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

The role of DNA methylation in the maintenance of phenotypic variation induced by grafting chimerism in Brassica

Grafting facilitates the interaction between heterologous cells with different genomes, resulting in abundant phenotypic variation, which provides opportunities for crop improvement. However, how grafting-induced variation occurs and is transmitted to progeny remains elusive. A graft chimera, especially a periclinal chimera, which has genetically distinct cell layers throughout the plant, is an excellent model to probe the molecular mechanisms of grafting-induced variation maintenance. Here we regenerated a plant from the T-cell layer of a periclinal chimera, TCC (where the apical meristem was artificially divided into three cell layers - from outside to inside, L1, L2, and L3; T = Tuber mustard, C = red Cabbage), named rTTT0 (r = regenerated). Compared with the control (rsTTT, s = self-grafted), rTTT0 had multiple phenotypic variations, especially leaf shape variation, which could be maintained in sexual progeny. Transcriptomes were analyzed and 58 phenotypic variation-associated genes were identified. Whole-genome bisulfite sequencing analyses revealed that the methylome of rTTT0 was changed, and the CG methylation level was significantly increased by 8.74%. In rTTT0, the coding gene bodies are hypermethylated in the CG context, while their promoter regions are hypomethylated in the non-CG context. DNA methylation changes in the leaf shape variation-associated coding genes, ARF10, IAA20, ROF1, and TPR2, were maintained for five generations of rTTT0. Interestingly, grafting chimerism also affected transcription of the microRNA gene (MIR), among which the DNA methylation levels of the promoters of three MIRs associated with leaf shape variation were changed in rTTT0, and the DNA methylation modification of MIR319 was maintained to the fifth generation of selfed progeny of rTTT0 (rTTT5). These findings demonstrate that DNA methylation of coding and non-coding genes plays an important role in heterologous cell interaction-induced variation formation and its transgenerational inheritance.

Plant gene silencing signals move from the phloem to influence gene expression in shoot apical meristems

BACKGROUND

Small RNAs (sRNA) are potent regulators of gene expression that can diffuse short distances between cells and move long distances through plant vasculature. However, the degree to which sRNA silencing signals can move from the phloem to the shoot apical meristem (SAM) remains unclear.

RESULTS

Two independent transgenic approaches were used to examine whether phloem sRNA silencing can reach different domains of the SAM and silence SAM-expressed genes. First, the phloem companion-cell specific SUCROSE-PROTON SYMPORTER2 (SUC2) promoter was used to drive expression of an inverted repeat to target the FD gene, an exclusively SAM-localized floral regulator. Second, the SUC2 promoter was used to express an artificial microRNA (aMiR) designed to target a synthetic CLAVATA3 (CLV3) transgene in SAM stem cells. Both phloem silencing signals phenocopied the loss of function of their targets and altered target gene expression suggesting that a phloem-to-SAM silencing communication axis exists, connecting distal regions of the plant to SAM stem cells.

CONCLUSIONS

Demonstration of phloem-to-SAM silencing reveals a regulatory link between somatic sRNA expressed in distal regions of the plant and the growing shoot. Since the SAM stem cells ultimately produce the gametes, we discuss the intriguing possibility that phloem-to-SAM sRNA trafficking could allow transient somatic sRNA expression to manifest stable, transgenerational epigenetic changes.

Warming-induced changes of broccoli head to cauliflower-like curd in Brassica oleracea are regulated by DNA methylation as revealed by methylome and transcriptome co-profiling

