Polyploidization-driven differentiation of freezing tolerance in Solidago canadensis

Weed biology and management in the multi-omics era: Progress and perspectives

Weeds pose a significant threat to crop production, resulting in substantial yield reduction. In addition, they possess robust weedy traits that enable them to survive in extreme environments and evade human control. In recent years, the application of multi-omics biotechnologies has helped to reveal the molecular mechanisms underlying these weedy traits. In this review, we systematically describe diverse applications of multi-omics platforms for characterizing key aspects of weed biology, including the origins of weed species, weed classification, and the underlying genetic and molecular bases of important weedy traits such as crop-weed interactions, adaptability to different environments, photoperiodic flowering responses, and herbicide resistance. In addition, we discuss limitations to the application of multi-omics techniques in weed science, particularly compared with their extensive use in model plants and crops. In this regard, we provide a forward-looking perspective on the future application of multi-omics technologies to weed science research. These powerful tools hold great promise for comprehensively and efficiently unraveling the intricate molecular genetic mechanisms that underlie weedy traits. The resulting advances will facilitate the development of sustainable and highly effective weed management strategies, promoting greener practices in agriculture.

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.

Polyploidization-enhanced effective clonal reproduction endows the successful invasion of Solidago canadensis

Clonality and ploidy levels are positively associated with plant invasiveness. However, there is still no consensus on whether polyploidization can promote the invasion of alien plants by enhancing clonality. Our recent long-term community succession study found that the more vigorous clone of introduced polyploid Solidago canadensis succeeded into mono-dominant community, which seems to be a positive correlationship between polyploidization and clonal reproduction. However, the formation process of clonal ramet and how polyploidization improves the clonal reproduction of S. canadensis remains unknown. Here, we compared clonal growth ability among diploids and polyploids of S. canadensis from native and introduced ranges in a common garden. Results showed that the rhizomes of S. canadensis originated from axillary buds of dense nodes at the basal stem of seedling and then produced into clonal ramets from the rhizomes. Diploids had denser nodes and more buds, developed more rhizomes per unit mass and produced more clonal propagules at the early growth stage compared with polyploids. However, the number of juvenile and secondary rhizomes, as well as the diameter and length of rhizomes in polyploid populations was significantly higher or greater than those of diploids, and those clonal traits in introduced polyploids were significantly higher than in native polyploids. Moreover, a phalanx growth form was observed in native and introduced diploid populations, which allocated about 3% and 5% of the total biomass to rhizomes, respectively, resulting in short and weak rhizomes. However, native and introduced polyploids allocated about 35% and 40%, respectively, of the total biomass to rhizomes, resulting in long and strong rhizomes, which were guerrilla growth forms. This study firstly shows that polyploidization enhanced the effective clonal reproduction of S. canadensis through pre-adaptation and rapid post-adaptation evolution, and consequently contributed to its successful invasion.

The metabolism of nonstructural carbohydrates, lipids, and energy in two Cycas species with differential tolerance to unexpected freezing stress

Introduction

With the climate warming, the occurrence of freezing events is projected to increase in late spring and early autumn in the Northern Hemisphere. Observation of morphological traits showed that Cycas panzhihuaensis was more tolerant to unexpected freezing stress than C. bifida. Energy balance is crucial for plant tolerance to stress. Here, we aimed to determine whether the different responses of the two species to the unpredicted freezing stress were associated with the metabolism of energy and related substances.

Methods

The effects of unexpected freezing temperatures on C. panzhihuaensis and C. bifida were studied by measuring chlorophyll fluorescence parameters, energy charge and the profile of nonstructural carbohydrates (NSC) and lipids.

Results

C. panzhihuaensis exhibited higher stability of photosynthetic machinery than C. bifida under unpredicted freezing events. Significant interaction between species and treatments were observed in the energy charge, the level of NSC and its most components and the amount of most lipid categories and lipid classes. The decrease of soluble sugar and the increase of neutral glycerolipids at the early freezing stage, the accumulation of membrane glycerolipids at the late freezing stage and the continuous decrease of energy charge during the freezing period were the characteristics of C. panzhihuaensis responding to unexpected freezing stress. The degradation of membrane glycerolipids and the continuous decrease of soluble sugar during the freezing period and the accumulation of neutral glycerolipids and energy charge at the late freezing stage represented the characteristics of C. bifida responses.

