The polyploidy and its key role in plant breeding

Systematic approach of polyploidy as an evolutionary genetic and genomic phenomenon in horticultural crops

Polyploidy is thought to be an evolutionary and systematic mechanism for gene flow and phenotypic advancement in flowering plants. It is a natural phenomenon that promotes diversity by creating new permutations enhancing the prime potentials as compared to progenitors. Two different pathways have been recognized in studying polyploidy in nature; mitotic or somatic chromosome doubling and cytogenetics variation. Secondly, the vital influence of being polyploid is its heritable property (unreduced reproductive cells) formed during first and second-division restitution (FDR & SDR). Different approaches either chemical (Colchicine, Oryzalin, Caffeine, Trifuralin, or phosphoric amides) or gaseous i.e. Nitrous oxide have been deliberated as strong polyploidy causing agents. A wide range of cytogenetic practices like chromosomes study, ploidy, genome analysis, and plant morphology and anatomy have been studied in different plant species. Flow cytometry for ploidy and chromosome analysis through fluorescence and genomic in situ hybridization (FISH & GISH) are the basic methods to evaluate heredity substances sampled from leaves and roots. Many horticultural crops have been developed successfully and released commercially for consumption. Moreover, some deep detailed studies are needed to check the strong relationship between unique morphological features and genetic makeup concerning genes and hormonal expression in a strong approach.

Identification and Evaluation of Diploid and Tetraploid Passiflora edulis Sims

Passiflora edulis Sims (2n = 18) is a perennial plant with high utilization values, but its spontaneous polyploidy in nature has yet to be seen. Thus, this study aims to enhance our understanding of polyploidy P. edulis and provide rudimentary knowledge for breeding new cultivars. In this study, colchicine-induced tetraploid P. edulis (2n = 36) was used as experimental material (T1, T2, and T3) to explore the variances between it and its diploid counterpart in morphology, physiology, and biochemical characteristics, and a comparison of their performance under cold stress was conducted. We measured and collected data on phenotype parameters, chlorophyll contents, chlorophyll fluorescence, photosynthesis, osmotic substances, and antioxidant enzymes. The results showed that tetraploid P. edulis exhibited a shorter phenotype, more giant leaves, darker leaf color, and longer and fewer roots. Moreover, the physiological and biochemical analysis indicated that the tetraploid P. edulis had better photosynthesis systems and higher chlorophyll fluorescence parameters than the diploid P. edulis. Additionally, the tetraploid P. edulis had higher activity of antioxidant enzymes (SOD, POD, CAT) and lower MDA content to maintain better resistance in low temperatures. Overall, we conclude that there were apparent differences in the morphological, physiological, and biochemical traits of the tetraploid and diploid P. edulis. The tetraploid plants showed better photosynthesis systems, higher osmotic substance content, and antioxidant enzyme activity than the diploid, even under cold stress. Our results suggest that tetraploids with more abundant phenotype variation and better physiological and biochemical traits may be used as a new genetic germplasm resource for producing new P. edulis cultivars.

Revisiting Citrus Rootstocks Polyploidy as a Means to Improve Drought Resilience: Sometimes Less Is More

Polyploid varieties have been suggested as an alternative approach to promote drought tolerance in citrus crops. In this study, we compared the responses of diploid and tetraploid Sunki 'Tropical' rootstocks to water deficit when grafted onto 'Valencia' sweet orange trees and subjected to water withholding in isolation or competition experiments under potted conditions. Our results revealed that, when grown in isolation, tetraploid rootstocks took longer to show drought symptoms, but this advantage disappeared when grown in competition under the same soil moisture conditions. The differences in drought responses were mainly associated with variations in endogenous leaf levels of abscisic acid (ABA), hydrogen peroxide (H₂O₂) and carbohydrates among treatments. Overall, tetraploids were more affected by drought in individual experiments, showing higher H₂O₂ production, and in competition experiments, rapidly increasing ABA production to regulate stomatal closure and reduce water loss through transpiration. Therefore, our results highlight the crucial importance of evaluating diploid and tetraploid rootstocks under the same soil moisture conditions to better simulate field conditions, providing important insights to improve selection strategies for more resilient citrus rootstocks.

Polyphest: fast polyploid phylogeny estimation

MOTIVATION

Despite the widespread occurrence of polyploids across the Tree of Life, especially in the plant kingdom, very few computational methods have been developed to handle the specific complexities introduced by polyploids in phylogeny estimation. Furthermore, methods that are designed to account for polyploidy often disregard incomplete lineage sorting (ILS), a major source of heterogeneous gene histories, or are computationally very demanding. Therefore, there is a great need for efficient and robust methods to accurately reconstruct polyploid phylogenies.

RESULTS

We introduce Polyphest (POLYploid PHylogeny ESTimation), a new method for efficiently and accurately inferring species phylogenies in the presence of both polyploidy and ILS. Polyphest bypasses the need for extensive network space searches by first generating a multilabeled tree based on gene trees, which is then converted into a (uniquely labeled) species phylogeny. We compare the performance of Polyphest to that of two polyploid phylogeny estimation methods, one of which does not account for ILS, namely PADRE, and another that accounts for ILS, namely MPAllopp. Polyphest is more accurate than PADRE and achieves comparable accuracy to MPAllopp, while being significantly faster. We also demonstrate the application of Polyphest to empirical data from the hexaploid bread wheat and confirm the allopolyploid origin of bread wheat along with the closest relatives for each of its subgenomes.

AVAILABILITY AND IMPLEMENTATION

Polyphest is available at https://github.com/NakhlehLab/Polyphest.

Defining autopolyploidy: Cytology, genetics, and taxonomy

Autopolyploidy is taxonomically defined as the presence of more than two copies of each genome within an organism or species, where the genomes present must all originate within the same species. Alternatively, "genetic" or "cytological" autopolyploidy is defined by polysomic inheritance: random pairing and segregation of the four (or more) homologous chromosomes present, with no preferential pairing partners. In this review, we provide an overview of methods used to categorize species as taxonomic and cytological autopolyploids, including both modern and obsolete cytological methods, marker-segregation-based and genomics methods. Subsequently, we also investigated how frequently polysomic inheritance has been reliably documented in autopolyploids. Pure or predominantly polysomic inheritance was documented in 39 of 43 putative autopolyploid species where inheritance data was available (91%) and in seven of eight synthetic autopolyploids, with several cases of more mixed inheritance within species. We found no clear cases of autopolyploids with disomic inheritance, which was likely a function of our search methodology. Interestingly, we found seven species with purely polysomic inheritance and another five species with partial or predominant polysomic inheritance that appear to be taxonomic allopolyploids. Our results suggest that observations of polysomic inheritance can lead to relabeling of taxonomically allopolyploid species as autopolyploid and highlight the need for further cytogenetic and genomic investigation into polyploid origins and inheritance types.

Exploring floral morphoanatomy and embryology in wild populations of Chrysolaena flexuosa (Vernonia, Asteraceae): a contribution to understanding its ornamental potential

Chrysolaena flexuosa (Sims.) H. Rob. is a South American species in the tribe Vernonieae, with potential ornamental value: it has attractive inflorescences, is suitable for pot cultivation, and its cypselae are useful for dried flower arrangements. Apart from studies on the growth dynamics of this species under cultivation, chromosome number, DNA content, ploidy level, size, pollen viability, and the characterization of phenotypic and genetic variability, it is noteworthy that other aspects regarding the floral architecture, reproductive mode, and gametophyte formation of C. flexuosa have not yet been studied. For this reason, our study encompasses a floral morphoanatomical survey and a comprehensive assessment of gametophyte development in the species. As a result of this study, we report new floral morphotypes, confirming that the morphological variability of the species might be greater than speculated. The morphoanatomy of the androecium and gynoecium and the male and female gametophyte developmental characteristics are uniform in all the populations studied despite the different ploidy levels. Chrysolaena flexuosa has five tetrasporangiate stamens of the dicotyledonous type of development; all the populations studied displayed a unilocular inferior ovary with a single anatropous, unitegumented, and tenuinucellar ovule. Given that all the embryo sacs observed were of the Polygonum-type development regardless of the ploidy level, we infer that the populations analyzed are fertile and undergo sexual reproduction. Our results not only contribute further research in the field of breeding systems and propagation of this species, but also promote the successful introduction of C. flexuosa to the plant ornamental market.

