutations, epigenetic phenomena, and polyploidy, contribute to rapid evolutionary changes. The saltational model proposes that certain evolutionary changes, such as the rise of new species, may result suddenly from single macromutations rather than from gradual changes in DNA sequences and allele frequencies within a species over time. These events, observed in domesticated and wild higher plants, provide well-defined mechanistic bases, revealing their profound impact on plant diversity and rapid evolutionary events. Notably, next-generation sequencing exposes the likely crucial role of allopolyploidy and autopolyploidy (saltational events) in generating new plant species, each characterized by distinct chromosomal complements. In conclusion, through this review, we offer a thorough exploration of the ongoing dissertation on the saltational model, elucidating its implications for our understanding of plant evolutionary processes and paving the way for continued research in this intriguing field.

HD-ZIP Transcription Factors and Brassinosteroid Signaling Play a Role in Capitulum Patterning in Chrysanthemum

Chrysanthemum is a genus in the Asteraceae family containing numerous cut flower varieties with high ornamental value. It owes its beauty to the composite flower head, which resembles a compact inflorescence. This structure is also known as a capitulum, in which many ray and disc florets are densely packed. The ray florets are localized at the rim, are male sterile, and have large colorful petals. The centrally localized disc florets develop only a small petal tube but produce fertile stamens and a functional pistil. Nowadays, varieties with more ray florets are bred because of their high ornamental value, but, unfortunately, this is at the expense of their seed setting. In this study, we confirmed that the disc:ray floret ratio is highly correlated to seed set efficiency, and therefore, we further investigated the mechanisms that underlie the regulation of the disc:ray floret ratio. To this end, a comprehensive transcriptomics analysis was performed in two acquired mutants with a higher disc:ray floret ratio. Among the differentially regulated genes, various potential brassinosteroid (BR) signaling genes and HD-ZIP class IV homeodomain transcription factors stood out. Detailed follow-up functional studies confirmed that reduced BR levels and downregulation of HD-ZIP IV gene Chrysanthemum morifolium PROTODERMAL FACTOR 2 (CmPDF2) result in an increased disc:ray floret ratio, thereby providing ways to improve seed set in decorative chrysanthemum varieties in the future.

Floral Development Stage-Specific Transcriptomic Analysis Reveals the Formation Mechanism of Different Shapes of Ray Florets in Chrysanthemum

The formation mechanism of different ray floret shapes of chrysanthemum (Chrysanthemum × morifolium) remains elusive due to its complex genetic background. C. vestitum, with the basic ray floret shapes of the flat, spoon, and tubular types, is considered a model material for studying ray floret morphogenesis. In this study, the flat and tubular type lines of C. vestitum at specific stages were used to investigate the key genes that regulate morphological differences in ray florets. We found that the expression levels of genes related to auxin synthesis, transport, and response were generally higher in the tubular type than in the flat type. CvARF3 was highly expressed in the flat type, while CvARF5 and CvARF6 were highly expressed in the tubular type. Additionally, the transcription levels of Class B and E genes closely related to petal development, including CvPI, CvAP3, Cvdefh21, CvSEP3, and CvCDM77, were expressed at higher levels in the tubular type than the flat type. Based on the results, it is proposed that auxin plays a key role in the development of ray florets, and auxin-related genes, especially CvARFs, may be key genes to control the morphological difference of ray florets. Simultaneously, MADS-box genes are involved in the co-regulation of ray floret morphogenesis. The results provide novel insights into the molecular mechanism of different petal type formation and lay a theoretical foundation for the directional breeding of petal type in chrysanthemums.

Advances in Research on the Regulation of Floral Development by CYC-like Genes

CYCLOIDEA (CYC)-like genes belong to the TCP transcription factor family and play important roles associated with flower development. The CYC-like genes in the CYC1, CYC2, and CYC3 clades resulted from gene duplication events. The CYC2 clade includes the largest number of members that are crucial regulators of floral symmetry. To date, studies on CYC-like genes have mainly focused on plants with actinomorphic and zygomorphic flowers, including Fabaceae, Asteraceae, Scrophulariaceae, and Gesneriaceae species and the effects of CYC-like gene duplication events and diverse spatiotemporal expression patterns on flower development. The CYC-like genes generally affect petal morphological characteristics and stamen development, as well as stem and leaf growth, flower differentiation and development, and branching in most angiosperms. As the relevant research scope has expanded, studies have increasingly focused on the molecular mechanisms regulating CYC-like genes with different functions related to flower development and the phylogenetic relationships among these genes. We summarize the status of research on the CYC-like genes in angiosperms, such as the limited research conducted on CYC1 and CYC3 clade members, the necessity to functionally characterize the CYC-like genes in more plant groups, the need for investigation of the regulatory elements upstream of CYC-like genes, and exploration of the phylogenetic relationships and expression of CYC-like genes with new techniques and methods. This review provides theoretical guidance and ideas for future research on CYC-like genes.

Genome-Wide Analysis of WOX Multigene Family in Sunflower (Helianthus annuus L.)

The WUSCHEL-related homeobox (WOX) is a family of specific transcription factors involved in plant development and response to stress, characterized by the presence of a homeodomain. This study represents the first comprehensive characterization of the WOX family in a member of the Asteraceae family, the sunflower (H. annuus L.). Overall, we identified 18 putative HaWOX genes divided by phylogenetic analysis in three major clades (i.e., ancient, intermediate, and WUS). These genes showed conserved structural and functional motifs. Moreover, HaWOX has homogeneously distributed on H. annuus chromosomes. In particular, 10 genes originated after whole segment duplication events, underpinning a possible evolution of this family along with the sunflower genome. In addition, gene expression analysis evidenced a specific pattern of regulation of the putative 18 HaWOX during embryo growth and in ovule and inflorescence meristem differentiation, suggesting a pivotal role for this multigenic family in sunflower development. The results obtained in this work improved the understanding of the WOX multigenic family, providing a resource for future study on functional analysis in an economically valuable species such as sunflower.

