Horizontal genome transfer as an asexual path to the formation of new species

Plant grafting: Molecular mechanisms and applications

People have grafted plants since antiquity for propagation, to increase yields, and to improve stress tolerance. This cutting and joining of tissues activates an incredible regenerative ability as different plants fuse and grow as one. For over a hundred years, people have studied the scientific basis for how plants graft. Today, new techniques and a deepening knowledge of the molecular basis for graft formation have allowed a range of previously ungraftable combinations to emerge. Here, we review recent developments in our understanding of graft formation, including the attachment and vascular formation steps. We analyze why plants graft and how biotic and abiotic factors influence successful grafting. We also discuss the ability and inability of plants to graft, and how grafting has transformed both horticulture and fundamental plant science. As our knowledge about plant grafting improves, new combinations and techniques will emerge to allow an expanded use of grafting for horticultural applications and to address fundamental research questions.

Genome-wide analysis of horizontal transfer in non-model wild species from a natural ecosystem reveals new insights into genetic exchange in plants

Horizontal transfer (HT) refers to the exchange of genetic material between divergent species by mechanisms other than reproduction. In recent years, several studies have demonstrated HTs in eukaryotes, particularly in the context of parasitic relationships and in model species. However, very little is known about HT in natural ecosystems, especially those involving non-parasitic wild species, and the nature of the ecological relationships that promote these HTs. In this work, we conducted a pilot study investigating HTs by sequencing the genomes of 17 wild non-model species from a natural ecosystem, the Massane forest, located in southern France. To this end, we developed a new computational pipeline called INTERCHANGE that is able to characterize HTs at the whole genome level without prior annotation and directly in the raw sequencing reads. Using this pipeline, we identified 12 HT events, half of which occurred between lianas and trees. We found that mainly low copy number LTR-retrotransposons from the Copia superfamily were transferred between these wild plant species, especially those of the Ivana and Ale lineages. This study revealed a possible new route for HTs between non-parasitic plants and provides new insights into the genomic characteristics of horizontally transferred DNA in plant genomes.

Grafting in plants: recent discoveries and new applications

Grafting is a traditional horticultural technique that makes use of plant wound healing mechanisms to join two different genotypes together to form one plant. In many agricultural systems, grafting with rootstocks controls the vigour of the scion and/or provides tolerance to deleterious soil conditions such as the presence of soil pests or pathogens or limited or excessive water or mineral nutrient supply. Much of our knowledge about the limits to grafting different genotypes together comes from empirical knowledge of horticulturalists. Until recently, researchers believed that grafting monocotyledonous plants was impossible, because they lack a vascular cambium, and that graft compatibility between different scion/rootstock combinations was restricted to closely related genotypes. Recent studies have overturned these ideas and open up the possibility of new research directions and applications for grafting in agriculture. The objective of this review is to describe and assess these recent advances in the field of grafting and, in particular, the molecular mechanisms underlining graft union formation and graft compatibility between different genotypes. The challenges of characterizing the different stages of graft union formation and phenotyping graft compatibility are examined.

Sidestepping Darwin: horizontal gene transfer from plants to insects

Horizontal transfer of genetic material (HT) is the passage of DNA between organisms by means other than reproduction. Increasing numbers of HT are reported in insects, with bacteria, fungi, plants, and insects acting as the main sources of these transfers. Here, we provide a detailed account of plant-to-insect HT events. At least 14 insect species belonging to 6 orders are known to have received plant genetic material through HT. One of them, the whitefly Bemisia tabaci (Middle East Asia Minor 1), concentrates most of these transfers, with no less than 28 HT events yielding 55 plant-derived genes in this species. Several plant-to-insect HT events reported so far involve gene families known to play a role in plant-parasite interactions. We highlight methodological approaches that may further help characterize these transfers. We argue that plant-to-insect HT is likely more frequent than currently appreciated and that in-depth studies of these transfers will shed new light on plant-insect interactions.

Scion-to-Rootstock Mobile Transcription Factor CmHY5 Positively Modulates the Nitrate Uptake Capacity of Melon Scion Grafted on Squash Rootstock

It is generally recognized that the root uptake capacity of grafted plants strongly depends on the rootstocks' well-developed root system. However, we found that grafted plants showed different nitrate uptake capacities when different varieties of oriental melon scion were grafted onto the same squash rootstock, suggesting that the scion regulated the nitrate uptake capacity of the rootstock root. In this study, we estimated the nitrate uptake capacity of grafted plants with the different oriental melon varieties' seedlings grafted onto the same squash rootstocks. The results indicated a significant difference in the nitrate uptake rate and activity of two heterologous grafting plants. We also showed a significant difference in CmoNRT2.1 expression in the roots of two grafting combinations and verified the positive regulation of nitrate uptake by CmoNRT2.1 expression. In addition, the two varieties of oriental melon scion had highly significant differences in CmHY5 expression, which was transported to the rootstock and positively induced CmoHY5-1 and CmoHY5-2 expression in the rootstock roots. Meanwhile, CmHY5 could positively regulate CmoNRT2.1 expression in the rootstock roots. Furthermore, CmoHY5-1 and CmoHY5-2 also positively regulated CmoNRT2.1 expression, respectively, and CmoHY5-1 dominated the positive regulation of CmoNRT2.1, while CmHY5 could interact with CmoHY5-1 and CmoHY5-2, respectively, to jointly regulate CmoNRT2.1 expression. The oriental melon scion regulated the nitrate uptake capacity of the melon/squash grafting plant roots, and the higher expression of CmHY5 in the oriental melon scion leaves, the more substantial the nitrate uptake capacity of squash rootstock roots.

Comparative study on comprehensive quality of Xinhui chenpi by two main plant propagation techniques

Xinhui chenpi (XHCP), the sun-dried peel of the mandarin orange, Citrus reticulata "Chachi," is the most famous crude drug, as well as a traditional seasoning in Chinese cooking. The main cultivation methods of XHCP are cutting and grafting, but it is generally considered that the quality of XHCP after cutting is superior to that obtained from plants propagated by graftings, which had a negative impact on the marketing of the finished product. In our study, a total of 25 samples of XHCP obtained from plants cultivated by either traditional methods (i.e., from cuttings) or by grafting were collected to compare the contents of four types of metabolites (essential oils, flavonoids, synephrine, and total polysaccharides) as well as antioxidant activity. The results revealed that the quality of XHCP did not decline after cutting, and marked individual differences between XHCP samples, even when prepared from plants grown in the same way. In general, grafting had no significant effect on the most essential oils components, total polysaccharides, synephrine, total flavonoids, total polymethoxylated flavones, hesperidin, nobiletin, tangeretin content, and antioxidant activity. Nevertheless, five volatile compounds can be used as potential chemical markers (p < 0.05) to distinguish between cutting XHCP and grafted XHCP, while four volatile compounds showed high content in grafted XHCP. Our study is expected to provide a theoretical basis for XHCP breeding and cultivation, and thereby further standardize the market of XHCP.