Haplotype-resolved genomes of octoploid species in Phyllanthaceae family reveal a critical role for polyploidization and hybridization in speciation

The Phyllanthaceae family comprises a diverse range of plants with medicinal, edible, and ornamental value, extensively cultivated worldwide. Polyploid species commonly occur in Phyllanthaceae. Due to the rather complex genomes and evolutionary histories, their speciation process has been still lacking in research. In this study, we generated chromosome-scale haplotype-resolved genomes of two octoploid species (Phyllanthus emblica and Sauropus spatulifolius) in Phyllanthaceae family. Combined with our previously reported one tetraploid (Sauropus androgynus) and one diploid species (Phyllanthus cochinchinensis) from the same family, we explored their speciation history. The three polyploid species were all identified as allopolyploids with subgenome A/B. Each of their two distinct subgenome groups from various species was uncovered to independently share a common diploid ancestor (Ancestor-AA and Ancestor-BB). Via different evolutionary routes, comprising various scenarios of bifurcating divergence, allopolyploidization (hybrid polyploidization), and autopolyploidization, they finally evolved to the current tetraploid S. androgynus, and octoploid S. spatulifolius and P. emblica, respectively. We further discuss the variations in copy number of alleles and the potential impacts within the two octoploids. In addition, we also investigated the fluctuation of metabolites with medical values and identified the key factor in its biosynthesis process in octoploids species. Our study reconstructed the evolutionary history of these Phyllanthaceae species, highlighting the critical roles of polyploidization and hybridization in their speciation processes. The high-quality genomes of the two octoploid species provide valuable genomic resources for further research of evolution and functional genomics.

Physiological Responses of C4 Perennial Bioenergy Grasses to Climate Change: Causes, Consequences, and Constraints

C4 perennial bioenergy grasses are an economically and ecologically important group whose responses to climate change will be important to the future bioeconomy. These grasses are highly productive and frequently possess large geographic ranges and broad environmental tolerances, which may contribute to the evolution of ecotypes that differ in physiological acclimation capacity and the evolution of distinct functional strategies. C4 perennial bioenergy grasses are predicted to thrive under climate change-C4 photosynthesis likely evolved to enhance photosynthetic efficiency under stressful conditions of low [CO2], high temperature, and drought-although few studies have examined how these species will respond to combined stresses or to extremes of temperature and precipitation. Important targets for C4 perennial bioenergy production in a changing world, such as sustainability and resilience, can benefit from combining knowledge of C4 physiology with recent advances in crop improvement, especially genomic selection.

Evolutionary genomics of climatic adaptation and resilience to climate change in alfalfa

Given the escalating impact of climate change on agriculture and food security, gaining insights into the evolutionary dynamics of climatic adaptation and uncovering climate-adapted variation can empower the breeding of climate-resilient crops to face future climate change. Alfalfa (Medicago sativa subsp. sativa), the queen of forages, shows remarkable adaptability across diverse global environments, making it an excellent model for investigating species responses to climate change. In this study, we performed population genomic analyses using genome resequencing data from 702 accessions of 24 Medicago species to unravel alfalfa's climatic adaptation and genetic susceptibility to future climate change. We found that interspecific genetic exchange has contributed to the gene pool of alfalfa, particularly enriching defense and stress-response genes. Intersubspecific introgression between M. sativa subsp. falcata (subsp. falcata) and alfalfa not only aids alfalfa's climatic adaptation but also introduces genetic burden. A total of 1671 genes were associated with climatic adaptation, and 5.7% of them were introgressions from subsp. falcata. By integrating climate-associated variants and climate data, we identified populations that are vulnerable to future climate change, particularly in higher latitudes of the Northern Hemisphere. These findings serve as a clarion call for targeted conservation initiatives and breeding efforts. We also identified pre-adaptive populations that demonstrate heightened resilience to climate fluctuations, illuminating a pathway for future breeding strategies. Collectively, this study enhances our understanding about the local adaptation mechanisms of alfalfa and facilitates the breeding of climate-resilient alfalfa cultivars, contributing to effective agricultural strategies for facing future climate change.

In vitro induction of tetraploids and their phenotypic and transcriptome analysis in Glehnia littoralis

BACKGROUND

Glehnia littoralis is a medicinal and edible plant species having commercial value and has several hundred years of cultivation history. Polyploid breeding is one of the most important and fastest ways to generate novel varieties. To obtain tetraploids of G. littoralis in vitro, colchicine treatment was given to the seeds and then were screened based on morphology, flow cytometry, and root tip pressing assays. Furthermore, transcriptome analysis was performed to identity the differentially expressed genes associated with phenotypic changes in tetraploid G. littoralis.

RESULTS

The results showed that 0.05% (w/v) colchicine treatment for 48 h was effective in inducing tetraploids in G. littoralis. The tetraploid G. littoralis (2n = 4x = 44) was superior in leaf area, leaf thickness, petiole diameter, SPAD value (Chl SPAD), stomatal size, epidermal tissues thickness, palisade tissues thickness, and spongy tissues thickness to the diploid ones, while the stomatal density of tetraploids was significantly lower. Transcriptome sequencing revealed, a total of 1336 differentially expressed genes (DEGs) between tetraploids and diploids. Chromosome doubling may lead to DNA content change and gene dosage effect, which directly affects changes in quantitative traits, with changes such as increased chlorophyll content, larger stomata and thicker tissue of leaves. Several up-regulated DEGs were found related to growth and development in tetraploid G. littoralis such as CKI, PPDK, hisD and MDP1. KEGG pathway enrichment analyses showed that most of DEGs were enriched in metabolic pathways.

CONCLUSIONS

This is the first report of the successful induction of tetraploids in G. littoralis. The information presented in this study facilitate breeding programs and molecular breeding of G. littoralis varieties.

Exploring the mechanism of transformation in Acacia nilotica (Linn.) triggered by colchicine seed treatment

BACKGROUND

Acacia nilotica Linn. is a widely distributed tree known for its applications in post-harvest and medicinal horticulture. However, its seed-based growth is relatively slow. Seed is a vital component for the propagation of A. nilotica due to its cost-effectiveness, genetic diversity, and ease of handling. Colchicine, commonly used for polyploidy induction in plants, may act as a pollutant at elevated levels. Its optimal concentration for Acacia nilotica's improved growth and development has not yet been determined, and the precise mechanism underlying this phenomenon has not been established. Therefore, this study investigated the impact of optimized colchicine (0.07%) seed treatment on A. nilotica's morphological, anatomical, physiological, fluorescent, and biochemical attributes under controlled conditions, comparing it with a control.

RESULTS

Colchicine seed treatment significantly improved various plant attributes compared to control. This included increased shoot length (84.6%), root length (53.5%), shoot fresh weight (59.1%), root fresh weight (42.8%), shoot dry weight (51.5%), root dry weight (40%), fresh biomass (23.6%), stomatal size (35.9%), stomatal density (41.7%), stomatal index (51.2%), leaf thickness (11 times), leaf angle (2.4 times), photosynthetic rate (40%), water use efficiency (2.2 times), substomatal CO2 (36.6%), quantum yield of photosystem II (13.1%), proton flux (3.1 times), proton conductivity (2.3 times), linear electron flow (46.7%), enzymatic activities of catalase (25%), superoxide dismutase (33%), peroxidase (13.5%), and ascorbate peroxidase (28%), 2,2-diphenyl-1-picrylhydrazyl-radical scavenging activities(23%), total antioxidant capacity (59%), total phenolic (23%), and flavonoid content (37%) with less number of days to 80% germination (57.1%), transpiration rate (53.9%), stomatal conductance (67.1%), non-photochemical quenching (82.8%), non-regulatory energy dissipation (24.3%), and H2O2 (25%) and O-2 levels (30%).

CONCLUSION

These findings elucidate the intricate mechanism behind the morphological, anatomical, physiological, fluorescent, and biochemical transformative effects of colchicine seed treatment on Acacia nilotica Linn. and offer valuable insights for quick production of A. nilotica's plants with modification and enhancement from seeds through an eco-friendly approach.

Octoploids Show Enhanced Salt Tolerance through Chromosome Doubling in Switchgrass (Panicum virgatum L.)

Polyploid plants often exhibit enhanced stress tolerance. Switchgrass is a perennial rhizomatous bunchgrass that is considered ideal for cultivation in marginal lands, including sites with saline soil. In this study, we investigated the physiological responses and transcriptome changes in the octoploid and tetraploid of switchgrass (Panicum virgatum L. 'Alamo') under salt stress. We found that autoploid 8× switchgrass had enhanced salt tolerance compared with the amphidiploid 4× precursor, as indicated by physiological and phenotypic traits. Octoploids had increased salt tolerance by significant changes to the osmoregulatory and antioxidant systems. The salt-treated 8× Alamo plants showed greater potassium (K+) accumulation and an increase in the K+/Na+ ratio. Root transcriptome analysis for octoploid and tetraploid plants with or without salt stress revealed that 302 upregulated and 546 downregulated differentially expressed genes were enriched in genes involved in plant hormone signal transduction pathways and were specifically associated with the auxin, cytokinin, abscisic acid, and ethylene pathways. Weighted gene co-expression network analysis (WGCNA) detected four significant salt stress-related modules. This study explored the changes in the osmoregulatory system, inorganic ions, antioxidant enzyme system, and the root transcriptome in response to salt stress in 8× and 4× Alamo switchgrass. The results enhance knowledge of the salt tolerance of artificially induced homologous polyploid plants and provide experimental and sequencing data to aid research on the short-term adaptability and breeding of salt-tolerant biofuel plants.

The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

Coffea arabica, an allotetraploid hybrid of Coffea eugenioides and Coffea canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabica accession and modern representatives of its diploid progenitors, C. eugenioides and C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000-610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred ~30.5 thousand years ago, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with C. canephora, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of C. arabica.