Impact of transposable elements on the evolution of complex living systems and their epigenetic control

Transposable elements (TEs) contribute to genomic innovations, as well as genome instability, across a wide variety of species. Popular designations such as 'selfish DNA' and 'junk DNA,' common in the 1980s, may be either inaccurate or misleading, while a more enlightened view of the TE-host relationship covers a range from parasitism to mutualism. Both plant and animal hosts have evolved epigenetic mechanisms to reduce the impact of TEs, both by directly silencing them and by reducing their ability to transpose in the genome. However, TEs have also been co-opted by both plant and animal genomes to perform a variety of physiological functions, ranging from TE-derived proteins acting directly in normal biological functions to innovations in transcription factor activity and also influencing gene expression. Their presence, in fact, can affect a range of features at genome, phenotype, and population levels. The impact TEs have had on evolution is multifaceted, and many aspects still remain unexplored. In this review, the epigenetic control of TEs is contextualized according to the evolution of complex living systems.

Ray flower initiation in the Helianthus radula inflorescence is influenced by a functional allele of the HrCYC2c gene

The radiate pseudanthium, with actinomorphic disk flowers surrounded by showy marginal zygomorphic ray flowers, is the most common inflorescence in the Helianthus genus. In Helianthus radula, ray flower primordia are normally absent at the dorsal domain of the inner phyllaries (discoid heads) while the occurrence of radiate inflorescences is uncommon. In Helianthus spp., flower symmetry and inflorescence architecture are mainly controlled by CYCLOIDEA (CYC)-like genes but the putative role of these genes in the development of discoid inflorescences has not been investigate. Three CYC genes of H. radula with a role in ray flower identity (HrCYC2c, HrCYC2d, and HrCYC2e) were isolated. The phylogenetic analysis placed these genes within the CYC2 subclade. We identified two different alleles for the HrCYC2c gene. A mutant allele, designed HrCYC2c-m, shows a thymine to adenine transversion, which generates a TGA stop codon after a translation of 14 amino acids. We established homozygous dominant (HrCYC2c/HrCYC2c) and recessive (HrCYC2c-m/HrCYC2c-m) plants for this nonsense mutation. Inflorescences of both HrCYC2c/HrCYC2c and HrCYC2c/HrCYC2c-m plants initiated ray flowers, despite at low frequency. By contrast, plants homozygous for the mutant allele (HrCYC2c-m/HrCYC2c-m) failed at all to develop ray flowers. The results support, for the first time, a role of the HrCYC2c gene on the initiation of ray flower primordia. However, also in the two dominant phenotypes, discoid heads are the prevalent architecture suggesting that this gene is required but not sufficient to initiate ray flowers in pseudanthia. Other unknown major genes are most likely required in the shift from discoid to radiate inflorescence.

Parallelism in Flower Evolution and Development

Flower evolution is characterized by widespread repetition, with adaptations to pollinator environment evolving in parallel. Recent studies have expanded our understanding of the developmental basis of adaptive floral novelties—petal fusion, bilateral symmetry, heterostyly, and floral dimensions. In this article, we describe patterns of trait evolution and review developmental genetic mechanisms underlying floral novelties. We discuss the diversity of mechanisms for parallel adaptation, the evidence for constraints on these mechanisms, and how constraints help explain observed macroevolutionary patterns. We describe parallel evolution resulting from similarities at multiple hierarchical levels—genetic, developmental, morphological, functional—which indicate general principles in floral evolution, including the central role of hormone signaling. An emerging pattern is mutational bias that may contribute to rapid patterns of parallel evolution, especially if the derived trait can result from simple degenerative mutations. We argue that such mutational bias may be less likely to govern the evolution of novelties patterned by complex developmental pathways.

Characterization of lingering hope, a new brachytic mutant in sunflower (Helianthus annuus L.) with altered salicylic acid metabolism

Dwarf mutants are useful to elucidate regulatory mechanisms of plant growth and development. A brachytic mutant, named lingering hope (linho), was recently isolated from sunflower (Helianthus annuus). The aim of this report is the characterization of the mutant through genetic, morphometric, physiological and gene expression analyses. The brachytic trait is controlled by a recessive gene. The reduction of plant height depends on shorter apical internodes. The mutant shows an altered ratio length/width of the leaf blade, chlorosis and defects in inflorescence development. The brachytic trait is not associated to a specific hormonal deficiency, but an increased level of several gibberellins is detected in leaves. Notably, the endogenous salicylic acid (SA) content in young leaves of the mutant is very high despite a low level of SA 2-O-β-d-glucoside (SAG). The CO₂ assimilation rate significantly decreases in the second pair of leaves of linho, due to effects of both stomatal and non-stomatal constraints. In addition, the reduction of both actual and potential photochemical efficiency of photosystem II is associated with a reduced content of chlorophylls and carotenoids, a lower chlorophyll a to chlorophyll b ratio and a higher SA content. In comparison to wild type, linho shows a different pattern of gene expression with respect two pathogenesis-related genes and two genes involved in SA biosynthesis and SA metabolism. linho is the first mutant described in sunflower with altered SA metabolism and this genotype could be useful to improve information about the effects of high endogenous content of SA on plant development, reproductive growth and photosynthesis, in a major crop.