Authors: Seunghyun Ban, Je Hyeong Jung
Categories: Review, apple, bud sports, citrus, fruit crops, grape, molecular mechanisms, peach, somatic mutation
Source: Plants
Somatic mutations are genetic changes that occur in non-reproductive cells. In fruit trees, such as apple, grape, orange, and peach, somatic mutations are typically observed as “bud sports” that remain stable during vegetative propagation. Bud sports exhibit various horticulturally important traits that differ from those of their parent plants. Somatic mutations are caused by internal factors, such as DNA replication error, DNA repair error, transposable elements, and deletion, and external factors, such as strong ultraviolet radiation, high temperature, and water availability. There are several methods for detecting somatic mutations, including cytogenetic analysis, and molecular techniques, such as PCR-based methods, DNA sequencing, and epigenomic profiling. Each method has its advantages and limitations, and the choice of method depends on the research question and the available resources. The purpose of this review is to provide a comprehensive understanding of the factors that cause somatic mutations, techniques used to identify them, and underlying molecular mechanisms. Furthermore, we present several case studies that demonstrate how somatic mutation research can be leveraged to discover novel genetic variations. Overall, considering the diverse academic and practical value of somatic mutations in fruit crops, especially those that require lengthy breeding efforts, related research is expected to become more active.
Keywords: somatic mutation, bud sports, fruit crops, molecular mechanisms, apple, grape, citrus, peach
Somatic mutation is a natural process that occurs in both plants and animals and leads to genetic diversity [1]. Unlike mutations that occur in gametes and are passed on to the next generation, somatic mutations occur in somatic cells and are usually not passed on to offspring. However, somatic mutations in plants can still potentially affect the reproductive organs of a plant, even though the mutation originally occurred in non-reproductive cells. This is because the mutated cells may still have the ability to develop into buds or flowers and contribute to the plant’s reproductive process. Especially for fruit crops, somatic mutations can lead to the emergence of novel traits, such as alterations in fruit size [2,3], color [4,5,6], or taste [7,8], which could be commercially valuable. In orchards, lateral shoots, floral clusters, or individual flowers/fruits on trees can be found with noticeably different phenotypes from the rest of the plant [9]. These are called “bud sports”, and enable the propagation of new mutations through asexual propagation while maintaining the name recognition of the existing variety and potentially gaining a market advantage with novel or improved characteristics added to the existing ones. According to Okie [10], more than 170 commercially available varieties of peaches and nectarines are derived from bud-sport mutations. At least 38 bud-sport mutations from ‘Gala’ have been reported since the original release of the ‘Gala’ apple cultivar in 1965 [11], whereas 91 bud-sport mutations have been reported from ‘Fuji’ [12].
Bud sports, clones, and crosses are all important for plant genetic diversity in horticulture and agriculture [13]. Clones are created through asexual propagation, where genetically identical plants are produced from a single parent plant through methods such as rooting, cuttings, or grafting. Grafting is a major propagation method for fruit trees. In contrast, crosses are formed by a sexual reproduction process that involves the crossing of two genetically different plants to produce offspring with new genetic combinations. Bud sports are genetic mutations that occur in a single bud or shoot of a plant, leading to a branch or portion of the plant with different characteristics. Each of these methods can contribute to plant genetic diversity in different ways. Understanding how somatic mutations arise and how they interact with other genetic processes can reveal the evolutionary history of fruit crops and clarify their connections to other plant species. In addition, somatic mutants are known to have a nearly identical genetic background to that of the original cultivars [14,15], making them an important source of material for research in plant genetics and physiology to understand the molecular mechanisms responsible for the variation in traits of interest.
This review aims to provide a comprehensive understanding of somatic mutations in fruit crops, covering their definitions, types, mechanisms, and genetic causes. We also explore recent studies and progress in somatic mutation research for diverse fruit crops, such as apples, grapes, and citrus. Additionally, this review paper identifies the challenges and future directions for research on somatic mutations in fruit crops.
Depending on the plant, the frequency and type of somatic mutations that occur may differ based on differences in genetic background [16]. For example, some plants may have higher natural mutation rates due to the presence and action of transposable elements, whereas others may have lower mutation rates due to DNA repair mechanisms [17]. Somatic mutations are caused by both internal and external factors (Figure 1).