Horizontal gene transfer from genetically modified plants - Regulatory considerations

Gene technology regulators receive applications seeking permission for the environmental release of genetically modified (GM) plants, many of which possess beneficial traits such as improved production, enhanced nutrition and resistance to drought, pests and diseases. The regulators must assess the risks to human and animal health and to the environment from releasing these GM plants. One such consideration, of many, is the likelihood and potential consequence of the introduced or modified DNA being transferred to other organisms, including people. While such gene transfer is most likely to occur to sexually compatible relatives (vertical gene transfer), horizontal gene transfer (HGT), which is the acquisition of genetic material that has not been inherited from a parent, is also a possibility considered during these assessments. Advances in HGT detection, aided by next generation sequencing, have demonstrated that HGT occurrence may have been previously underestimated. In this review, we provide updated evidence on the likelihood, factors and the barriers for the introduced or modified DNA in GM plants to be horizontally transferred into a variety of recipients. We present the legislation and frameworks the Australian Gene Technology Regulator adheres to with respect to the consideration of risks posed by HGT. Such a perspective may generally be applicable to regulators in other jurisdictions as well as to commercial and research organisations who develop GM plants.

Systematic Analysis of the Grafting-Related Glucanase-Encoding GH9 Family Genes in Pepper, Tomato and Tobacco

Grafting is an important agricultural practice to control soil-borne diseases, alleviate continuous cropping problems and improve stress tolerance in vegetable industry, but it is relatively less applied in pepper production. A recent study has revealed the key roles of β-1, 4-glucanase in graft survival. We speculated that the GH9 family gene encoding glucanase may be involved in the obstacles of pepper grafting. Therefore, we performed a systematic analysis of the GH9 family in pepper, tomato and tobacco. A total of 25, 24 and 42 GH9 genes were identified from these three species. Compared with the orthologues of other solanaceous crops, the deduced pepper GH9B3 protein lacks a conserved motif (Motif 5). Promoter cis-element analysis revealed that a wound-responsive element exists in the promoter of tobacco NbGH9B3, but it is absent in the GH9B3 promoter of most solanaceous crops. The auxin-responsive related element is absent in CaGH9B3 promoter, but it presents in the promoter of tobacco, tomato, potato and petunia GH9B3. Tissue and induction expression profiles indicated that GH9 family genes are functionally differentiated. Nine GH9 genes, including CaGH9B3, were detected expressing in pepper stem. The expression patterns of NbGH9B3 and CaGH9B3 in grafting were different in our test condition, with obvious induction in tobacco but repression in pepper. Furthermore, weighted correlation network analysis (WGCNA) revealed 58 transcription factor genes highly co-expressed with NbGH9B3. Eight WRKY binding sites were detected in the promoter of NbGH9B3, and several NbWRKYs were highly co-expressed with NbGH9B3. In conclusion, the missing of Motif 5 in CaGH9B3, and lacking of wound- and auxin-responsive elements in the gene promoter are the potential causes of grafting-related problems in pepper. WRKY family transcription factors could be important regulator of NbGH9B3 in tobacco grafting. Our analysis points out the putative regulators of NbGH9B3, which would be helpful to the functional validation and the study of signal pathways related to grafting in the future.

Drought tolerance memory transmission by citrus buds

Plants face recurrent drought events, and previous stresses can influence their responses to subsequent stress episodes. Studies on drought stress memory are recent in citriculture, although they show promise as a tool for crop improvement. Here, we investigated whether stress memory mechanisms can be detected in citrus plants grafted with buds from plants subjected to recurrent water deficit. Three rootstock varieties, namely 'Rangpur Santa Cruz' lime, 'Sunki Maravilha' mandarin and 'Sunki Tropical' mandarin, in combination with 'Valencia' orange, were either maintained under full irrigation or subjected to one, two, or three water deficit cycles. Buds from 'Valencia' orange were grafted onto 'Swingle' citrumelo rootstocks and were evaluated. This combination displayed improved physiological and biochemical performance under water limitation, especially 'Valencia' buds grafted onto 'Sunki Maravilha', with better photosynthetic performance under water deficit. These findings indicate that genotype-dependent epigenetic memory is a key factor in restoring citrus plants' capacity to rely on previous stress experiences to restore better photosynthetic and physiological responses when undergoing new water deficit events. Therefore, epigenetic marks can be stored and transmitted to new citrus plants and are a promising alternative to enable increased water deficit tolerance when plants are then challenged by drought-prone environments.

Comparative Transcriptomic, Anatomical and Phytohormone Analyses Provide New Insights Into Hormone-Mediated Tetraploid Dwarfing in Hybrid Sweetgum (Liquidambar styraciflua × L. formosana)

Polyploid breeding is an effective approach to improve plant biomass and quality. Both fast growth and dwarf types of in vitro or ex vitro plants are produced after polyploidization. However, little is known regarding the dwarf type mechanism in polyploids grown in vitro. In this study, the morphological and cytological characteristics were measured in tetraploid and diploid hybrid sweetgum (Liquidambar styraciflua × L. formosana) with the same genetic background. RNA sequencing (RNA-Seq) was used to analyse shoot and root variations between tetraploid and diploid plants; important metabolites were validated. The results showed that the shoot and root lengths were significantly shorter in tetraploids than in diploids after 25 d of culture. Most tetraploid root cells were wider and more irregular, and the length of the meristematic zone was shorter, while tetraploid cells were significantly larger than diploid cells. Differentially expressed genes (DEGs) were significantly enriched in the plant growth and organ elongation pathways, such as plant hormone biosynthesis and signal transduction, sugar and starch metabolism, and cell cycles. Hormone biosynthesis and signal transduction genes, such as YUCCA, TAA1, GH3, SAUR, CPS, KO, KAO, GA20ox, GA3ox, BAS1 and CYCD3, which help to regulate organ elongation, were generally downregulated. The auxin, gibberellin, and brassinolide (BL) contents in roots and stems were significantly lower in tetraploids than in diploids, which may greatly contribute to slow growth in the roots and stems of tetraploid regenerated plants. Exogenous gibberellic acid (GA₃) and indole-3-acetic acid (IAA), which induced plant cell elongation, could significantly promote growth in the stems and roots of tetraploids. In summary, comparative transcriptomics and metabolite analysis showed that the slow growth of regenerated tetraploid hybrid sweetgum was strongly related to auxin and gibberellin deficiency. Our findings provide insights into the molecular mechanisms that underlie dwarfism in allopolyploid hybrid sweetgum.