Identification of two mutant JASON-RELATED genes associated with unreduced pollen production in potato

KEY MESSAGE

Multiple QTLs control unreduced pollen production in potato. Two major-effect QTLs co-locate with mutant alleles of genes with homology to AtJAS, a known regulator of meiotic spindle orientation. In diploid potato the production of unreduced gametes with a diploid (2n) rather than a haploid (n) number of chromosomes has been widely reported. Besides their evolutionary important role in sexual polyploidisation, unreduced gametes also have a practical value for potato breeding as a bridge between diploid and tetraploid germplasm. Although early articles argued for a monogenic recessive inheritance, the genetic basis of unreduced pollen production in potato has remained elusive. Here, three diploid full-sib populations were genotyped with an amplicon sequencing approach and phenotyped for unreduced pollen production across two growing seasons. We identified two minor-effect and three major-effect QTLs regulating this trait. The two QTLs with the largest effect displayed a recessive inheritance and an additive interaction. Both QTLs co-localised with genes encoding for putative AtJAS homologs, a key regulator of meiosis II spindle orientation in Arabidopsis thaliana. The function of these candidate genes is consistent with the cytological phenotype of mis-oriented metaphase II plates observed in the parental clones. The alleles associated with elevated levels of unreduced pollen showed deleterious mutation events: an exonic transposon insert causing a premature stop, and an amino acid change within a highly conserved domain. Taken together, our findings shed light on the natural variation underlying unreduced pollen production in potato and will facilitate interploidy breeding by enabling marker-assisted selection for this trait.

Synthetic polyploidization induces enhanced phytochemical profile and biological activities in Thymus vulgaris L. essential oil

Essential oil from Thymus vulgaris L. has valuable therapeutic potential that is highly desired in pharmaceutical, food, and cosmetic industries. Considering these advantages and the rising market demand, induced polyploids were obtained using oryzalin to enhance essential oil yield. However, their therapeutic values were unexplored. So, this study aims to assess the phytochemical content, and antimicrobial, antioxidant, and anti-inflammatory activities of tetraploid and diploid thyme essential oils. Induced tetraploids had 41.11% higher essential oil yield with enhanced thymol and γ-terpinene content than diploid. Tetraploids exhibited higher antibacterial activity against all tested microorganisms. Similarly, in DPPH radical scavenging assay tetraploid essential oil was more potent with half-maximal inhibitory doses (IC50) of 180.03 µg/mL (40.05 µg TE/mg) than diploid with IC50 > 512 µg/mL (12.68 µg TE/mg). Tetraploids exhibited more effective inhibition of in vitro catalytic activity of pro-inflammatory enzyme cyclooxygenase-2 (COX-2) than diploids at 50 µg/mL concentration. Furthermore, molecular docking revealed higher binding affinity of thymol and γ-terpinene towards tested protein receptors, which explained enhanced bioactivity of tetraploid essential oil. In conclusion, these results suggest that synthetic polyploidization using oryzalin could effectively enhance the quality and quantity of secondary metabolites and can develop more efficient essential oil-based commercial products using this induced genotype.

Allelic Variations in Vernalization (Vrn) Genes in Triticum spp

Rapid climate changes, with higher warming rates during winter and spring seasons, dramatically affect the vernalization requirements, one of the most critical processes for the induction of wheat reproductive growth, with severe consequences on flowering time, grain filling, and grain yield. Specifically, the Vrn genes play a major role in the transition from vegetative to reproductive growth in wheat. Recent advances in wheat genomics have significantly improved the understanding of the molecular mechanisms of Vrn genes (Vrn-1, Vrn-2, Vrn-3, and Vrn-4), unveiling a diverse array of natural allelic variations. In this review, we have examined the current knowledge of Vrn genes from a functional and structural point of view, considering the studies conducted on Vrn alleles at different ploidy levels (diploid, tetraploid, and hexaploid). The molecular characterization of Vrn-1 alleles has been a focal point, revealing a diverse array of allelic forms with implications for flowering time. We have highlighted the structural complexity of the different allelic forms and the problems linked to the different nomenclature of some Vrn alleles. Addressing these issues will be crucial for harmonizing research efforts and enhancing our understanding of Vrn gene function and evolution. The increasing availability of genome and transcriptome sequences, along with the improvements in bioinformatics and computational biology, offers a versatile range of possibilities for enriching genomic regions surrounding the target sites of Vrn genes, paving the way for innovative approaches to manipulate flowering time and improve wheat productivity.

Polyploidization: A Biological Force That Enhances Stress Resistance

Organisms with three or more complete sets of chromosomes are designated as polyploids. Polyploidy serves as a crucial pathway in biological evolution and enriches species diversity, which is demonstrated to have significant advantages in coping with both biotic stressors (such as diseases and pests) and abiotic stressors (like extreme temperatures, drought, and salinity), particularly in the context of ongoing global climate deterioration, increased agrochemical use, and industrialization. Polyploid cultivars have been developed to achieve higher yields and improved product quality. Numerous studies have shown that polyploids exhibit substantial enhancements in cell size and structure, physiological and biochemical traits, gene expression, and epigenetic modifications compared to their diploid counterparts. However, some research also suggested that increased stress tolerance might not always be associated with polyploidy. Therefore, a more comprehensive and detailed investigation is essential to complete the underlying stress tolerance mechanisms of polyploids. Thus, this review summarizes the mechanism of polyploid formation, the polyploid biochemical tolerance mechanism of abiotic and biotic stressors, and molecular regulatory networks that confer polyploidy stress tolerance, which can shed light on the theoretical foundation for future research.

Growth, ultrastructural and physiological characteristics of Abelmoschus cytotypes under elevated ozone stress: a study on ploidy-specific responses

Tropospheric ozone (O3 ) is a significant abiotic stressor whose rising concentration negatively influences plant growth. Studies related to the differential response of Abelmoschus cytotypes to elevated O3 treatment are scarce and need further exploration to recognise the role of polyploidisation in stress tolerance. In this study, we analysed the changes in growth pattern, ultrastructure, physiology and foliar protein profile occurring under O3 stress in Abelmoschus moschatus (monoploid), Abelmoschus esculentus (diploid) and Abelmoschus caillei (triploid). Our findings showed that higher stomatal conductance in A. moschatus triggered higher O3 intake, causing damage to stomatal cells and photosynthetic pigments. Additionally, it caused a reduction in photosynthetic rates, leading to reduced plant growth, total biomass and economic yield. This O3 -induced toxicity was less in diploid and triploid cytotypes of Abelmoschus . Protein profiling by sodium dodecyl sulpate-polyacrylamide gel electrophoresis showed a significant decrease in the commonly found RuBisCO larger and smaller subunits. The decrease was more prominent in monoploid compared to diploid and triploid. This study provides crucial data for research that aim to enhance plant ability to withstand O3 induced oxidative stress. Our findings may help in developing a tolerant variety through plant breeding techniques, which will be economically more advantageous in reaching the objective of sustainable production at the high O3 levels projected under a climate change scenario.

Transcriptomic and Phenotypic Analyses Reveal the Molecular Mechanism of Dwarfing in Tetraploid Robinia pseudoacacia L

Polyploid breeding techniques aid in the cultivation of new forestry cultivars, thus expanding the suite of strategies for the improvement of arboreal traits and innovation within the field of forestry. Compared to diploid Robinia pseudoacacia L. (black locust) 'D26-5①' (2×), its dwarfed homologous tetraploid 'D26-5②' (4×) variety has better application prospects in garden vegetation guardrails and urban landscape. However, the molecular mechanism of the generation and growth of this dwarf variety is still unclear. Here, plant growth and development as well as histological differences between the diploid and its autotetraploid were investigated. Levels of endogenous hormones at three different developmental stages (20, 40, and 70 days) of 2× and homologous 4× tissue culture plantlets were assessed, and it was found that the brassinosteroid (BR) contents of the former were significantly higher than the latter. Transcriptome sequencing data analysis of 2× and homologous 4× showed that differentially expressed genes (DEGs) were significantly enriched in plant hormone synthesis and signal transduction, sugar and starch metabolism, and the plant circadian rhythm pathway, which are closely related to plant growth and development. Therefore, these biological pathways may be important regulatory pathways leading to dwarfism and slow growth in tetraploids. Additionally, utilizing weighted gene coexpression network analysis (WGCNA), we identified three crucial differentially expressed genes (DEGs)-PRR5, CYP450, and SPA1-that potentially underlie the observed ploidy variation. This study provides a new reference for the molecular mechanism of dwarfism in dwarfed autotetraploid black locusts. Collectively, our results of metabolite analysis and comparative transcriptomics confirm that plant hormone signaling and the circadian rhythm pathway result in dwarfism in black locusts.