Figure 1 Overview of factors, inducing somatic mutations and methods for analysis in fruit crops.
Examples of internal factors include DNA replication errors [18], DNA repair errors [19], transposable elements [20,21], and deletion [22]. Environmental factors can also affect the frequency and type of somatic mutations [23]. For example, the continuous exposure of plants to mutagens in the environment, such as strong ultraviolet radiation [24], increases the likelihood of somatic mutations [25]. In addition, high temperature [26,27], salt stress [28], water availability [29], and other environmental factors can induce somatic mutations. The induction and types of somatic mutations can also be influenced by the physiological conditions of plants [30]. For example, somatic mutations are more likely to occur in actively growing tissues, such as meristems, than in mature tissues. One of the reasons for this is that the activity of transposons varies depending on the developmental stage of the plant [20,21]. Epigenetic factors can influence the stability of plant genomes and their susceptibility to mutagens [31,32]. For example, alterations in DNA methylation patterns can affect the expression of genes involved in cell-cycle regulation and DNA repair, which can consequently influence the frequency of somatic mutations. According to a recent study by Monroe et al., the frequency of mutations in Arabidopsis is lower in functional and essential genes, and more than 90% of genome-wide patterns of mutation bias are explained by epigenomic and physical features [33].
The various methods for verifying that putative somatic mutations show characteristics different from those of the original cultivar discovered by a breeder in an orchard are shown in Table 1.
Cytogenetic techniques are used to examine the number, structure, and behavior of chromosomes to identify abnormalities such as aneuploidy, polyploidy, deletions, and translocations [34]. Flow cytometry can be used in a similar manner to cytogenetic techniques to examine chromosomes by measuring the amount of DNA in each cell and identifying aneuploidy and polyploidy, as well as changes in DNA content within individual cells [35]. DNA fingerprinting analyzes DNA fragments to distinguish genetic variations between individuals. Some examples of DNA fingerprinting techniques used for this purpose are restriction fragment length polymorphism (RFLP) [36], amplified fragment length polymorphism (AFLP) [37], and simple sequence repeats (SSR) analysis [38]. Microarray analysis can compare the levels of gene expression between somatic mutations and their original variety, enabling the identification of candidate genes for large-scale somatic mutation screening in a cost-effective and efficient manner [39,40]. RNA-Seq can also compare gene expression levels at the transcriptome level, which can be used to select candidate gene regions for somatic mutation [41,42,43]. If certain genes are not expressed in mutants, it is possible to conduct additional experiments, such as comparing the nucleotide sequences of the targeted genomic DNA regions. Recent advances in next-generation sequencing (NGS) technology have enabled the detection of whole-genome sequences in an individual laboratory, allowing for the identification of somatic mutations by comparing the DNA sequence of a mutant sample to that of the original variety [3,44].
We have summarized 36 studies (13 on apple, 9 on grape, 4 on citrus, 4 on pear, 3 on peach, 2 on orange, and 1 on plum) that characterized the somatic mutations in fruit crops (Table 2).
Regardless of the plant species, the most frequent type of research has been related to fruit color. This is because somatic mutants that differ from the original strain in fruit color are easier to detect than other types of somatic mutants. Additionally, fruit color has a significant impact on consumer preference [73,74,75], which likely explains why researchers have shown particular interest in elucidating the underlying mechanisms of these anthocyanin variants. Research on somatic mutations related to fruit maturation and ripening has been actively conducted in apples [22,44,47], citrus [56], grapes [61], peaches [66], and plums [72]. This is because the selling time of a crop variety is determined by its maturation date, and distinct storage techniques and durations are necessary based on the maturation date and ripening characteristics. Therefore, comprehensive studies on fruit maturation and ripening mechanisms have been conducted for most fruit crops.