Walnut Genotypes for High Density Orchards

The aim of this review is to check the possibilities and circumstances regarding how to create a high-density Persian walnut orchard. Increasing yields, decreasing tree size, limiting juveniles, and lowering total costs are the most important objectives of breeders and horticulturists. Reducing the size of walnut trees can increase yield. Breeding programs in several countries have led to the production of walnut dwarf rootstocks. For example, Daixiang and Daihui in China, Alvand in Iran, and Fernette in France are all novel-bred dwarfing Persian walnut rootstocks. These precocious walnuts are considered to be a rare resource in the study of precociousness as well as juvenile and flowering mechanisms. Moreover, they play a potential role in breeding and modifying cultivars by genetic engineering, through walnut ameliorating programs. The CRISPR (clustered regularly interspaced short palindromic repeat) technique is used to improve walnuts, which will be used in the near future.

Rootstock-scion combination contributes to shape diversity and composition of microbial communities associated with grapevine root system

To alleviate biotic and abiotic stresses and enhance fruit yield, many crops are cultivated in the form of grafted plants, in which the shoot (scion) and root (rootstock) systems of different species are joined together. Because (i) the plant species determines the microbial recruitment from the soil to the root and (ii) both scion and rootstock impact the physiology, morphology and biochemistry of the grafted plant, it can be expected that their different combinations should affect the recruitment and assembly of plant microbiome. To test our hypothesis, we investigated at a field scale the bacterial and fungal communities associated with the root system of seven grapevine rootstock–scion combinations cultivated across 10 different vineyards. Following the soil type, which resulted in the main determinant of the grapevine root microbial community diversity, the rootstock–scion combination resulted more important than the two components taken alone. Notably, the microbiome differences among the rootstock–scion combinations were mainly dictated by the changes in the relative abundance of microbiome members rather than by their presence/absence. These results reveal that the microbiome of grafted grapevine root systems is largely influenced by the combination of rootstock and scion, which affects the microbial diversity uptaken from soil.

Horizontal transfer and evolution of the biosynthetic gene cluster for benzoxazinoids in plants

Benzoxazinoids are a class of protective and allelopathic plant secondary metabolites that have been identified in multiple grass species and are encoded by the Bx biosynthetic gene cluster (BGC) in maize. Data mining of 41 high-quality grass genomes identified complete Bx clusters (containing genes Bx1-Bx5 and Bx8) in three genera (Zea, Echinochloa, and Dichanthelium) of Panicoideae and partial clusters in Triticeae. The Bx cluster probably originated from gene duplication and chromosomal translocation of native homologs of Bx genes. An ancient Bx cluster that included additional Bx genes (e.g., Bx6) is presumed to have been present in ancestral Panicoideae. The ancient Bx cluster was putatively gained by the Triticeae ancestor via horizontal transfer (HT) from the ancestral Panicoideae and later separated into multiple segments on different chromosomes. Bx6 appears to have been under less constrained selection compared with the Bx cluster during the evolution of Panicoideae, as evidenced by the fact that it was translocated away from the Bx cluster in Zea mays, moved to other chromosomes in Echinochloa, and even lost in Dichanthelium. Further investigations indicate that purifying selection and polyploidization have shaped the evolutionary trajectory of Bx clusters in the grass family. This study provides the first candidate case of HT of a BGC between plants and sheds new light on the evolution of BGCs.

Long-distance transport RNAs between rootstocks and scions and graft hybridization

The present review addresses the advances of the identification methods, functions, and transportation mechanism of long-distance transport RNAs between rootstock and scion. In addition, we highlight the cognitive processes and potential mechanisms of graft hybridization. Phloem, the main transport channel of higher plants, plays an important role in the growth and development of plants. Numerous studies have identified a large number of RNAs, including mRNAs, miRNAs, siRNAs, and lncRNAs, in the plant phloem. They can not only be transported to long distances across the grafting junction in the phloem, but also act as signal molecules to regulate the growth, development, and stress resistance of remote cells or tissues, resulting in changes in the traits of rootstocks and scions. Many mobile RNAs have been discovered, but their detection methods, functions, and long-distance transport mechanisms remain to be elucidated. In addition, grafting hybridization, a phenomenon that has been questioned before, and which has an important role in selecting for superior traits, is gradually being recognized with the emergence of new evidence and the prevalence of horizontal gene transfer between parasitic plants. In this review, we outline the species, functions, identification methods, and potential mechanisms of long-distance transport RNAs between rootstocks and scions after grafting. In addition, we summarize the process of recognition and the potential mechanisms of graft hybridization. This study aimed to emphasize the role of grafting in the study of long-distance signals and selection for superior traits and to provide ideas and clues for further research on long-distance transport RNAs and graft hybridization.

Grafting: a potential method to reveal the differential accumulation mechanism of secondary metabolites

Plant secondary metabolites make a great contribution to the agricultural and pharmaceutical industries. Their accumulation is determined by the integrated transport of target compounds and their biosynthesis-related RNA, protein, or DNA. However, it is hard to track the movement of these biomolecules in vivo. Grafting may be an ideal method to solve this problem. The differences in genetic and metabolic backgrounds between rootstock and scion, coupled with multiple omics approaches and other molecular tools, make it feasible to determine the movement of target compounds, RNAs, proteins, and DNAs. In this review, we will introduce methods of using the grafting technique, together with molecular biological tools, to reveal the differential accumulation mechanism of plant secondary metabolites at different levels. Details of the case of the transport of one diterpene alkaloid, fuziline, will be further illustrated to clarify how the specific accumulation model is shaped with the help of grafting and multiple molecular biological tools.

Root-to-Shoot Long-Distance Mobile miRNAs Identified from Nicotiana Rootstocks

Root-derived mobile signals play critical roles in coordinating a shoot's response to underground conditions. However, the identification of root-to-shoot long-distance mobile signals has been scant. In this study, we aimed to characterize root-to-shoot endogenous mobile miRNAs by using an Arabidopsis/Nicotiana interfamilial heterograft in which these two taxonomically distant species with clear genetic backgrounds had sufficient diversity in differentiating miRNA sources. Small RNA deep sequencing analysis revealed that 82 miRNAs from the Arabidopsis scion could travel through the graft union to reach the rootstock, whereas only a very small subset of miRNA (6 miRNAs) preferred the root-to-shoot movement. We demonstrated in an ex vivo RNA imaging experiment that the root-to-shoot mobile Nb-miR164, Nb-miR395 and Nb-miR397 were targeted to plasmodesmata using the bacteriophage coat protein MS2 system. Furthermore, the Nb-miR164 was shown to move from the roots to the shoots to induce phenotypic changes when its overexpressing line was used as rootstock, strongly supporting that root-derived Nb-miR164 was able to modify the scion trait via its long-distance movement.