Discussion

The different freezing sensitivity between C. panzhihuaensis and C. bifida might be associated with the differential patterns of the metabolism of energy, NSC and lipids. C. panzhihuaensis possesses the potential to be introduced to the areas of higher latitudes and altitudes.

Expression dosage effects of a small number of genes after the artificial doubling of weeping forsythia

Whole genome doubling (WGD) plays a critical role in plant evolution, yet the mechanisms underlying the maintenance of overall equilibrium following an artificial doubling event, as well as its impact on phenotype and adaptability, remain unclear. By comparing the gene expression of naturally occurring weeping forsythia diploids and colchicine-induced autotetraploids under normal growth conditions and cold stress, we identified gene expression dosage responses resulting from ploidy change. Only a small proportion of effectively expressed genes showed dosage effect, and most genes did not exhibit significant expression differences. However, the genes that showed expression dosage effect were largely random. The autotetraploids had slower overall growth rates, possibly resulting from negative gene dosage effects on zeatin synthesis and multiple metabolic delays caused by other negative dosage genes. Our comparative analysis of cold response genes in diploids and autotetraploids revealed that genes related to "response to abscisic acid" and "cold acclimation" were key factors contributing to greater cold tolerance in the autotetraploids. In particular, gene expression related to "cold acclimation" might mitigate the effects of cold stress. Taken together, our findings suggested that overall gene expression equilibrium following WGD of weeping forsythia autotetraploids was achieved through the inactivation of the majority of duplicated genes. Our research provides new insights into the mechanisms regulating expression dosage balance following polyploidization events.

Weed genomics: yielding insights into the genetics of weedy traits for crop improvement

Weeds cause tremendous economic and ecological damage worldwide. The number of genomes established for weed species has sharply increased during the recent decade, with some 26 weed species having been sequenced and de novo genomes assembled. These genomes range from 270 Mb (Barbarea vulgaris) to almost 4.4 Gb (Aegilops tauschii). Importantly, chromosome-level assemblies are now available for 17 of these 26 species, and genomic investigations on weed populations have been conducted in at least 12 species. The resulting genomic data have greatly facilitated studies of weed management and biology, especially origin and evolution. Available weed genomes have indeed revealed valuable weed-derived genetic materials for crop improvement. In this review, we summarize the recent progress made in weed genomics and provide a perspective for further exploitation in this emerging field.

Transcriptome Analysis of Low-Temperature-Treated Tetraploid Yellow Actinidia chinensis Planch. Tissue Culture Plantlets

Simple Summary

Yellow kiwifruit (Actinidia chinensis Planch.) is popular in the market. However, it is highly susceptible to severe weather, including as low temperatures and frost, which may affect its production in the coming year. The cold-resistant mechanism of yellow kiwifruit associated with gene regulation is poorly investigated. To better understand cold-adaptive mechanisms, we grew plants under low-temperature conditions, which was followed by transcriptome analysis to discern the genes that play an active role in growth under low temperatures. The findings and dataset obtained in this study advance our knowledge of the cold-adaptive genes in regulatory networks and helps us to understand the cold-tolerance mechanisms in the tetraploid yellow kiwifruit.

Abstract

The cold-resistant mechanism of yellow kiwifruit associated with gene regulation is poorly investigated. In this study, to provide insight into the causes of differences in low-temperature tolerance and to better understand cold-adaptive mechanisms, we treated yellow tetraploid kiwifruit ‘SWFU03’ tissue culture plantlets at low temperatures, used these plantlets for transcriptome analysis, and validated the expression levels of ten selected genes by real-time quantitative polymerase chain reaction (RT-qPCR) analysis. A number of 1630 differentially expressed genes (DEGs) were identified, of which 619 pathway genes were up-regulated, and 1011 were down-regulated in the cold treatment group. The DEGs enriched in the cold tolerance-related pathways mainly included the plant hormone signal transduction and the starch and sucrose metabolism pathway. RT-qPCR analysis confirmed the expression levels of eight up-regulated genes in these pathways in the cold-resistant mutants. In this study, cold tolerance-related pathways (the plant hormone signal transduction and starch and sucrose metabolism pathway) and genes, e.g., CEY00_Acc03316 (abscisic acid receptor PYL), CEY00_Acc13130 (bZIP transcription factor), CEY00_Acc33627 (TIFY protein), CEY00_Acc26744 (alpha-trehalose-phosphate synthase), CEY00_Acc28966 (beta-amylase), CEY00_Acc16756 (trehalose phosphatase), and CEY00_Acc08918 (beta-amylase 4) were found.