Increasingly warming temperature impacts on all aspects of growth and development in plants. Flower development is a complex process that is very sensitive to ambient temperature, and warming temperatures often lead to abnormal flower development and remarkably reduce the quality and yield of inflorescent vegetables and many other crops, which can be exemplified by Brassica oleracea cv. Green Harmony F1, a broccoli cultivar, whose floral development is ceased at inflorescence meristem (at 28 °C) or floral primordium stage (at 22 °C), forming a cauliflower-like curd (28 °C) or intermediate curd (22 °C) instead of normal broccoli head at 16 °C. However, the underlying molecular regulatory mechanisms are not well understood. Here we report that warming temperature (28 °C or 22 °C) induced hypermethylation of the genome, especially the promoter regions of such sets of genes as ribosome biogenesis-related and others, leading to the suppression of the apex-highly-expressed distinctive genes, subsequently resulting in the abnormal floral development, as revealed by methylome and transcriptome co-profiling. The regulation of warming-induced abnormal floral development in broccoli was further verified by the fact that the DNA methylation inhibitor 5-azacytidine (5-azaC) released the expression of genes from the warming temperature-induced suppression, and restored the broccoli development to normalcy at warming temperature. The research provided new approaches to breeding broccoli and other crops for growing in wider or warmer temperature zones. Graphical Abstract.

Maintenance of grafting reducing cadmium accumulation in soybean (Glycinemax) is mediated by DNA methylation

Cadmium (Cd) pollution in farmland soil increases the probability of wastage of land resources and compromised food safety. Grafting can change the absorption rates of elements in crops; however, there are few studies on grafting in bulk grain and cash crops. In this study, Glycine max was used as a scion and Luffa aegyptiaca as a rootstock for grafting experiments. The changes in total sulfur and Cd content in the leaves and grains of grafted species were determined for three consecutive generations, and the gene expression and DNA methylation status of the leaves were analyzed. The results show that grafting significantly reduced the total sulfur and Cd content in soybean leaves and grains; the Cd content in soybean leaves and grains decreased by >50 %. The plant's primary sulfur metabolism pathway was not significantly affected. Glucosinolates and DNA methylation may play important roles in reducing total sulfur and Cd accumulation. Notably, low sulfur and low Cd traits can be maintained over two generations. Our study establishes that grafting can reduce the total sulfur and Cd content in soybean, and these traits can be inherited. In summary, grafting technology can be used to prevent soybean from accumulating Cd in farmland soil. This provides a theoretical basis for grafting to cultivate crops with low Cd accumulation.

Potato Periderm Development and Tuber Skin Quality

The periderm is a corky tissue that replaces the epidermis when the latter is damaged, and is critical for preventing pathogen invasion and water loss. The periderm is formed through the meristematic activity of phellogen cells (cork cambium). The potato skin (phellem cells) composes the outer layers of the tuber periderm and is a model for studying cork development. Early in tuber development and following tuber expansion, the phellogen becomes active and produces the skin. New skin layers are continuously added by division of the phellogen cells until tuber maturation. Some physiological disorders of the potato tuber are related to abnormal development of the skin, including skinning injuries and russeting of smooth-skinned potatoes. Thus, characterizing the potato periderm contributes to modeling cork development in plants and helps to resolve critical agricultural problems. Here, we summarize the data available on potato periderm formation, highlighting tissue characteristics rather than the suberization processes.

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.

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.

Genome of a citrus rootstock and global DNA demethylation caused by heterografting

Grafting is an ancient technique used for plant propagation and improvement in horticultural crops for at least 1,500 years. Citrus plants, with a seed-to-seed cycle of 5-15 years, are among the fruit crops that were probably domesticated by grafting. Poncirus trifoliata, a widely used citrus rootstock, can promote early flowering, strengthen stress tolerance, and improve fruit quality via scion-rootstock interactions. Here, we report its genome assembly using PacBio sequencing. We obtained a final genome of 303 Mb with a contig N50 size of 1.17 Mb and annotated 25,680 protein-coding genes. DNA methylome and transcriptome analyses indicated that the strong adaptability of P. trifoliata is likely attributable to its special epigenetic modification and expression pattern of resistance-related genes. Heterografting by using sweet orange as scion and P. trifoliata as rootstock and autografting using sweet orange as both scion and rootstock were performed to investigate the genetic effects of the rootstock. Single-base methylome analysis indicated that P. trifoliata as a rootstock caused DNA demethylation and a reduction in 24-nt small RNAs (sRNAs) in scions compared to the level observed with autografting, implying the involvement of sRNA-mediated graft-transmissible epigenetic modifications in citrus grafting. Taken together, the assembled genome for the citrus rootstock and the analysis of graft-induced epigenetic modifications provide global insights into the genetic effects of rootstock-scion interactions and grafting biology.