Screening for Resistance Resources against Bacterial Wilt in Wild Potato

Potato is an important crop, used not only for food production but also for various industrial applications. With the introduction of the potato as a staple food strategy, the potato industry in China has grown rapidly. However, issues related to bacterial wilt, exacerbated by factors such as seed potato transportation and continuous cropping, have become increasingly severe in the primary potato cultivation regions of China, leading to significant economic losses. The extensive genetic diversity of Ralstonia solanacearum (R. solanacearum), which is the pathogen of bacterial wilt, has led to a lack of highly resistant potato genetic resources. There is a need to identify and cultivate potato varieties with enhanced resistance to reduce the adverse impact of this disease on the industry. We screened 55 accessions of nine different wild potato species against the bacterial wilt pathogen R. solanacearum PO2-1, which was isolated from native potato plants and belongs to phylotype II. Three accessions of two species (ACL24-2, PNT880-3, and PNT204-23) were identified with high resistance phenotypes to the tested strains. We found these accessions also showed high resistance to different phylotype strains. Among them, only PNT880-3 was capable of flowering and possessed viable pollen, and it was diploid. Consistent with the high resistance, decreased growth of R. solanacearum was detected in PNT880-3. All these findings in our study reveal that the wild potato PNT880-3 was a valuable resistance source to bacterial wilt with breeding potential.

Synthetic Tetraploid of Oncidium crispum Lodd. (Orchidaceae)

In ornamental plants, artificial polyploidization has enabled the creation of new cultivars. Due to their high commercial value in the international flower market and their ornamental characteristics, such as the shape, size, color, and durability of their flower, orchids have received great attention in studies of artificial polyploidization. Here we described the protocol used for polyploid induction in Oncidium crispum, an epiphyte species native of southeastern Brazil, of great ornamental interest and widely sold in flower shops. The species stands out for having inflorescence with large flowers, brown in color with yellow spots. In addition, O. crispum has great potential for use in genetic improvement programs since the species is widely used in interspecific crosses. Closed capsules containing mature O. crispum seeds were subjected to running sterilized water for 10 min and then to a 1.5% sodium hypochlorite solution for 10 min. Small portions of seeds were introduced into 50 mL of water-soluble fertilizer with macro- and micronutrients (B>M) plus 0.7% agar. Explants originating from seeds previously in vitro germinated were submitted to 0.05% and 0.1% of colchicine for 4 days and 8 days. Flow cytometry and chromosome counts confirmed that the protocol successfully produced synthetic polyploid plants.

Phytochemical Composition of Different Red Clover Genotypes Based on Plant Part and Genetic Traits

Red clover (Trifolium pratense L.) is an important legume that is also known as a rich source of isoflavones, which are compounds with mild estrogenic activity. Therefore, this plant is often used as a raw material in the production of dietary supplements recommended in menopause. Many factors can influence isoflavone content, but those genetically related are considered to be the most important. Therefore, the aim of this study was to evaluate the phytochemical profile of different plant parts of 30 red clover genotypes grouped according to ploidy and country of seed origin by analyzing the content of dominant isoflavones, total phenolic content (TPC) and antioxidant activity. It was found that there are significant differences in the examined traits among plant parts. Red clover leaves had the highest total isoflavone content, with biochanin A as the dominant compound, while flower extracts had the highest TPC and antioxidant activity. Diploid and tetraploid genotypes were significantly different concerning the content of daidzein, genistein, formononetin and TPC with higher quantities in tetraploid samples. On the other hand, seed origin was not a useful separating factor for the analyzed samples. The results of this research indicate that ploidy, as a previously poorly studied factor, could influence isoflavone content in red clover.

Polyploid Genome Assembly Provides Insights into Morphological Development and Ascorbic Acid Accumulation of Sauropus androgynus

Sauropus androgynus (S. androgynus) (2n = 4x = 52) is one of the most popular functional leafy vegetables in South and Southeast Asia. With its rich nutritional and pharmaceutical values, it has traditionally had widespread use for dietary and herbal purposes. Here, the genome of S. androgynus was sequenced and assembled, revealing a genome size of 1.55 Gb with 26 pseudo-chromosomes. Phylogenetic analysis traced back the divergence of Sauropus from Phyllanthus to approximately 29.67 million years ago (Mya). Genome analysis revealed that S. androgynus polyploidized around 20.51 Mya and shared a γ event about 132.95 Mya. Gene function analysis suggested that the expansion of pathways related to phloem development, lignin biosynthesis, and photosynthesis tended to result in the morphological differences among species within the Phyllanthaceae family, characterized by varying ploidy levels. The high accumulation of ascorbic acid in S. androgynus was attributed to the high expression of genes associated with the L-galactose pathway and recycling pathway. Moreover, the expanded gene families of S. androgynus exhibited multiple biochemical pathways associated with its comprehensive pharmacological activity, geographic adaptation and distinctive pleasurable flavor. Altogether, our findings represent a crucial genomic asset for S. androgynus, casting light on the intricate ploidy within the Phyllanthaceae family.

Phenotypic characterization, plant growth and development, genome methylation, and mineral elements composition of neotetraploid lettuce (Lactuca sativa L.)

Stable neotetraploid lines of lettuce (Lactuca sativa L.) were produced from three phenotypically distinct cultivars (Annapolis, Eruption, Merlot) and an advanced breeding line (SM13-L2) using colchicine treatment of seeds or young seedlings. When tested under the greenhouse and field conditions, neotetraploids initially grew more rapidly than their diploid progenitors, however they reached their reproductive stage (bolting, flower bud formation, and flowering) substantially later. Seeds production on neotetraploids was delayed by more than 30 days compared to diploids. Tetraploid plants had fewer, but larger stomata and leaves, less chlorophyll per area, higher photosystem II photochemical efficiency, generally lighter root system, and produced less than 1% of seeds in comparison with diploids. Field-grown neotetraploids of all lines displayed a significant reduction in tipburn (1.8% vs. 22.2%, respectively), a highly undesirable physiological disorder. Changes in leaf and root mineral composition were detected in neotetraploids. Several elements were found in lower abundance than in diploids, most notably iron, calcium, and silicon. Whole genome bisulfite sequencing (WGBS) revealed 498 differentially methylated regions (DMR), with 106 of these regions having at least 50% difference in the level of methylation between neotetraploids and their diploid progenitors. At least 18 of the most prominent DMR were detected in proximity to genes predicted to be involved in plant development or reaction to biotic and abiotic stressors. Because neotetraploid lines have low seed production, they are not suitable for commercial cultivation. They can be used, however, in research to study the factors contributing to tipburn, traits affected by stomata size or density, and the effect of ploidy on resistance to environmental stressors.

Induction of tetraploids in Paper Mulberry (Broussonetia papyrifera (L.) L'Hér. ex Vent.) by colchicine

BACKGROUND

Broussonetia papyrifera (L.) L'Hér. ex Vent. has the characteristics of strong stress resistance, high crude protein content, and pruning tolerance. It is an ecological, economic, and medicinal plant. Polyploid plants usually perform better than their corresponding diploid plants in terms of nutrients, active substances, and stress resistance.

RESULTS

In this study, the leaves, calli, and seeds of diploid B. papyrifera were used for tetraploid induction by colchicine. The induction effect of colchicine on B. papyrifera was summarized through the early morphology, chromosome count and flow cytometry. It was concluded that the best induction effect (18.6%) was obtained when the leaves of B. papyrifera were treated in liquid MS (Murashige and Skoog) medium containing 450 mg·L-1 colchicine for 3 d. The comparative analysis of the growth characteristics of diploid and tetraploid B. papyrifera showed that tetraploid B. papyrifera has larger ground diameter, larger stomata, thicker palisade tissue and thicker sponge tissue than diploid B. papyrifera. In addition, the measurement of photosynthetic features also showed that tetraploids had higher chlorophyll content and higher photosynthetic rates.

CONCLUSION

This study showed that tetraploid B. papyrifera could be obtained by treating leaves, callus and seeds with liquid and solid colchicine, but the induction efficiency was different. Moreover, there were differences in stomata, leaf cell structure and photosynthetic features between tetraploid B. papyrifera and its corresponding diploid. The induced tetraploid B. papyrifera can provide a technical basis and breeding material for the creation of B. papyrifera germplasm resources in the future.

Transcriptome Shock in Developing Embryos of a Brassica napus and Brassica rapa Hybrid

Interspecific crosses that fuse the genomes of two different species may result in overall gene expression changes in the hybrid progeny, called 'transcriptome shock'. To better understand the expression pattern after genome merging during the early stages of allopolyploid formation, we performed RNA sequencing analysis on developing embryos of Brassica rapa, B. napus, and their synthesized allotriploid hybrids. Here, we show that the transcriptome shock occurs in the developing seeds of the hybrids. Of the homoeologous gene pairs, 17.1% exhibit expression bias, with an overall expression bias toward B. rapa. The expression level dominance also biases toward B. rapa, mainly induced by the expression change in homoeologous genes from B. napus. Functional enrichment analysis revealed significant differences in differentially expressed genes (DEGs) related to photosynthesis, hormone synthesis, and other pathways. Further study showed that significant changes in the expression levels of the key transcription factors (TFs) could regulate the overall interaction network in the developing embryo, which might be an essential cause of phenotype change. In conclusion, the present results have revealed the global changes in gene expression patterns in developing seeds of the hybrid between B. rapa and B. napus, and provided novel insights into the occurrence of transcriptome shock for harnessing heterosis.