In addition to studies on the overall common interests of fruit crops, studies on crop-specific traits have also been actively conducted. The seedless characteristics of grapes and apples are particularly important for consumers when purchasing fruit [76]; therefore, researchers have attempted to understand the molecular mechanism using seedless somatic mutants [49,63,64]. Research on apple tree morphology is a representative example of crop-specific research. In the 1960s, a bud mutation called ‘Wijcik McIntosh’ was discovered in McIntosh apples that exhibited vertically growing branches and a reduced number of branches [77]. This trait has received continued interest from the apple community as it requires less pruning and is suitable for mechanical fruit harvesting; this has led to active research and the discovery of its molecular mechanism [50,51,52,53]. In the case of peach fruit, the typical shape is round; however, since the discovery of flat peach fruit [78,79], the associated molecular mechanisms have been actively researched. Fruit shape in peaches has a significant impact on consumer preference, and as the popularity of flat fruits increases, these studies help increase the understanding of fruit shape [67,68,80].
Numerous studies have been conducted on somatic mutations; however, these studies have various challenges and limitations. One of the main challenges is to distinguish between true mutations and genetic variations. For example, differences in transcription-factor genes such as MYB1 [4,5,59,60], MYB10 [6,70,71], and MYB90 [46] cause different coloration in mutants compared to the original variety. Although differences in the expression and methylation of MYB could explain the variation in fruit color, there is still a possibility that a true mutation may have caused these differences. However, traits that are influenced by multiple genes in complex pathways, such as fruit development, pose significant challenges to research. Maturation and ripening of fruits are complex traits that involve various genes in the fruit development process; therefore, the results of mutation studies are diverse. Most studies have reported results by listing numerous differentially expressed genes with varying expression patterns [47,56,57,61,66], or by listing SNPs or Indels at the genomic level [44,72]. Of course, the importance of these studies is evident because the candidate genes identified in these studies will lead to further research.
A good example of a study that has identified the genetic cause of somatic mutation and validated candidate genes concerned tree growth habits in apples [52]. The study used fine mapping to narrow down the trait-associated region and identified a long terminal repeat (LTR) retrotransposon insertion in that region. The candidate genes were then screened using RNA-Seq, and transgenic lines were created using the candidate gene to verify phenotypic differences. In a second example, a 2.8 Mb hemizygous deletion, which is considered the cause of late maturation in somatic mutations, was identified [22]. Candidate genes were narrowed down using RNA-Seq data from fruit development stages, and transgenic lines were created using the candidate gene MdACT7 for phenotype verification in Arabidopsis. As in the above example, we hope that more somatic mutation studies will be conducted in the future, from the proposed genetic causes to the validation of candidate genes.
This review provides an overview of the factors that induce somatic mutations, methods used to detect them, and molecular mechanisms involved. Furthermore, we present several case studies demonstrating the potential of somatic mutation research to identify new sources of genetic variation and enhance fruit crop variety. The detection and identification of genes and pathways affected by somatic mutations can also improve our understanding of fruit crop biology and enable precise breeding efforts. As somatic mutation research continues to evolve, several areas warrant further investigation. Further research is needed to understand the genetic and environmental factors that influence somatic mutation rates in different fruit crop species. Advances in molecular techniques, such as NGS, have the potential to greatly expand our understanding of somatic mutations in fruit crops. In addition, the development of various bioinformatics tools and the use of multi-omics analysis systems are expected to facilitate a comprehensive understanding of somatic mutations.
In conclusion, somatic mutation research represents a promising avenue for improving fruit crops and expanding our knowledge of fruit crop biology. By continuing to study somatic mutations and developing new methods for their detection and analysis, we can uncover new sources of genetic variation and facilitate more targeted breeding efforts in fruit crops. In the near future, it is hoped that a smart factory designed to induce somatic mutations in fruit trees will be developed. This smart factory is expected to be capable of creating various environmental stresses to induce mutations that exhibit superior quality or resistance to specific diseases, with a non-destructive screening system for somatic mutations. If such a smart factory can achieve these capabilities, it is anticipated to have tremendous value.
Conceptualization, S.B. and J.H.J.; resources, J.H.J.; data curation, S.B.; writing—original draft preparation, S.B.; writing—review and editing, S.B. and J.H.J.; and supervision, J.H.J. All authors have read and agreed to the published version of the manuscript.
Not applicable.
Not applicable.
The authors declare no conflict of interest.
This work was supported by intramural grants (2Z06831) from the Korea Institute of Science and Technology (KIST).
Not applicable.