Cell-to-Cell Connection in Plant Grafting-Molecular Insights into Symplasmic Reconstruction

Grafting is a means to connect tissues from two individual plants and grow a single chimeric plant through the establishment of both apoplasmic and symplasmic connections. Recent molecular studies using RNA-sequencing data have provided genetic information on the processes involved in tissue reunion, including wound response, cell division, cell-cell adhesion, cell differentiation and vascular formation. Thus, studies on grafting increase our understanding of various aspects of plant biology. Grafting has also been used to study systemic signaling and transport of micromolecules and macromolecules in the plant body. Given that graft viability and molecular transport across graft junctions largely depend on vascular formation, a major focus in grafting biology has been the mechanism of vascular development. In addition, it has been thought that symplasmic connections via plasmodesmata are fundamentally important to share cellular information among newly proliferated cells at the graft interface and to accomplish tissue differentiation correctly. Therefore, this review focuses on plasmodesmata formation during grafting. We take advantage of interfamily grafts for unambiguous identification of the graft interface and summarize morphological aspects of de novo formation of plasmodesmata. Important molecular events are addressed by re-examining the time-course transcriptome of interfamily grafts, from which we recently identified the cell-cell adhesion mechanism. Plasmodesmata-associated genes upregulated during graft healing that may provide a link to symplasm establishment are described. We also discuss future research directions.

Comparative Transcriptome Analysis in Homo- and Hetero-Grafted Cucurbit Seedlings

Watermelon (Citrullus lanatus) is a valuable horticultural crop with nutritional benefits grown worldwide. It is almost exclusively cultivated as grafted scions onto interspecific squash rootstock (Cucurbita maxima × Cucurbita moschata) to improve the growth and yield and to address the problems of soilborne diseases and abiotic stress factors. This study aimed to examine the effect of grafting (homo- and hetero-grafting) on the transcriptome level of the seedlings. Therefore, we compared homo-grafted watermelon (WW) with non-grafted watermelon control (W), homo-grafted squash (SS) with non-grafted squash control (S), hetero-grafted watermelon onto squash (WS) with SS, and WS with WW. Different numbers of differentially expressed genes (DEGs) were identified in each comparison. In total, 318 significant DEGs were detected between the transcriptomes of hetero-grafts and homo-grafts at 16 h after grafting. Overall, a significantly higher number of downregulated transcripts was detected among the DEGs. Only one gene showing increased expression related to the cytokinin synthesis was common in three out of four comparisons involving WS, SS, and S. The highest number of differentially expressed (DE) transcripts (433) was detected in the comparison between SS and S, followed by the 127 transcripts between WW and W. The study provides a description of the transcriptomic nature of homo- and hetero-grafted early responses, while the results provide a start point for the elucidation of the molecular mechanisms and candidate genes for the functional analyses of hetero-graft and homo-graft systems in Cucurbitaceae and generally in the plants.

Engineering Metabolism in Nicotiana Species: A Promising Future

Molecular farming intends to use crop plants as biofactories for high value-added compounds following application of a wide range of biotechnological tools. In particular, the conversion of nonfood crops into efficient biofactories is expected to be a strong asset in the development of a sustainable bioeconomy. The 'nonfood' status combined with the high metabolic versatility and the capacity of high-yield cultivation highlight the plant genus Nicotiana as one of the most appropriate 'chassis' for molecular farming. Nicotiana species are a rich source of valuable industrial, active pharmaceutical ingredients and nutritional compounds, synthesized from highly complex biosynthetic networks. Here, we review and discuss approaches currently used to design enriched Nicotiana species for molecular farming using new plant breeding techniques (NPBTs).

Horizontal Gene Transfers in Plants

In plants, as in all eukaryotes, the vertical transmission of genetic information through reproduction ensures the maintenance of the integrity of species. However, many reports over the past few years have clearly shown that horizontal gene transfers, referred to as HGTs (the interspecific transmission of genetic information across reproductive barriers) are very common in nature and concern all living organisms including plants. The advent of next-generation sequencing technologies (NGS) has opened new perspectives for the study of HGTs through comparative genomic approaches. In this review, we provide an up-to-date view of our current knowledge of HGTs in plants.

Light quality and quantity affect graft union formation of tomato plants

It is already known that there are many factors responsible for the successful formation of a graft union. However, the role of light has been little studied. In an anatomical study, Scanning Electronic Microscope (SEM) was used to explore the effects of different light-emitting diodes (LEDs) on graft union formation in grafted tomato. In addition, the expression genes related to Auxin hormone signaling pathway (SAUR67, AUX1, ARF30, and LAX3) was investigated. The obtained results showed that the concrescence process occurred faster under R7:B3 light conditions, as compared to blue (B) and white fluorescent (WFL) lights. Red light application caused a delay in the vascular tissue differentiation, which may lead to callus development on both sides, causing junctional failure and resulting in ineffective graft junctional arrangement. The expression of genes related to Auxin hormone significantly increased by R7:B3 application. We suggest that LED spectra affects the graft development of tomato plants and can improve the performance of grafted tomato seedlings.

New plant breeding techniques and their regulatory implications: An opportunity to advance metabolomics approaches

Over the previous decades, biotechnological innovations have led to improved agricultural productivity, more nutritious foods and lower chemical usage. Both in western societies and Low Medium Income Countries (LMICs). However, the projected increases in the global population, means the production of nutritious food stuffs must increase dramatically. Building on existing genetic modification technologies a series of New Plant Breeding Technologies (NPBT) has recently emerged. These approaches include, Agro-infiltration, grafting, cis and intragenesis and gene editing technologies. How these new techniques should be regulated has fostered considerable debate. Concerns have also been raised, to ensure over-regulation does not arise, creating administrative and economic burden. In this article the existing landscape of genetically modified crops is reviewed and the potential of several New Plant Breeding Techniques (NPBT) described. Metabolomics is an omic technology that has developed in a concurrent manner with biotechnological advances in plant breeding. There is potentially further opportunities to advance our metabolomic technologies to characterise the outputs of New Plant Breeding Technologies, in a manner that is beneficial both from an academic, biosafety and industrial perspective.