Effects of polyploidization and their evolutionary implications are revealed by heritable polyploidy in the haplodiploid wasp Nasonia vitripennis

Recurrent polyploidization occurred in the evolutionary history of most Eukaryota. However, how neopolyploid detriment (sterility, gigantism, gene dosage imbalances) has been overcome and even been bridged to evolutionary advantage (gene network diversification, mass radiation, range expansion) is largely unknown, particularly for animals. We used the parasitoid wasp Nasonia vitripennis, a rare insect system with heritable polyploidy, to begin addressing this knowledge gap. In Hymenoptera the sexes have different ploidies (haploid males, diploid females) and neopolyploids (diploid males, triploid females) occur for various species. Although such polyploids are usually sterile, those of N. vitripennis are reproductively capable and can even establish stable polyploid lines. To assess the effects of polyploidization, we compared a long-established polyploid line, the Whiting polyploid line (WPL) and a newly generated transformer knockdown line (tKDL) for fitness traits, absolute gene expression, and cell size and number. WPL polyploids have high male fitness and low female fecundity, while tKDL polyploids have poor male mate competition ability and high fertility. WPL has larger cells and cell number reduction, but the tKDL does not differ in this respect. Expression analyses of two housekeeping genes indicated that gene dosage is linked to sex irrespective of ploidy. Our study suggests that polyploid phenotypic variation may explain why some polyploid lineages thrive and others die out; a commonly proposed but difficult-to-test hypothesis. This documentation of diploid males (tKDL) with impaired competitive mating ability; triploid females with high fitness variation; and hymenopteran sexual dosage compensation (despite the lack of sex chromosomes) all challenges general assumptions on hymenopteran biology. We conclude that polyploidization is dependent on the duplicated genome characteristics and that genomes of different lines are unequally suited to survive diploidization. These results demonstrate the utility of N. vitripennis for delineating mechanisms of animal polyploid evolution, analogous to more advanced polyploid plant models.

Deciphering peanut complex genomes paves a way to understand its origin and domestication

Peanut (Arachis) is a key oil and protein crop worldwide with large genome. The genomes of diploid and tetraploid peanuts have been sequenced, which were compared to decipher their genome structures, evolutionary, and life secrets. Genome sequencing efforts showed that different cultivars, although Bt homeologs being more privileged in gene retention and gene expression. This subgenome bias, extended to sequence variation and point mutation, might be related to the long terminal repeat (LTR) explosions after tetraploidization, especially in At subgenomes. Except that, whole-genome sequences revealed many important genes, for example, fatty acids and triacylglycerols pathway, NBS-LRR (nucleotide-binding site-leucine-rich repeats), and seed size decision genes, were enriched after recursive polyploidization. Each ancestral polyploidy, with old ones having occurred hundreds of thousand years ago, has thousands of duplicated genes in extant genomes, contributing to genetic novelty. Notably, although full genome sequences are available, the actual At subgenome ancestor has still been elusive, highlighted with new debate about peanut origin. Although being an orphan crop lagging behind other crops in genomic resources, the genome sequencing achievement has laid a solid foundation for advancing crop enhancement and system biology research of peanut.

Phenotypic Diversity in Domesticated and Wild Timothy Grass, and Closely Related Species for Forage Breeding

Timothy grass (Phleum pratense L.) is one of the most important forage crops in temperate regions. Forage production, however, faces many challenges, and new cultivars adapted to a changing climate are needed. Wild populations and relatives of timothy may serve as valuable genetic resources in the breeding of improved cultivars. The aim of our study is to provide knowledge about the phenotypic diversity in domesticated (cultivars, breeding lines and landraces) and wild timothy and two closely related species, P. nodosum (lowland species) and P. alpinum, (high altitude species) to identify potential genetic resources. A total of 244 accessions of timothy and the two related species were studied for growth (plant height, fresh and dry weight) and plant development (days to stem elongation, days to booting and days to heading) in the field and in a greenhouse. We found a large diversity in development and growth between the three Phleum species, as well as between the accessions within each species. Timothy showed the highest growth, but no significant difference was found between wild accessions and cultivars of timothy in fresh and dry weight. However, these two groups of accessions showed significant differences in plant development, where timothy cultivars as a group reached flowering earlier than the wild accessions. This suggests that there has not been a strong directional selection towards increased yield during the domestication and breeding of timothy; rather, timothy has been changed for other traits such as earlier heading. Principal component analysis and cluster analysis based on all traits revealed distinct clusters. Accessions falling within the same cluster showed similarities in the development and growth rather than the type of accession. The large diversity found in this study shows the potential of using timothy accessions as genetic resources in crosses with existing cultivars. Also, accessions of P. nodosum with favorable traits can be candidates for the domestication of a novel forage crop, and the high-altitude relative P. alpinum may be a source of genes for the development of more cold and stresstolerant cultivars.

The Abundant and Unique Transcripts and Alternative Splicing of the Artificially Autododecaploid London Plane (Platanus × acerifolia)

Transcription and alternative splicing (AS) are now appreciated in plants, but few studies have examined the effects of changing ploidy on transcription and AS. In this study, we showed that artificially autododecaploid plants of London plane (Platanus × acerifolia (Aiton) Willd) had few flowers relative to their hexaploid progenitors. Transcriptome analysis based on full-length Oxford Nanopore Technologies (ONTs) and next-generation sequencing (NGS) revealed that the increased ploidy level in P. × acerifolia led to more transcribed isoforms, accompanied by an increase in the number of isoforms per gene. The functional enrichment of genes indicated that novel genes transcribed specifically in the dodecaploids may have been highly correlated with the ability to maintain genome stability. The dodecaploids showed a higher number of genes with upregulated differentially expressed genes (DEGs) compared with the hexaploid counterpart. The genome duplication of P. × acerifolia resulted mainly in the DEGs involved in basic biological pathways. It was noted that there was a greater abundance of alternative splicing (AS) events and AS genes in the dodecaploids compared with the hexaploids in P. × acerifolia. In addition, a significant difference between the structure and expression of AS events between the hexaploids and dodecaploids of Platanus was found. Of note, some DEGs and differentially spliced genes (DSGs) related to floral transition and flower development were consistent with the few flower traits in the dodecaploids of P. × acerifolia. Collectively, our findings explored the difference in transcription and AS regulation between the hexaploids and dodecaploids of P. × acerifolia and gained new insight into the molecular mechanisms underlying the few-flower phenotype of P. × acerifolia. These results contribute to uncovering the regulatory role of transcription and AS in polyploids and breeding few-flower germplasms.

Autotetraploid Origin of Chinese Cherry Revealed by Chromosomal Karyotype and In Situ Hybridization of Seedling Progenies

Polyploidy is considered a driving force in plant evolution and diversification. Chinese cherry [Cerasus pseudocerasus (Lindl.) G.Don], an economically important fruit crop native to China, has evolved at the tetraploid level, with a few pentaploid and hexaploid populations. However, its auto- or allo-polyploid origin remains unclear. To address this issue, we analyzed the ploidy levels and rDNA chromosomal distribution in self- and open-pollinated seedling progenies of tetraploid and hexaploid Chinese cherry. Genomic in situ hybridization (GISH) analysis was conducted to reveal the genomic relationships between Chinese cherry and diploid relatives from the genus Cerasus. Both self- and open-pollinated progenies of tetraploid Chinese cherry exhibited tetraploids, pentaploids, and hexaploids, with tetraploids being the most predominant. In the seedling progenies of hexaploid Chinese cherry, the majority of hexaploids and a few pentaploids were observed. A small number of aneuploids were also observed in the seedling progenies. Chromosome 1, characterized by distinct length characteristics, could be considered the representative chromosome of Chinese cherry. The basic Chinese cherry genome carried two 5S rDNA signals with similar intensity, and polyploids had the expected multiples of this copy number. The 5S rDNA sites were located at the per-centromeric regions of the short arm on chromosomes 4 and 5. Three 45S rDNA sites were detected on chr. 3, 4 and 7 in the haploid complement of Chinese cherry. Tetraploids exhibited 12 signals, while pentaploids and hexaploids showed fewer numbers than expected multiples. Based on the GISH signals, Chinese cherry demonstrated relatively close relationships with C. campanulata and C. conradinae, while being distantly related to another fruiting cherry, C. avium. In combination with the above results, our findings suggested that Chinese cherry likely originated from autotetraploidy.