Traces of Genetic but Not Epigenetic Adaptation in the Invasive Goldenrod Solidago canadensis Despite the Absence of Population Structure

Biological invasions may result from multiple introductions, which might compensate for reduced gene pools caused by bottleneck events, but could also dilute adaptive processes. A previous common-garden experiment showed heritable latitudinal clines in fitness-related traits in the invasive goldenrod Solidago canadensis in Central Europe. These latitudinal clines remained stable even in plants chemically treated with zebularine to reduce epigenetic variation. However, despite the heritability of traits investigated, genetic isolation-by-distance was non-significant. Utilizing the same specimens, we applied a molecular analysis of (epi)genetic differentiation with standard and methylation-sensitive (MSAP) AFLPs. We tested whether this variation was spatially structured among populations and whether zebularine had altered epigenetic variation. Additionally, we used genome scans to mine for putative outlier loci susceptible to selection processes in the invaded range. Despite the absence of isolation-by-distance, we found spatial genetic neighborhoods among populations and two AFLP clusters differentiating northern and southern Solidago populations. Genetic and epigenetic diversity were significantly correlated, but not linked to phenotypic variation. Hence, no spatial epigenetic patterns were detected along the latitudinal gradient sampled. Applying genome-scan approaches (BAYESCAN, BAYESCENV, RDA, and LFMM), we found 51 genetic and epigenetic loci putatively responding to selection. One of these genetic loci was significantly more frequent in populations at the northern range. Also, one epigenetic locus was more frequent in populations in the southern range, but this pattern was lost under zebularine treatment. Our results point to some genetic, but not epigenetic adaptation processes along a large-scale latitudinal gradient of S. canadensis in its invasive range.

Integrated analysis of mRNA-seq and miRNA-seq reveals the advantage of polyploid Solidago canadensis in sexual reproduction

BACKGROUND

The invasion of Solidago canadensis probably related to polyploidy, which may promotes its potential of sexual reproductive. S. canadensis as an invasive species which rapidly widespread through yield huge numbers of seed, but the mechanism remains unknown. To better understand the advantages of sexual reproduction in hexaploid S. canadensis, transcriptome and small RNA sequencing of diploid and hexaploid cytotypes in flower bud and fruit development stages were performed in this study.

RESULTS

The transcriptome analysis showed that in the flower bud stage, 29 DEGs were MADS-box related genes with 14 up-regulated and 15 down-regulated in hexaploid S. canadensis; 12 SPL genes were detected differentially expressed with 5 up-regulated and 7 down-regulated. In the fruit development stage, 26 MADS-box related genes with 20 up-regulated and 6 down-regulated in hexaploid S. canadensis; 5 SPL genes were all up-regulated; 28 seed storage protein related genes with 18 were up-regulated and 10 down-regulated. The weighted gene co-expression network analysis (WGCNA) identified 19 modules which consisted of co-expressed DEGs with functions such as sexual reproduction, secondary metabolism and transcription factors. Furthermore, we discovered 326 miRNAs with 67 known miRNAs and 259 novel miRNAs. Some of miRNAs, such as miR156, miR156a and miR156f, which target the sexual reproduction related genes.

CONCLUSION

Our study provides a global view of the advantages of sexual reproduction in hexaploid S. canadensis based on the molecular mechanisms, which may promote hexaploid S. canadensis owing higher yield and fruit quality in the process of sexual reproduction and higher germination rate of seeds, and finally conductive to diffusion, faster propagation process and enhanced invasiveness.