A Panicum-derived chromosomal segment captured by Hordeum a few million years ago preserves a set of stress-related genes

Intra-specific variability is a cornerstone of evolutionary success of species. Acquiring genetic material from distant sources is an important adaptive mechanism in bacteria, but it can also play a role in eukaryotes. In this paper, we investigate the nature and evolution of a chromosomal segment of panicoid (Poaceae, Panicoideae) origin occurring in the nuclear genomes of species of the barley genus Hordeum (Pooideae). The segment, spanning over 440 kb in the Asian Hordeum bogdanii and 219 kb in the South American Hordeum pubiflorum, resides on a pair of nucleolar organizer region (NOR)-bearing chromosomes. Conserved synteny and micro-collinearity of the segment in both species indicate a common origin of the segment, which was acquired before the split of the respective barley lineages 5-1.7 million years ago. A major part of the foreign DNA consists of several approximately 68 kb long repeated blocks containing five stress-related protein-coding genes and transposable elements (TEs). Whereas outside these repeats, the locus was invaded by multiple TEs from the host genome, the repeated blocks are rather intact and appear to be preserved. The protein-coding genes remained partly functional, as indicated by conserved reading frames, a low amount of non-synonymous mutations, and expression of mRNA. A screen across Hordeum species targeting the panicoid protein-coding genes revealed the presence of the genes in all species of the section Stenostachys. In summary, our study shows that grass genomes can contain large genomic segments obtained from distantly related species. These segments usually remain undetected, but they may play an important role in the evolution and adaptation of species.

Epigenetic Changes and Transcriptional Reprogramming Upon Woody Plant Grafting for Crop Sustainability in a Changing Environment

Plant grafting is an ancient agricultural practice widely employed in crops such as woody fruit trees, grapes, and vegetables, in order to improve plant performance. Successful grafting requires the interaction of compatible scion and rootstock genotypes. This involves an intricate network of molecular mechanisms operating at the graft junction and associated with the development and the physiology of the scion, ultimately leading to improved agricultural characteristics such as fruit quality and increased tolerance/resistance to abiotic and biotic factors. Bidirectional transfer of molecular signals such as hormones, nutrients, proteins, and nucleic acids from the rootstock to the scion and vice versa have been well documented. In recent years, studies on rootstock-scion interactions have proposed the existence of an epigenetic component in grafting reactions. Epigenetic changes such as DNA methylation, histone modification, and the action of small RNA molecules are known to modulate chromatin architecture, leading to gene expression changes and impacting cellular function. Mobile small RNAs (siRNAs) migrating across the graft union from the rootstock to the scion and vice versa mediate modifications in the DNA methylation pattern of the recipient partner, leading to altered chromatin structure and transcriptional reprogramming. Moreover, graft-induced DNA methylation changes and gene expression shifts in the scion have been associated with variations in graft performance. If these changes are heritable they can lead to stably altered phenotypes and affect important agricultural traits, making grafting an alternative to breeding for the production of superior plants with improved traits. However, most reviews on the molecular mechanisms underlying this process comprise studies related to vegetable grafting. In this review we will provide a comprehensive presentation of the current knowledge on the epigenetic changes and transcriptional reprogramming associated with the rootstock-scion interaction focusing on woody plant species, including the recent findings arising from the employment of advanced-omics technologies as well as transgrafting methodologies and their potential exploitation for generating superior quality grafts in woody species. Furthermore, will discuss graft-induced heritable epigenetic changes leading to novel plant phenotypes and their implication to woody crop improvement for yield, quality, and stress resilience, within the context of climate change.

Vegetable Grafting From a Molecular Point of View: The Involvement of Epigenetics in Rootstock-Scion Interactions

Vegetable grafting is extensively used today in agricultural production to control soil-borne pathogens, abiotic and biotic stresses and to improve phenotypic characteristics of the scion. Commercial vegetable grafting is currently practiced in tomato, watermelon, melon, eggplant, cucumber, and pepper. It is also regarded as a rapid alternative to the relatively slow approach of breeding for increased environmental-stress tolerance of fruit vegetables. However, even though grafting has been used for centuries, until today, there are still many issues that have not been elucidated. This review will emphasize on the important mechanisms taking place during grafting, especially the genomic interactions between grafting partners and the impact of rootstocks in scion's performance. Special emphasis will be drawn on the relation between vegetable grafting, epigenetics, and the changes in morphology and quality of the products. Recent advances in plant science such as next-generation sequencing provide new information regarding the molecular interactions between rootstock and scion. It is now evidenced that genetic exchange is happening across grafting junctions between rootstock and scion, potentially affecting grafting-mediated effects already recorded in grafted plants. Furthermore, significant changes in DNA methylation are recorded in grafted scions, suggesting that these epigenetic mechanisms could be implicated in grafting effects. In this aspect, we also discuss the process and the molecular aspects of rootstock scion communication. Finally, we provide with an extensive overview of gene expression changes recorded in grafted plants and how these are related to the phenotypic changes observed. Τhis review finally seeks to elucidate the dynamics of rootstock-scion interactions and thus stimulate more research on grafting in the future. In a future where sustainable agricultural production is the way forward, grafting could play an important role to develop products of higher yield and quality in a safe and "green" way.

Horizontal genome transfer by cell-to-cell travel of whole organelles

Recent work has revealed that both plants and animals transfer genomes between cells. In plants, horizontal transfer of entire plastid, mitochondrial, or nuclear genomes between species generates new combinations of nuclear and organellar genomes, or produces novel species that are allopolyploid. The mechanisms of genome transfer between cells are unknown. Here, we used grafting to identify the mechanisms involved in plastid genome transfer from plant to plant. We show that during proliferation of wound-induced callus, plastids dedifferentiate into small, highly motile, amoeboid organelles. Simultaneously, new intercellular connections emerge by localized cell wall disintegration, forming connective pores through which amoeboid plastids move into neighboring cells. Our work uncovers a pathway of organelle movement from cell to cell and provides a mechanistic framework for horizontal genome transfer.

Genetic developmental timing revealed by inter-species transplantations in fish

The path from a fertilised egg to an embryo involves the coordinated formation of cell types, tissues and organs. Developmental modules comprise discrete units specified by self-sufficient genetic programs that can interact with each other during embryogenesis. Here, we have taken advantage of the different span of embryonic development between two distantly related teleosts, zebrafish (Danio rerio) and medaka (Oryzias latipes) (3 and 9 days, respectively), to explore modularity principles. We report that inter-species blastula transplantations result in the ectopic formation of a retina formed by donor cells - a module. We show that the time taken for the retina to develop follows a genetic program: an ectopic zebrafish retina in medaka develops with zebrafish dynamics. Heterologous transplantation results in a temporal decoupling between the donor retina and host organism, illustrated by two paradigms that require retina-host interactions: lens recruitment and retino-tectal projections. Our results uncover a new experimental system for addressing temporal decoupling along embryonic development, and highlight the presence of largely autonomous but interconnected developmental modules that orchestrate organogenesis.