Cultivar-dependent phenotypic and chemotypic responses of drug-type Cannabis sativa L. to polyploidization

Cannabis sativa L. is a plant with a wide range of potential medicinal applications. In recent years, polyploidy has gained attention as a potential strategy for rapidly improving C. sativa, which, unlike other modern crops, has not yet benefitted from this established biotechnological application. Currently, no reports on high THCA and CBDA drug-type polyploid cultivars have been published. Moreover, it still needs to be clarified if different cultivars react similarly to polyploidization. For these reasons, we set out to evaluate and compare the phenotype and chemotype of three high Δ9-tetrahydrocannabinolic acid (THCA) and one high cannabidiolic acid (CBDA) drug-type cultivars in their diploid, triploid and tetraploid state through agronomic and metabolomic approaches. Our observations on plant morphology revealed a significant increase in plant height and leaf size with increasing ploidy levels in a cultivar-dependent manner. In contrast, cannabinoids were negatively affected by polyploidization, with the concentration of total cannabinoids, THCA, CBDA and cannabigerolic acid (CBGA) decreasing significantly in higher ploidy levels across all four cultivars. Headspace analysis of volatiles revealed that total volatile content decreased in triploids. On the other hand, tetraploids reacted differently depending on the cultivars. Two THCA dominant cultivars showed an increase in concentrations, while in the other two cultivars, concentrations decreased. Additionally, several rare compounds not present in diploids appeared in higher ploidy levels. Moreover, in one high THCA cultivar, a couple of elite tetraploid genotypes for cannabinoid and volatile production were identified, highlighting the role of cultivar and genotypic variability as an important factor in Cannabis sativa L. polyploids. Overall, our observations on plant morphology align with the giga phenotype observed in polyploids of other plant species. The decrease in cannabinoids and volatiles production in triploids have relevant implications regarding their commercial use. On the other hand, this study found that tetraploidization is a suitable approach to improve Cannabis sativa L. medicinal potential, although the response is cultivar and genotype-dependent. This work lays the ground for further improving, evaluating and harnessing Cannabis sativa L. chemical diversity by the breeding, biotechnological and pharmaceutical sectors.

Genetic factors inherited from both diploid parents interact to affect genome stability and fertility in resynthesized allotetraploid Brassica napus

Established allopolyploids are known to be genomically stable and fertile. However, in contrast, most newly resynthesized allopolyploids are infertile and meiotically unstable. Identifying the genetic factors responsible for genome stability in newly formed allopolyploid is key to understanding how 2 genomes come together to form a species. One hypothesis is that established allopolyploids may have inherited specific alleles from their diploid progenitors which conferred meiotic stability. Resynthesized Brassica napus lines are often unstable and infertile, unlike B. napus cultivars. We tested this hypothesis by characterizing 41 resynthesized B. napus lines produced by crosses between 8 Brassica rapa and 8 Brassica oleracea lines for copy number variation resulting from nonhomologous recombination events and fertility. We resequenced 8 B. rapa and 5 B. oleracea parent accessions and analyzed 19 resynthesized lines for allelic variation in a list of meiosis gene homologs. SNP genotyping was performed using the Illumina Infinium Brassica 60K array for 3 individuals per line. Self-pollinated seed set and genome stability (number of copy number variants) were significantly affected by the interaction between both B. rapa and B. oleracea parental genotypes. We identified 13 putative meiosis gene candidates which were significantly associated with frequency of copy number variants and which contained putatively harmful mutations in meiosis gene haplotypes for further investigation. Our results support the hypothesis that allelic variants inherited from parental genotypes affect genome stability and fertility in resynthesized rapeseed.

Quantification of pollen viability in Lantana camara by digital holographic microscopy

Pollen grains represent the male gametes of seed plants and their viability is critical for sexual reproduction in the plant life cycle. Palynology and viability studies have traditionally been used to address a range of botanical, ecological and geological questions, but recent work has revealed the importance of pollen viability in invasion biology as well. Here, we report an efficient visual method for assessing the viability of pollen using digital holographic microscopy (DHM). Imaging data reveal that quantitative phase information provided by the technique can be correlated with viability as indicated by the outcome of the colorimetric test. We successfully test this method on pollen grains of Lantana camara, a well-known alien invasive plant in the tropical world. Our results show that pollen viability may be assessed accurately without the usual staining procedure and suggest potential applications of the DHM methodology to a number of emerging areas in plant science.

Characterisation of a Spontaneous Mutant of Lemna gibba G3 (Lemnaceae)

A spontaneous mutant of the duckweed Lemna gibba clone no. 7796 (known as strain G3, WT) was discovered. In this mutant clone, L. gibba clone no. 9602 (mt), the morphological parameters (frond length, frond width, root length, root diameter) indicated an enlarged size. A change in the frond shape was indicated by the decreased frond length/width ratio, which could have taxonomic consequences. Several different cell types in both the frond and the root were also enlarged. Flow cytometric measurements disclosed the genome size of the WT as 557 Mbp/1C and that of the mt strain as 1153 Mbp/1C. This represents the results of polyploidisation of a diploid clone to a tetraploid one. The mutant clone flowered under the influence of long day-treatment in half-strength Hutner's medium in striking contrast to the diploid WT. Low concentration of salicylic acid (<1 µM) induced flowering in the tetraploid mutant but not in the diploid plants. The transcript levels of nuclear-encoded genes of the photosynthetic apparatus (CAB, RBCS) showed higher abundance in light and less dramatic decline in darkness in the mt than in WT, while this was not the case with plastid-encoded genes (RBCL, PSAA, PSBA, PSBC).

Cytogenotoxic effects of 3-epicaryoptin in Allium cepa L. root apical meristem cells

Diterpenoid 3-epicaryoptin (C₂₆H₃₆O₉) is abundant in the leaves of Clerodendrum inerme, a traditionally used medicinal plant, and has insect antifeedant activities. Here, we aim to explore the cytogenotoxic effects of compound 3-epicaryoptin in Allium cepa root apical meristem cells. 3-epicaryoptin (concentrations of 100, 150, and 200 µg mL^-1) and the standard compound colchicine (200 µg mL^-1) were applied to A. cepa roots for 2, 4, and 4 + 16 h (4-h treatment followed by 16-h recovery). Cytogenotoxicity was analyzed by studying the root growth retardation (RGR), mitotic index (MI), and chromosomal aberrations. The result showed statistically significant (p < 0.01), concentration-dependent RGR effects of 3-epicaryoptin treatment compared with the negative control. A study of cell frequency in different phases of cell division observed a significant (p < 0.001) increase in the metaphase cell percentage (66.2 ± 0.58%, 150 µg mL^-1), which subsequently caused an increase in the frequency of MI (12.29 ± 0.34%, 150 µg mL^-1) at 4 h of 3-epicaryoptin treatment and that was comparable with the colchicine action. The cytological study revealed that the 3-epicaryoptin treatment could induce different types of chromosomal abnormalities, such as colchicine-like metaphase, vagrant chromosomes, sticky chromosomes, anaphase bridge, lagging chromosomes, multipolar anaphase-telophase, and an increased frequency of micronuclei and polyploid cells. These findings indicate that 3-epicaryoptin is cytogenotoxic, and thus, C. inerme should be used with caution in traditional medicine.

Embryonic abnormalities and genotoxicity induced by 2,4-dichlorophenoxyacetic acid during indirect somatic embryogenesis in Coffea

Indirect somatic embryogenesis (ISE) is a morphogenetic pathway in which somatic cells form callus and, later, somatic embryos (SE). 2,4-dichlorophenoxyacetic acid (2,4-D) is a synthetic auxin that promotes the proliferation and dedifferentiation of somatic cells, inducing the ISE. However, 2,4-D can cause genetic, epigenetic, physiological and morphological disorders, preventing the regeneration and/or resulting abnormal somatic embryos (ASE). We aimed to evaluate the toxic 2,4-D effect during the Coffea arabica and C. canephora ISE, assessing the SE morphology, global 5-methylcytosine levels (5-mC%) and DNA damage. Leaf explants were inoculated in media with different 2,4-D concentrations. After 90 days, the friable calli were transferred to the regeneration medium, and the number of normal and abnormal SE was monthly counted. The increase of the 2,4-D concentration increased the number of responsive explants in both Coffea. At 9.06, 18.08 and 36.24 μM 2,4-D, C. arabica presented the highest values of responsive explants, differing from C. canephora. Normal and abnormal SE regeneration increased in relation to the time and 2,4-D concentration. Global 5-mC% varied at different stages of the ISE in both Coffea. Furthermore, the 2,4-D concentration positively correlated with global 5-mC%, and with the mean number of ASE. All ASE of C. arabica and C. canephora exhibited DNA damage and showed higher global 5-mC%. The allotetraploid C. arabica exhibited greater tolerance to the toxic effect of 2,4-D than the diploid C. canephora. We conclude that synthetic 2,4-D auxin promotes genotoxic and phytotoxic disorders and promotes epigenetic changes during Coffea ISE.

