Induced mutagenesis is one of the most effective strategies for trait improvement without altering the well-optimized genetic background of the cultivars. In this review, several currently accessible methods such as physical, chemical and insertional mutagenesis have been discussed concerning their efficient exploration for the tomato crop improvement. Similarly, challenges for the adaptation of genome-editing, a newly developed technique providing an opportunity to induce precise mutation, have been addressed. Several efforts of genome-editing have been demonstrated in tomato and other crops, exploring its effectiveness and convenience for crop improvement. Descriptive data compiled here from such efforts will be helpful for the efficient exploration of technological advances. However, uncertainty about the regulation of genome-edited crops is still a significant concern, particularly when timely trait improvement in tomato cultivars is needed. In this regard, random approaches of induced mutagenesis are still promising if efficiently explored in breeding applications. Precise identification of casual mutation is a prerequisite for the molecular understanding of the trait development as well as its utilization for the breeding program. Recent advances in sequencing techniques provide an opportunity for the precise detection of mutagenesis-induced sequence variations at a large scale in the genome. Here, we reviewed several novel next-generation sequencing based mutation mapping approaches including Mutmap, MutChromeSeq, and whole-genome sequencing-based mapping which has enormous potential to accelerate the mutation breeding in tomato. The proper utilization of the existing well-characterized tomato mutant resources combined with novel mapping approaches would inevitably lead to rapid enhancement of tomato quality and yield. This article provides an overview of the principles and applications of mutagenesis approaches in tomato and discusses the current progress and challenges involved in tomato mutagenesis research.

MicroRNAs (miRNAs) are small non-coding endogenous RNA molecules, 18–24 nucleotides long, that control multiple gene regulatory pathways via post-transcriptional gene silencing in eukaryotes. To develop a comprehensive picture of the evolutionary history of miRNA biogenesis and action in land plants, studies on bryophyte representatives are needed. Here, we review current understanding of liverwort MIR gene structure, miRNA biogenesis, and function, focusing on the simple thalloid Pellia endiviifolia and the complex thalloid Marchantia polymorpha. We review what is known about conserved and non-conserved miRNAs, their targets, and the functional implications of miRNA action in M. polymorpha and P. endiviifolia. We note that most M. polymorpha miRNAs are encoded within protein-coding genes and provide data for 23 MIR gene structures recognized as independent transcriptional units. We identify M. polymorpha genes involved in miRNA biogenesis that are homologous to those identified in higher plants, including those encoding core microprocessor components and other auxiliary and regulatory proteins that influence the stability, folding, and processing of pri-miRNAs. We analyzed miRNA biogenesis proteins and found similar domain architecture in most cases. Our data support the hypothesis that almost all miRNA biogenesis factors in higher plants are also present in liverworts, suggesting that they emerged early during land plant evolution.

A wide variety of functional regulatory non-coding RNAs (ncRNAs) have been identified as essential regulators of plant growth and development. Depending on their category, ncRNAs are not only involved in modulating target gene expression at the transcriptional and post-transcriptional levels but also are involved in processes like RNA splicing and RNA-directed DNA methylation. To fulfill their molecular roles properly, ncRNAs must be precisely processed by multiprotein complexes. In the case of small RNAs, DICER-LIKE (DCL) proteins play critical roles in the production of mature molecules. Land plant genomes contain at least four distinct classes of DCL family proteins (DCL1–DCL4), of which DCL1, DCL3 and DCL4 are also present in the genomes of bryophytes, indicating the early divergence of these genes. The liverwort Marchantia polymorpha has become an attractive model species for investigating the evolutionary history of regulatory ncRNAs and proteins that are responsible for ncRNA biogenesis. Recent studies on Marchantia have started to uncover the similarities and differences in ncRNA production and function between the basal lineage of bryophytes and other land plants. In this review, we summarize findings on the essential role of regulatory ncRNAs in Marchantia development. We provide a comprehensive overview of conserved ncRNA–target modules among M. polymorpha, the moss Physcomitrium patens and the dicot Arabidopsis thaliana, as well as Marchantia-specific modules. Based on functional studies and data from the literature, we propose new connections between regulatory pathways involved in Marchantia’s vegetative and reproductive development and emphasize the need for further functional studies to understand the molecular mechanisms that control ncRNA-directed developmental processes.

SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE ( SPL ) genes encode plant-specific transcription factors which have been found to be conserved in green plants lineage. SPL proteins are important regulators of diverse plant developmental processes in bryophytes and vascular plants. In our study, we took advantage of available genome sequences of representatives of each bryophyte clade to investigate the relationships of SPL genes between bryophytes and model angiosperm Arabidopsis thaliana . We have identified four SPL genes in each of the two hornworts species, Anthoceros agrestis and Anthoceros punctatus , what is similar to the set of SPL genes present in the liverwort Marchantia polymorpha . Thus, the analyzed hornworts and liverwort genomes encode a minimal set of SPL genes in comparison to other land plants that may resemble an archetype of SPL genes present in the ancestor of land plants. The phylogenetic analysis revealed the presence of four SPL groups. Comparative gene structure analysis showed that SPLs share similar exon-intron organization within the same phylogenetic group with some exceptions in hornworts. While we have identified conserved protein motifs between bryophytes and Arabidopsis in three out of four phylogenetic groups, the motif content differed explicitly in the fourth group. Since current understanding of SPL genes mostly arises from seed plants, the presented comparative and phylogenetic analysis will provide better understanding of SPL gene family from the representatives of the oldest living land plants.

SUMMARY: SQUAMOSA PROMOTER BINDING PROTEIN‐LIKE ( SPL ) genes encode plant‐specific transcription factors that are widely distributed across the plant kingdom. In angiosperms, the multimember SPL family regulates various biological processes, including vegetative‐to‐reproductive phase transition, inflorescence architecture, and lateral organ development. In contrast, the liverwort Marchantia polymorpha genome encodes only four SPL genes, with functional studies available only for microRNA‐targeted members, Mp SPL1 and Mp SPL2 . Mp SPL1 was shown to control the meristem dormancy to modulate the thallus architecture, whereas Mp SPL2 was found to promote the transition from vegetative‐to‐reproductive phase. Here, we investigate the impact of the Mp SPL3 gene on M. polymorpha development. We demonstrate that Mp SPL3 influences coordination of the vegetative growth and the reproductive phase transition. Knockout of Mp SPL3 leads to strong growth retardation with disordered thallus morphology, reduced gemma cup number, and, most strikingly, complete loss of gametangiophore formation. Interestingly, overexpression of Mp SPL3.2 , the shorter isoform, has no detectable morphological effect, whereas the overexpression of Mp SPL3.1 , the longer isoform encoding a protein with an additional 61‐aa long fragment, results in a delay in timing and reduced efficiency of gametangiophore production. Moreover, all the observed developmental abnormalities might be a consequence of the altered expression of genes essential for proper vegetative development and responsible for germ cell specification in Mp SPL3 knockout and overexpression plants. Altogether, our findings demonstrate that Mp SPL3 is important in regulating gametophyte development and ensuring reproductive success in M. polymorpha .