Possibility of Increasing the Growth and Photosynthetic Properties of Precocious Walnut by Grafting

Plant growth characteristics after grafting are mainly dependent on photosynthesis performance, which may be influenced by grafting combinations with different rootstocks and scions. In this study, we used one-year-old walnut grafts to investigate the grafting compatibility between precocious (‘Liaoning 1’, L) and hybrid (‘Zhong Ning Sheng’, Z) walnut, as well as rootstock and scion impact on the growth and photosynthetic properties of walnut trees. The results showed that grafting compatibility between the two varieties is high, with survival rates upward of 86%. Overwintering survival of grafted seedlings was as high as 100%, which indicated that the allopolyploid had good resistance to low-temperature stress. The homograft of the hybrid walnut had the highest net photosynthesis rate (18.77 μmol·m−2s−1, Z/Z) and growth characteristics, which could be due to its higher transpiration rate and stomatal conductance, whereas the homograft of precocious walnut presented the lowest net photosynthesis rate (15.08 μmol·m−2s−1, L/L) and growth characteristics. Significant improvements in the net photosynthesis rate (15.97 and 15.24 μmol·m−2s−1 for L/Z and Z/L, respectively) and growth characteristics of precocious walnut were noticed during grafting of the hybrid walnut, which could have been contributed by their transpiration rate. The results of this study serve as a guide for the selection and breeding of good rootstock to improve plant growth characteristics and photosynthetic efficiency. We conclude that good rootstock selection improves plant growth potential and could play an important role in sustainable production.

On the evolutionary significance of horizontal gene transfers in plants

Horizontal gene transfer (HGT) has long been seen as a crucial process in the evolution of prokaryotic species, but until recently it was thought to have little, if any, effect on the evolution of eukaryotic life forms. Detecting and describing HGT events in eukaryotes is difficult, making this phenomenon at times controversial. However, modern advances in genomics and bioinformatics have radically altered our view of HGT in eukaryotes, especially in plants. It now appears that HGT to and from plant lineages is more common than previously suspected. Importantly, the transfer of functional nuclear genes with adaptive significance has been reported in numerous taxa. Here we review several recent studies that have found evidence of the horizontal transfer of nuclear genes, and argue that HGT has undoubtedly had profound impacts on plant evolution as a whole.

Synthetic Polyploidy in Grafted Crops

Synthetic polyploids have been extensively studied for breeding in the last decade. However, the use of such genotypes at the agronomical level is still limited. Polyploidization is known to modify certain plant phenotypes, while leaving most of the fundamental characteristics apparently untouched. For this reason, polyploid breeding can be very useful for improving specific traits of crop varieties, such as quality, yield, or environmental adaptation. Nevertheless, the mechanisms that underlie polyploidy-induced novelty remain poorly understood. Ploidy-induced phenotypes might also include some undesired effects that need to be considered. In the case of grafted or composite crops, benefits can be provided both by the rootstock's adaptation to the soil conditions and by the scion's excellent yield and quality. Thus, grafted crops provide an extraordinary opportunity to exploit artificial polyploidy, as the effects can be independently applied and explored at the root and/or scion level, increasing the chances of finding successful combinations. The use of synthetic tetraploid (4x) rootstocks may enhance adaptation to biotic and abiotic stresses in perennial crops such as apple or citrus. However, their use in commercial production is still very limited. Here, we will review the current and prospective use of artificial polyploidy for rootstock and scion improvement and the implications of their combination. The aim is to provide insight into the methods used to generate and select artificial polyploids and their limitations, the effects of polyploidy on crop phenotype (anatomy, function, quality, yield, and adaptation to stresses) and their potential agronomic relevance as scions or rootstocks in the context of climate change.

Mechanisms Underlying Graft Union Formation and Rootstock Scion Interaction in Horticultural Plants

Grafting is a common practice for vegetative propagation and trait improvement in horticultural plants. A general prerequisite for successful grafting and long term survival of grafted plants is taxonomic proximity between the root stock and scion. For the success of a grafting operation, rootstock and scion should essentially be closely related. Interaction between the rootstock and scion involves complex physiological-biochemical and molecular mechanisms. Successful graft union formation involves a series of steps viz., lining up of vascular cambium, generation of a wound healing response, callus bridge formation, followed by vascular cambium formation and subsequent formation of the secondary xylem and phloem. For grafted trees compatibility between the rootstock/scion is the most essential factor for their better performance and longevity. Graft incompatibility occurs on account of a number of factors including of unfavorable physiological responses across the graft union, transmission of virus or phytoplasma and anatomical deformities of vascular tissue at the graft junction. In order to avoid the incompatibility problems, it is important to predict the same at an early stage. Phytohormones, especially auxins regulate key events in graft union formation between the rootstock and scion, while others function to facilitate the signaling pathways. Transport of macro as well as micro molecules across long distances results in phenotypic variation shown by grafted plants, therefore grafting can be used to determine the pattern and rate of recurrence of this transport. A better understanding of rootstock scion interactions, endogenous growth substances, soil or climatic factors needs to be studied, which would facilitate efficient selection and use of rootstocks in the future. Protein, hormones, mRNA and small RNA transport across the junction is currently emerging as an important mechanism which controls the stock/scion communication and simultaneously may play a crucial role in understanding the physiology of grafting more precisely. This review provides an understanding of the physiological, biochemical and molecular basis underlying grafting with special reference to horticultural plants.

Assisted Evolution in Astrobiology-Convergence of Ecology and Evolutionary Biology within the Context of Planetary Colonization

In ecology and conservation biology, the concept of assisted evolution aims at the optimization of the resilience of organisms and populations to changing environmental conditions. What has hardly been considered so far is that this concept is also relevant for future astrobiological research, since in artificial extraterrestrial habitats (e.g., plants and insects in martian greenhouses) novel environmental conditions will also affect the survival and performance of organisms. The question therefore arises whether and how space-relevant organisms can be artificially adapted to the desired circumstances in advance. Based on several adaptation and acclimatization strategies in wild ecosystems of Earth, I discuss which methods can be considered for assisted evolution in the context of astrobiological research. This includes enhanced selective breeding, induction of epigenetic inheritance, and genetic engineering, as well as possible problems of these applications. This short overview article aims to stimulate an emerging discussion as to whether humans, which are already prominent drivers of Earth's evolution, should consider such interventions for future planetary colonization as well.

Molecular Responses during Plant Grafting and Its Regulation by Auxins, Cytokinins, and Gibberellins

Plant grafting is an important horticulture technique used to produce a new plant after joining rootstock and scion. This is one of the most used techniques by horticulturists to enhance the quality and production of various crops. Grafting helps in improving the health of plants, their yield, and the quality of plant products, along with the enhancement of their postharvest life. The main process responsible for successful production of grafted plants is the connection of vascular tissues. This step determines the success rate of grafts and hence needs to be studied in detail. There are many factors that regulate the connection of scion and stock, and plant hormones are of special interest for researchers in the recent times. These phytohormones act as signaling molecules and have the capability of translocation across the graft union. Plant hormones, mainly auxins, cytokinins, and gibberellins, play a major role in the regulation of various key physiological processes occurring at the grafting site. In the current review, we discuss the molecular mechanisms of graft development and the phytohormone-mediated regulation of the growth and development of graft union.