Challenges and potentials of new breeding techniques in Cannabis sativa

Cannabis sativa L. is an ancient crop used for fiber and seed production and not least for its content of cannabinoids used for medicine and as an intoxicant drug. Due to the psychedelic effect of one of the compounds, tetrahydrocannabinol (THC), many countries had regulations or bands on Cannabis growing, also as fiber or seed crop. Recently, as many of these regulations are getting less tight, the interest for the many uses of this crop is increasing. Cannabis is dioecious and highly heterogenic, making traditional breeding costly and time consuming. Further, it might be difficult to introduce new traits without changing the cannabinoid profile. Genome editing using new breeding techniques might solve these problems. The successful use of genome editing requires sequence information on suitable target genes, a genome editing tool to be introduced into plant tissue and the ability to regenerate plants from transformed cells. This review summarizes the current status of Cannabis breeding, uncovers potentials and challenges of Cannabis in an era of new breeding techniques and finally suggests future focus areas that may help to improve our overall understanding of Cannabis and realize the potentials of the plant.

Clonal diploid and autopolyploid breeding strategies to harness heterosis: insights from stochastic simulation

KEY MESSAGE

Reciprocal recurrent selection sometimes increases genetic gain per unit cost in clonal diploids with heterosis due to dominance, but it typically does not benefit autopolyploids. Breeding can change the dominance as well as additive genetic value of populations, thus utilizing heterosis. A common hybrid breeding strategy is reciprocal recurrent selection (RRS), in which parents of hybrids are typically recycled within pools based on general combining ability. However, the relative performances of RRS and other breeding strategies have not been thoroughly compared. RRS can have relatively increased costs and longer cycle lengths, but these are sometimes outweighed by its ability to harness heterosis due to dominance. Here, we used stochastic simulation to compare genetic gain per unit cost of RRS, terminal crossing, recurrent selection on breeding value, and recurrent selection on cross performance considering different amounts of population heterosis due to dominance, relative cycle lengths, time horizons, estimation methods, selection intensities, and ploidy levels. In diploids with phenotypic selection at high intensity, whether RRS was the optimal breeding strategy depended on the initial population heterosis. However, in diploids with rapid-cycling genomic selection at high intensity, RRS was the optimal breeding strategy after 50 years over almost all amounts of initial population heterosis under the study assumptions. Diploid RRS required more population heterosis to outperform other strategies as its relative cycle length increased and as selection intensity and time horizon decreased. The optimal strategy depended on selection intensity, a proxy for inbreeding rate. Use of diploid fully inbred parents vs. outbred parents with RRS typically did not affect genetic gain. In autopolyploids, RRS typically did not outperform one-pool strategies regardless of the initial population heterosis.

Two-step model of paleohexaploidy, ancestral genome reshuffling and plasticity of heat shock response in Asteraceae

An ancient hexaploidization event in the most but not all Asteraceae plants, may have been responsible for shaping the genomes of many horticultural, ornamental, and medicinal plants that promoting the prosperity of the largest angiosperm family on the earth. However, the duplication process of this hexaploidy, as well as the genomic and phenotypic diversity of extant Asteraceae plants caused by paleogenome reorganization, are still poorly understood. We analyzed 11 genomes from 10 genera in Asteraceae, and redated the Asteraceae common hexaploidization (ACH) event ~70.7-78.6 million years ago (Mya) and the Asteroideae specific tetraploidization (AST) event ~41.6-46.2 Mya. Moreover, we identified the genomic homologies generated from the ACH, AST and speciation events, and constructed a multiple genome alignment framework for Asteraceae. Subsequently, we revealed biased fractionations between the paleopolyploidization produced subgenomes, suggesting the ACH and AST both are allopolyplodization events. Interestingly, the paleochromosome reshuffling traces provided clear evidence for the two-step duplications of ACH event in Asteraceae. Furthermore, we reconstructed ancestral Asteraceae karyotype (AAK) that has 9 paleochromosomes, and revealed a highly flexible reshuffling of Asteraceae paleogenome. Of specific significance, we explored the genetic diversity of Heat Shock Transcription Factors (Hsfs) associated with recursive whole-genome polyploidizations, gene duplications, and paleogenome reshuffling, and revealed that the expansion of Hsfs gene families enable heat shock plasticity during the genome evolution of Asteraceae. Our study provides insights on polyploidy and paleogenome remodeling for the successful establishment of Asteraceae, and is helpful for further communication and exploration of the diversification of plant families and phenotypes.

An efficient approach to synthesize sterile allopolyploids through the combined reproduction mode of ameiotic oogenesis and sperm-egg fusion in the polyploid Carassius complex

The association between polyploidy and reproduction transition, which is an intriguing issue in evolutionary genetics, can also be exploited as an approach for genetic improvement in agriculture. Recently, we generated novel amphitriploids (NA3n) by integrating the genomes of the gynogenetic Carassius gibelio and sexual C. auratus, and found gynogenesis was recovered in most NA3n females (NA3n♀I). Here, we discovered a unique reproduction mode, termed ameio-fusiongenesis, which combines the abilities of both ameiotic oogenesis and sperm-egg fusion, in a few NA3n females (NA3n♀II). These females inherited ameiotic oogenesis to produce unreduced eggs from gynogenetic C. gibelio and sperm-egg fusion from sexual C. auratus. Subsequently, we utilized this unique reproduction mode to generate a group of synthetic alloheptaploids by crossing NA3n♀II with Megalobrama amblycephala. They contained all chromosomes of maternal NA3n♀II and a chromosomal set of paternal M. amblycephala. Intergenomic chromosome translocations between NA3n♀II and M. amblycephala were also observed in a few somatic cells. Primary oocytes of the alloheptaploid underwent severe apoptosis owing to incomplete double-strand break repair at prophase I. Although spermatocytes displayed similar chromosome behavior at prophase I, they underwent apoptosis due to chromosome separation failure at metaphase I. Therefore, the alloheptaploid females and males were all sterile. Finally, we established a sustainable clone for the large-scale production of NA3n♀II and developed an efficient approach to synthesize diverse allopolyploids containing genomes of different cyprinid species. These findings not only broaden our understanding of reproduction transition but also offer a practical strategy for polyploidy breeding and heterosis fixing.

Effect of elevated ozone on the antioxidant response, genomic stability, DNA methylation pattern and yield in three species of Abelmoschus having different ploidy levels

The majority of polyploids can withstand many stresses better than their monoploid counterparts; however, there is no proven mechanism that can fully explain the level of tolerance at the biochemical and molecular levels. Here, we make an effort to provide an explanation for this intriguing but perplexing issue using the antioxidant responses, genomic stability, DNA methylation pattern and yield in relation to ploidy level under the elevated level of ozone in Abelmoschus cytotypes. The outcome of this study inferred that the elevated ozone causes an increase in reactive oxygen species leading to enhanced lipid peroxidation, DNA damage and DNA de-methylation in all the Abelmoschus cytotypes. The monoploid cytotype of Abelmoschus, that is Abelmoschus moschatus L., experienced the highest oxidative stress under elevated O₃, resulting in maximum DNA damage and DNA de-methylation leading to the maximum reduction in yield. While the diploid (Abelmoschus esculentus L.) and triploid (Abelmoschus caillei A. Chev.) cytotypes of Abelmoschus with lower oxidative stress result in lesser DNA damage and DNA de-methylation which ultimately leads to lower yield reduction. The result of this experiment explicitly revealed that polyploidy confers better adaptability in the case of Abelmoschus cytotypes under ozone stress. This study can further be used as a base to understand the mechanism behind the ploidy-induced stress tolerance in other plants mediated by gene dosage effect.

A wider spectrum of avoidance and tolerance mechanisms explained ozone sensitivity of two white poplar ploidy levels

BACKGROUND AND AIMS

Polyploidization can improve plant mass yield for bioenergy support, yet few studies have investigated ozone (O3) sensitivity linked to internal regulatory mechanisms at different ploidy levels.

METHODS

Diploid and triploid Populus tomentosa plants were exposed to ambient and ambient plus 60 ppb [O3]. We explored their differences in sensitivity (leaf morphological, physiological and biochemical traits, and plant mass) as well as mechanisms of avoidance (stomatal conductance, xanthophyll cycle, thermal dissipation) and tolerance (ROS scavenging system) in response to O3 at two developmental phases.

KEY RESULTS

Triploid plants had the highest plant growth under ambient O3, even under O3 fumigation. However, triploid plants were the most sensitive to O3 and under elevated O3 showed the largest decreases in photosynthetic capacity and performance, as well as increased shoot:root ratio, and the highest lipid peroxidation. Thus, plant mass production could be impacted in triploid plants under long-term O3 contamination. Both diploid and triploid plants reduced stomatal aperture in response to O3, thereby reducing O3 entrance, yet only in diploid plants was reduced stomatal aperture associated with minimal (non-significant) damage to photosynthetic pigments and lower lipid peroxidation.

CONCLUSIONS

Tolerance mechanisms of plants of both ploidy levels mainly focused on the enzymatic reduction of hydrogen peroxide through catalase and peroxidase, yet these homeostatic regulatory mechanisms were higher in diploid plants. Our study recommends triploid white poplar as a bioenergy species only under short-term O3 contamination. Under continuously elevated O3 over the long term, diploid white poplar may perform better.