MSH1-induced heritable enhanced growth vigor through grafting is associated with the RdDM pathway in plants

Plants transmit signals long distances, as evidenced in grafting experiments that create distinct rootstock-scion junctions. Noncoding small RNA is a signaling molecule that is graft transmissible, participating in RNA-directed DNA methylation; but the meiotic transmissibility of graft-mediated epigenetic changes remains unclear. Here, we exploit the MSH1 system in Arabidopsis and tomato to introduce rootstock epigenetic variation to grafting experiments. Introducing mutations dcl2, dcl3 and dcl4 to the msh1 rootstock disrupts siRNA production and reveals RdDM targets of methylation repatterning. Progeny from grafting experiments show enhanced growth vigor relative to controls. This heritable enhancement-through-grafting phenotype is RdDM-dependent, involving 1380 differentially methylated genes, many within auxin-related gene pathways. Growth vigor is associated with robust root growth of msh1 graft progeny, a phenotype associated with auxin transport based on inhibitor assays. Large-scale field experiments show msh1 grafting effects on tomato plant performance, heritable over five generations, demonstrating the agricultural potential of epigenetic variation.

The meiotic transmissibility and progeny phenotypic influence of graft-mediated epigenetic changes remain unclear. Here, the authors use the msh1 mutant in the rootstock to trigger heritable enhanced growth vigor in Arabidopsis and tomato, and show it is associated with the RNA-directed DNA methylation pathway.

Does variable epigenetic inheritance fuel plant evolution?

Epigenetic changes influence gene expression and contribute to the modulation of biological processes in response to the environment. Transgenerational epigenetic changes in gene expression have been described in many eukaryotes. However, plants appear to have a stronger propensity for inheriting novel epialleles. This mini-review discusses how plant traits, such as meristematic growth, totipotency, and incomplete epigenetic erasure in gametes promote epiallele inheritance. Additionally, we highlight how plant biology may be inherently tailored to reap the benefits of epigenetic metastability. Importantly, environmentally triggered small RNA expression and subsequent epigenetic changes may allow immobile plants to adapt themselves, and possibly their progeny, to thrive in local environments. The change of epigenetic states through the passage of generations has ramifications for evolution in the natural and agricultural world. In populations containing little genetic diversity, such as elite crop germplasm or habitually self-reproducing species, epigenetics may provide an important source of heritable phenotypic variation. Basic understanding of the processes that direct epigenetic shifts in the genome may allow for breeding or bioengineering for improved plant traits that do not require changes to DNA sequence.

Grafting induces flowering time and tuber formation changes in Brassica species involving FT signalling

Brassica species are widely cultivated and important biennial and annual crops. The transition from vegetative to reproductive development in Brassica species is critical in agriculture and horticulture. Grafting is a useful tool for improving agricultural production and investigating the movement of long-range signals. Here we established a hypocotyl micrografting system in B. rapa crops and successfully grafted the rootstock of turnip onto many different scion genotypes. Grafting with turnip rootstock prolonged vegetative growth, delayed flowering and improved seed yield in rapeseed. The late-flowering turnip rootstock could delay flowering of the scion of the early-flowering turnip accession. The BrrFLC1 (FLOWERING LOCUS C1 in B. rapa) transcript levels and H3K4me3 levels at the BrrFLC1 locus were up-regulated and subsequently suppressed the downstream FT (FLOWERING LOCUS T) signals in leaves of the scion to delay flowering. Vernalization treatment can efficiently promote flowering time in turnip. The non-vernalised turnip flowered early after grafting onto the rootstock of the vernalised turnip, which was accompanied by high levels of FT homologue expression in leaves of the scion. Hypocotyl excision experiments revealed that the process of tuber formation was suppressed by removing the hypocotyl tissue, which in turn repressed the expression of tuberization-related genes. Our findings suggest that the rootstock generates mobile signals that are transported from the rootstock to the scion to fine-tune FT signalling and modulate flowering time.

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.