Lamarck and Panspermia - On the Efficient Spread of Living Systems Throughout the Cosmos

We review the main lines of evidence (molecular, cellular and whole organism) published since the 1970s demonstrating Lamarckian Inheritance in animals, plants and microorganisms viz. the transgenerational inheritance of environmentally-induced acquired characteristics. The studies in animals demonstrate the genetic permeability of the soma-germline Weismann Barrier. The widespread nature of environmentally-directed inheritance phenomena reviewed here contradicts a key pillar of neo-Darwinism which affirms the rigidity of the Weismann Barrier. These developments suggest that neo-Darwinian evolutionary theory is in need of significant revision. We argue that Lamarckian inheritance strategies involving environmentally-induced rapid directional genetic adaptations make biological sense in the context of cosmic Panspermia allowing the efficient spread of living systems and genetic innovation throughout the Universe. The Hoyle-Wickramasinghe Panspermia paradigm also developed since the 1970s, unlike strictly geocentric neo-Darwinism provides a cogent biological rationale for the actual widespread existence of Lamarckian modes of inheritance - it provides its raison d'être. Under a terrestrially confined neo-Darwinian viewpoint such an association may have been thought spurious in the past. Our aim is to outline the conceptual links between rapid Lamarckian-based evolutionary hypermutation processes dependent on reverse transcription-coupled mechanisms among others and the effective cosmic spread of living systems. For example, a viable, or cryo-preserved, living system travelling through space in a protective matrix will need of necessity to rapidly adapt and proliferate on landing in a new cosmic niche. Lamarckian mechanisms thus come to the fore and supersede the slow (blind and random) genetic processes expected under a traditional neo-Darwinian evolutionary paradigm.

Living with Two Genomes: Grafting and Its Implications for Plant Genome-to-Genome Interactions, Phenotypic Variation, and Evolution

Plant genomes interact when genetically distinct individuals join, or are joined, together. Individuals can fuse in three contexts: artificial grafts, natural grafts, and host-parasite interactions. Artificial grafts have been studied for decades and are important platforms for studying the movement of RNA, DNA, and protein. Yet several mysteries about artificial grafts remain, including the factors that contribute to graft incompatibility, the prevalence of genetic and epigenetic modifications caused by exchanges between graft partners, and the long-term effects of these modifications on phenotype. Host-parasite interactions also lead to the exchange of materials, and RNA exchange actively contributes to an ongoing arms race between parasite virulence and host resistance. Little is known about natural grafts except that they can be frequent and may provide opportunities for evolutionary innovation through genome exchange. In this review, we survey our current understanding about these three mechanisms of contact, the genomic interactions that result, and the potential evolutionary implications.

Sequential horizontal gene transfers from different hosts in a widespread Eurasian parasitic plant, Cynomorium coccineum

PREMISE

Parasitic plants with large geographic ranges, and different hosts in parts of their range, may acquire horizontally transferred genes (HGTs), which might sometimes leave a footprint of gradual host and range expansion. Cynomorium coccineum, the only member of the Saxifragales family Cynomoriaceae, is a root holoparasite that occurs in water-stressed habitats from western China to the Canary Islands. It parasitizes at least 10 angiosperm families from different orders, some of them only in parts of its range. This parasite therefore offers an opportunity to trace HGTs as long as parasite-host pairs can be obtained and sequenced.

METHODS

By sequencing mitochondrial, plastid, and nuclear loci from parasite-host pairs from throughout the parasite's range and with prior information from completely assembled mitochondrial and plastid genomes, we detected 10 HGTs of five mitochondrial genes.

RESULTS

The 10 HGTs appear to have occurred sequentially as C. coccineum expanded from East to West. Molecular-clock models yield Cynomorium stem ages between 66 and 156 Myr, with relaxed clocks converging on 66-67 Myr. Chinese Sapindales, probably Nitraria, were the first source of transferred genes, followed by Iranian and Mediterranean Caryophyllales. The most recently acquired gene appears to come from a Tamarix host in the Iberian Peninsula.

CONCLUSIONS

Data on HGTs that have accumulated over the past 15 years, along with this discovery of multiple HGTs within a single widespread species, underline the need for more whole-genome data from parasite-host pairs to investigate whether and how transferred copies coexist with, or replace, native functional genes.

Merging genotypes: graft union formation and scion-rootstock interactions

Grafting has been utilised for at least the past 7000 years. Historically, grafting has been developed by growers without particular interest beyond the agronomical and ornamental effects, and thus knowledge about grafting has remained largely empirical. Much of the commercial production of fruit, and increasingly vegetables, relies upon grafting with rootstocks to provide resistance to soil-borne pathogens and abiotic stresses as well as to influence scion growth and performance. Although there is considerable agronomic knowledge about the use and selection of rootstocks for many species, we know little of the molecular mechanisms underlying rootstock adaptation to different soil environments and rootstock-conferred modifications of scion phenotypes. Furthermore, the processes involved in the formation of the graft union and graft compatibility are poorly understood despite over a hundred years of scientific study. In this paper, we provide an overview of what is known about grafting and the mechanisms underlying rootstock-scion interactions. We highlight recent studies that have advanced our understanding of graft union formation and outline subjects that require further development.

Root-expressed phytochromes B1 and B2, but not PhyA and Cry2, regulate shoot growth in nature

Although photoreceptors are expressed throughout all plant organs, most studies have focused on their function in aerial parts with laboratory-grown plants. Photoreceptor function in naturally dark-grown roots of plants in their native habitats is lacking. We characterized patterns of photoreceptor expression in field- and glasshouse-grown Nicotiana attenuata plants, silenced the expression of PhyB1/B2/A/Cry2 whose root transcripts levels were greater/equal to those of shoots, and by micrografting combined empty vector transformed shoots onto photoreceptor-silenced roots, creating chimeric plants with "blind" roots but "sighted" shoots. Micrografting procedure was robust in both field and glasshouse, as demonstrated by transcript accumulation patterns, and a spatially-explicit lignin visual reporter chimeric line. Field- and glasshouse-grown plants with PhyB1B2, but not PhyA or Cry2, -blind roots, were delayed in stalk elongation compared with control plants, robustly for two field seasons. Wild-type plants with roots directly exposed to FR phenocopied the growth of irPhyB1B2-blind root grafts. Additionally, root-expressed PhyB1B2 was required to activate the positive photomorphogenic regulator, HY5, in response to aboveground light. We conclude that roots of plants growing deep into the soil in nature sense aboveground light, and possibly soil temperature, via PhyB1B2 to control key traits, such as stalk elongation.