Mechanisms of salinity tolerance and their possible application in the breeding of vegetables

BACKGROUND

In dry and semi-arid areas, salinity is the most serious hazard to agriculture, which can affect plant growth and development adversely. Over-accumulation of Na⁺ in plant organs can cause an osmotic effect and an imbalance in nutrient uptake. However, its harmful impact can vary depending on genotype, period of exposure to stress, plant development stage, and concentration and content of salt. To overcome the unfavorable effect of salinity, plants have developed two kinds of tolerance strategies based on either minimizing the entrance of salts by the roots or administering their concentration and diffusion.

RESULTS

Having sufficient knowledge of Na⁺ accumulation mechanisms and an understanding of the function of genes involved in transport activity will present a new option to enhance the salinity tolerance of vegetables related to food security in arid regions. Considerable improvements in tolerance mechanisms can be employed for breeding vegetables with boosted yield performance under salt stress. A conventional breeding method demands exhaustive research work in crops, while new techniques of molecular breeding, such as cutting-edge molecular tools and CRISPR technology are now available in economically important vegetables and give a fair chance for the development of genetically modified organisms.

CONCLUSIONS

Therefore, this review highlights the molecular mechanisms of salinity tolerance, various molecular methods of breeding, and many sources of genetic variation for inducing tolerance to salinity stress.

The functional significance of the stomatal size to density relationship: Interaction with atmospheric [CO2] and role in plant physiological behaviour

The limits for stomatal conductance are set by stomatal size (SS) and density (SD). An inverse relationship between SS and SD has been observed in fossil and living plants. This has led to hypotheses proposing that the ratio of SS to SD influences the diffusion pathway for CO₂ and degree of physiological stomatal control. However, conclusive evidence supportive of a functional role of the SS-SD relationship is not evident, and patterns in SS-SD may simply reflect geometric constraints in stomatal spacing over a leaf surface. We examine published and new data to investigate the potential functional significance of the relationship between SS and SD to atmospheric [CO₂] in multiple generation adaptive responses and short-term acclamatory adjustment of stomatal morphology. Consistent patterns in SS and SD were not evident in fossil and living plants adapted to high [CO₂] over many generations. However, evolutionary adaptation to [CO₂] strongly affected SS and SD responses to elevated [CO₂], with plants adapted to the 'low' [CO₂] of the past 10 million years (Myr) showing adjustment of SS-SD, while members of the same species adapted to 'high' [CO₂] showed no response. This may suggest that SS and SD responses to future [CO₂] will likely constrain the stimulatory effect of 'CO₂-fertilisation' on photosynthesis. Angiosperms generally possessed higher densities of smaller stomata that corresponded to a greater degree of physiological stomatal control consistent with selective pressures induced by declining [CO₂] over the past 90 Myr. Atmospheric [CO₂] has likely shaped stomatal size and density relationships alongside the interaction with stomatal physiological behaviour. The rate and predicted extent of future increases in [CO₂] will have profound impacts on the selective pressures shaping SS and SD. Understanding the trade-offs involved in SS-SD and the interaction with [CO₂], will be central to the development of more productive climate resilient crops.

Colchicine-mediated in vitro polyploidization in gerbera hybrid

An efficient in vitro protocol for high-frequency polyploidization for the first time in gerbera hybrid (BGC-2019-01) was developed in the present study. Two-week-old in vitro-developed shoots (tips) were treated individually with 0.1%, 0.25% and 0.5% (w/v) colchicine solutions for 4, 6, 8, and 12 h. The colchicine-treated shoot tips were then inoculated on Murashige and Skoog (MS) medium fortified with 1.5 mg/l meta-Topolin for multiple shoot proliferation and later transferred into 1.5 mg/l indole-3-acetic acid-fortified MS medium for rooting of shoots. The ploidy levels of the colchicine-treated and regenerated plantlets along with the non-treated ones were confirmed via flow cytometry analysis and metaphasic chromosome count. The highest frequency of tetraploid plantlets (50%) were obtained when shoot tips were treated with 0.1% colchicine for 4 h. Morphological observations revealed that induced tetraploid plantlets exhibited delayed fresh shoot initiation, fewer but longer shoots, as well as fewer but broader leaves. Likewise, the study of stomata revealed that in comparison to their diploid counterparts, the tetraploid plantlets exhibited less frequent yet significantly larger stomata, and higher number of chloroplasts. The tetraploids were recorded with significantly higher chlorophyll, carotenoid, and anthocyanin content during the photosynthetic pigment analyses. During ex vitro acclimatization and field growth, the tetraploid plants exhibited delayed proliferation but with higher vigor and thickened broad leaves. The genetic uniformity among the diploid and the tetraploid plants was confirmed using conserved DNA-derived polymorphism (CDDP), directed amplification of minisatellite-region DNA (DAMD), inter simple sequence repeats (ISSR), and start codon targeted (SCoT) polymorphism marker systems. The tetraploids developed in the present study would be of immense importance for the genetic improvement of gerbera as far as its ornamental values are concerned.

Cytogeography of Naturalized Solidago canadensis Populations in Europe

Autopolyploidization has driven the successful invasion of Solidago canadensis in East Asia. However, it was believed that only diploid S. canadensis invaded Europe, whereas polyploids never did. Here, molecular identification, ploidy level, and morphological traits of ten S. canadensis populations collected in Europe were compared with previously identified S. canadensis populations from other continents and S. altissima populations. Furthermore, the ploidy-driven geographical differentiation pattern of S. canadensis in different continents was investigated. All ten European populations were identified as S. canadensis with five diploid and five hexaploid populations. Significant differences in morphological traits existed among diploids and polyploids (tetraploids and hexaploids), rather than between polyploids from different introduced ranges and between S. altissima and polyploidy S. canadensis. The invasive hexaploids and diploids had few differences in latitudinal distributions in Europe, which was similar to the native range but different from a distinct climate-niche differentiation in Asia. This may be attributed to the bigger difference in climate between Asia and Europe and North America. The morphological and molecular evidences proved the invasion of polyploid S. canadensis in Europe and suggest that S. altissima may be merged into a complex of S. canadensis species. Our study may be concluded that geographical and ecological niche differentiation of an invasive plant driven by ploidy depends on the degree of difference in the environmental factors between the introduced and native range, which provides new insight into the invasive mechanism.

Autoploid origin and rapid diploidization of the tetraploid Thinopyrum elongatum revealed by genome differentiation and chromosome pairing in meiosis

Polyploidy is a common mode of evolution in flowering plants. Both the natural tetraploid Thinopyrum elongatum and the diploid one from the same population show a diploid-like pairing in meiosis. However, debate on the chromosome composition and origin of the tetraploid Th. elongatum is ongoing. In the present study, we obtained the induced tetraploid Th. elongatum and found that the induced and natural tetraploids are morphologically close, except for slower development and lower seed setting. Using probes developed from single chromosome microdissection and a Fosmid library, obvious differentiations were discovered between two chromosome sets (E₁ and E₂ ) of the natural tetraploid Th. elongatum but not the induced one. Interestingly, hybrid F₁ derived from the two different wheat-tetraploid Th. elongatum amphiploids 8802 and 8803 produced seeds well. More importantly, analysis of meiosis in F₂ individuals revealed that chromosomes from E₁ and E₂ could pair well on the durum wheat background with the presence of Ph1. No chromosome set differentiation on the FISH level was discovered from the S1 to S4 generations in the induced one. In metaphase of the meiosis first division in the natural tetraploid, more pairings were bivalents and fewer quadrivalents with ratio of 13.94 II + 0.03 IV (n = 31). Chromosome pairing configuration in the induced tetraploid is 13.05 II + 0.47 IV (n = 19), with the quadrivalent ratio being only slightly higher than the ratio in the natural tetraploid. Therefore, the natural tetraploid Th. elongatum is of autoploid origin and the induced tetraploid Th. elongatum evolutionarily underwent rapid diploidization in the low generation.

Genomic and epigenomic variation in Psidium species and their outcome under the yield and composition of essential oils

Diploid and polyploid species derived from the euploid series x = 11 occur in the genus Psidium, as well as intraspecific cytotypes. Euploidy in the genus can alter the gene copy number, resulting in several "omics" variations. We revisited the euploidy, reported genomic (nuclear 2C value, GC%, and copy number of secondary metabolism genes) and epigenomic (5-mC%) differences in Psidium, and related them to essential oil yield and composition. Mean 2C values ranged from 0.90 pg (P. guajava) to 7.40 pg (P. gaudichaudianum). 2C value is intraspecifically varied in P. cattleyanum and P. gaudichaudianum, evidencing cytotypes that can be formed from euploid (non-reduced) and/or aneuploid reproductive cells. GC% ranged from 34.33% (P. guineense) to 48.95% (P. myrtoides), and intraspecific variations occurred even for species without 2C value intraspecific variation. Essential oil yield increased in relation to 2C value and to GC%. We showed that P. guajava (diploid) possesses two and P. guineense (tetraploid) four copies of the one specific TPS gene, as well as eight and sixteen copies respectively of the conserved regions that occur in eight TPS genes. We provide a wide "omics'' characterization of Psidium and show the outcome of the genome and epigenome variation in secondary metabolism.