Transcriptome and Metabolome Analysis Revealed the Freezing Resistance Mechanism in 60-Year-Old Overwintering Camellia sinensis

Simple Summary

The freezing stress during overwintering brings great challenges to the normal growth of Camellia sinensis. The current research on C. sinensis mainly focuses on cold resistance, but less on freezing resistance. In the present study, the transcriptome and metabolome of C. sinensis under freezing stress were studied. Results showed that Pyr/PYL-PP2C-SnRK2 played a critical role in the signal transduction of freezing stress. Three metabolic pathways including phenylpropanoid biosynthesis, flavone and flavonol biosynthesis, and flavonoid biosynthesis contributed to the freezing resistance of C. sinensis. This study provides substantial insights for the breeding of C. sinensis.

Abstract

Freezing stress in winter is the biggest obstacle to the survival of C. sinensis in mid-latitude and high-latitude areas, which has a great impact on the yield, quality, and even life of C. sinensis every year. In this study, transcriptome and metabolome were used to clarify the freezing resistance mechanism of 60-year-old natural overwintering C. sinensis under freezing stress. Next, 3880 DEGs and 353 DAMs were obtained. The enrichment analysis showed that pathways of MAPK and ABA played a key role in the signal transduction of freezing stress, and Pyr/PYL-PP2C-SnRK2 in the ABA pathway promoted stomatal closure. Then, the water holding capacity and the freezing resistance of C. sinensis were improved. The pathway analysis showed that DEGs and DAMs were significantly enriched and up-regulated in the three-related pathways of phenylpropanoid biosynthesis, flavone and flavonol biosynthesis, and flavonoid biosynthesis. In addition, the carbohydrate and fatty acid synthesis pathways also had a significant enrichment, and the synthesis of these substances facilitated the freezing resistance. These results are of great significance to elucidate the freezing resistance mechanism and the freezing resistance breeding of C. sinensis.

When everything changes at once: finding a new normal after genome duplication

Whole-genome duplication (WGD), which leads to polyploidy, is implicated in adaptation and speciation. But what are the immediate effects of WGD and how do newly polyploid lineages adapt to them? With many studies of new and evolved polyploids now available, along with studies of genes under selection in polyploids, we are in an increasingly good position to understand how polyploidy generates novelty. Here, I will review consistent effects of WGD on the biology of plants, such as an increase in cell size, increased stress tolerance and more. I will discuss how a change in something as fundamental as cell size can challenge the function of some cell types in particular. I will also discuss what we have learned about the short- to medium-term evolutionary response to WGD. It is now clear that some of this evolutionary response may 'lock in' traits that happen to be beneficial, while in other cases, it might be more of an 'emergency response' to work around physiological changes that are either deleterious, or cannot be undone in the polyploid context. Yet, other traits may return rapidly to a diploid-like state. Polyploids may, by re-jigging many inter-related processes, find a new, conditionally adaptive, normal.

Genomics of Evolutionary Novelty in Hybrids and Polyploids

It has long been recognized that hybridization and polyploidy are prominent processes in plant evolution. Although classically recognized as significant in speciation and adaptation, recognition of the importance of interspecific gene flow has dramatically increased during the genomics era, concomitant with an unending flood of empirical examples, with or without genome doubling. Interspecific gene flow is thus increasingly thought to lead to evolutionary innovation and diversification, via adaptive introgression, homoploid hybrid speciation and allopolyploid speciation. Less well understood, however, are the suite of genetic and genomic mechanisms set in motion by the merger of differentiated genomes, and the temporal scale over which recombinational complexity mediated by gene flow might be expressed and exposed to natural selection. We focus on these issues here, considering the types of molecular genetic and genomic processes that might be set in motion by the saltational event of genome merger between two diverged species, either with or without genome doubling, and how these various processes can contribute to novel phenotypes. Genetic mechanisms include the infusion of new alleles and the genesis of novel structural variation including translocations and inversions, homoeologous exchanges, transposable element mobilization and novel insertional effects, presence-absence variation and copy number variation. Polyploidy generates massive transcriptomic and regulatory alteration, presumably set in motion by disrupted stoichiometries of regulatory factors, small RNAs and other genome interactions that cascade from single-gene expression change up through entire networks of transformed regulatory modules. We highlight both these novel combinatorial possibilities and the range of temporal scales over which such complexity might be generated, and thus exposed to natural selection and drift.