Cross-Kingdom Commonality of a Novel Insertion Signature of RTE-Related Short Retroposons

In multicellular organisms, such as vertebrates and flowering plants, horizontal transfer (HT) of genetic information is thought to be a rare event. However, recent findings unveiled unexpectedly frequent HT of RTE-clade LINEs. To elucidate the molecular footprints of the genomic integration machinery of RTE-related retroposons, the sequence patterns surrounding the insertion sites of plant Au-like SINE families were analyzed in the genomes of a wide variety of flowering plants. A novel and remarkable finding regarding target site duplications (TSDs) for SINEs was they start with thymine approximately one helical pitch (ten nucleotides) downstream of a thymine stretch. This TSD pattern was found in RTE-clade LINEs, which share the 3'-end sequence of these SINEs, in the genome of leguminous plants. These results demonstrably show that Au-like SINEs were mobilized by the enzymatic machinery of RTE-clade LINEs. Further, we discovered the same TSD pattern in animal SINEs from lizard and mammals, in which the RTE-clade LINEs sharing the 3'-end sequence with these animal SINEs showed a distinct TSD pattern. Moreover, a significant correlation was observed between the first nucleotide of TSDs and microsatellite-like sequences found at the 3'-ends of SINEs and LINEs. We propose that RTE-encoded protein could preferentially bind to a DNA region that contains a thymine stretch to cleave a phosphodiester bond downstream of the stretch. Further, determination of cleavage sites and/or efficiency of primer sites for reverse transcription may depend on microsatellite-like repeats in the RNA template. Such a unique mechanism may have enabled retroposons to successfully expand in frontier genomes after HT.

Maintenance of grafting-induced epigenetic variations in the asexual progeny of Brassica oleracea and B. juncea chimera

Grafting-induced variations have been observed in many plant species, but the heritability of variation in progeny is not well understood. In our study, adventitious shoots from the C cell lineage of shoot apical meristem (SAM) grafting chimera TCC (where the origin of the outmost, middle and innermost cell layers, respectively, of SAM is designated by 'T' for tuber mustard and 'C' for red cabbage) were induced and identified as r-CCC (r = regenerated). To investigate the maintenance of grafting variations during cell propagation and regeneration, different generations of asexual progeny (r-CCCn, n = generation) were established through successive regeneration of axillary shoots from r-CCC. The fourth generation of r-CCC (r-CCC4) was selected to perform whole genome bisulfite sequencing for comparative analysis of hetero-grafting-induced global methylation changes relative to r-s-CCC4 (s = self-grafting). Increased CHH methylation levels and proportions were observed in r-CCC4, with substantial changes occurring in the repeat elements. Small RNA sequencing revealed 1135 specific small interfering RNA (siRNA) tags that were typically expressed in r-CCC, r-CCC2 and r-CCC4. Notably, 65% of these specific siRNAs were associated with repeat elements, termed RE siRNAs. Subsequent analysis revealed that the CHH methylation of RE siRNA-overlapping regions was mainly hypermethylation in r-CCC4, indicating that they were responsible for directing and maintaining grafting-induced CHH methylation. Moreover, the expression of 13 differentially methylated genes (DMGs) correlated with the phenotypic variation, showing differential expression levels between r-CCC4 and r-s-CCC4. These DMGs were predominantly CG hypermethylated, their methylation modifications corresponded to the transcription of relative methyltransferase.

"Cell grafting": a new approach for transferring cytoplasmic or nuclear genome between plants

KEY MESSAGE

A new method based on mixing and wounding of callus tissue was used to transfer plastid or nuclear DNA between cells. Methods alternative to sexual hybridization can be powerful tools for crop improvement. We have developed a new hybridization technology based on wounding a mixed population of cells of two parents growing in vitro as callus ("cell grafting"), and have demonstrated the utility of this system for plastid or nuclear genome transfer. In our proof-of concept experiments, non-organized growing tissue (callus) from tobacco var. Samsun, carrying the nuclear marker genes nptII and uidA (GUS), and tobacco var. Petit Havana, carrying aadA and gfp genes in the plastid genome, were mixed together, wounded with a razor blade and placed for regeneration on selection medium containing both spectinomycin (aadA) and paromomycin (nptII). Plants with aadA and gfp positive plastids and nptII plus uidA positive nuclear background were produced. Molecular analysis confirmed the presence of all four genes in these plants. Morphology and ploidy level analysis confirmed the production of "diploid" plants similar to var. Samsun possessing transformed plastids from var. Petit Havana. Reciprocal crosses between the experimentally produced plants and wild type tobacco confirmed maternal inheritance of aadA and gfp and Mendelian inheritance of nptII and uidA. For transfer of nuclear traits between plants we used two nuclear-transformed parents with different selectable markers; one with nptII (paromomycin resistant), and another with aadA (spectinomycin resistant). Plants resistant to both antibiotics which also had different visible markers were produced.

The Criticisms of Pangenesis: The Years of Controversy

When first published in 1868, Darwin's Pangenesis was almost uniformly rejected by his contemporaries. Until recently it has still been regarded as Darwin's biggest mistake or a brilliant blunder. There are three main reasons for this. First, Galton transfused the blood of one variety of rabbit into another, and then bred together the latter. The results of breeding showed no variations of characters in the offspring. Thus he concluded that Darwin's Pangenesis was incorrect. Second, there was no direct evidence for the existence of Darwin's imaginary gemmules. Third, Darwin's Pangenesis explained the Lamarckian inheritance of acquired characters, graft hybridization, xenia and telegony, which were largely thought to be doubtful phenomena. Now the discoveries of circulating cell-free DNA, mobile RNAs, prions and extracellular vesicles provide striking evidence for the chemical existence of Darwin's supposed gemmules. There is also convincing evidence for heritable changes induced by blood transfusion in which Galton failed to find such effects in his experiment. Moreover, there is increasing evidence for the inheritance of acquired characters, graft hybridization, xenia and other phenomena that Pangenesis was designed to explain. In light of the mounting evidence, it is not proper to continue to consider Pangenesis as Darwin's biggest mistake or a brilliant blunder.

Darwin's Pangenesis and Graft Hybridization

Although there were many records of graft-induced variations in ancient China, it was Darwin who coined the term "graft hybridization", the formation of hybrids between distinct species or varieties, through plant grafting, without the intervention of the sexual organs. He described many cases of the so-called "graft hybrids", in which shoots produced from grafted plants exhibited a combination of characters of both rootstock and scion, and explained their formation by his Pangenesis. Michurin invented "mentor-grafting" and "preliminary vegetative approximation" methods, which greatly increased the production of graft hybrids, thus providing a solution to Darwin's puzzle. Over the past decides, the existence of graft hybrids has been extensively documented, and graft hybridization is considered to be a simple and efficient means of plant breeding, and would be especially significant in the improvement of fruit trees. Graft hybridization is now explained by horizontal gene transfer and DNA transformation. In addition, the long-distance transport of mRNA and small RNAs is also considered to be involved in the formation of graft hybrids.