Next Article in Journal
Molecular Mechanisms of Regulation of Root Development by Plant Peptides
Next Article in Special Issue
Unique Salt-Tolerance-Related QTLs, Evolved in Vigna riukiuensis (Na+ Includer) and V. nakashimae (Na+ Excluder), Shed Light on the Development of Super-Salt-Tolerant Azuki Bean (V. angularis) Cultivars
Previous Article in Journal
Evaluation of Yield and Nutraceutical Traits of Orange-Fleshed Sweet Potato Storage Roots in Two Agro-Climatic Zones of Northern Ethiopia
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
Plants
Volume 12
Issue 6
10.3390/plants12061316
plants-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite question_answer Discuss in SciProfiles thumb_up
...
Endorse textsms
...
Comment
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Review

Somatic Mutations in Fruit Trees: Causes, Detection Methods, and Molecular Mechanisms

by
Seunghyun Ban
and
Je Hyeong Jung
*
Smart Farm Research Center, Korea Institute of Science and Technology (KIST), Gangneung 25451, Gangwon, Republic of Korea
*
Author to whom correspondence should be addressed.
Plants 2023, 12(6), 1316; https://doi.org/10.3390/plants12061316
Submission received: 22 February 2023 / Revised: 11 March 2023 / Accepted: 12 March 2023 / Published: 14 March 2023
(This article belongs to the Special Issue Exploring Genes for Crop Breeding and Improvement)
Browse Figure
Review Reports Versions Notes

Abstract

:
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.

1. Introduction

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.

2. Factors Affecting Somatic Mutation 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).
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].

3. Methods for Detecting Somatic Mutation

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].

4. Research on Somatic Mutation in Fruit Crops

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].

5. Challenges and Future Direction

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.

6. Conclusions

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.

Author Contributions

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.

Funding

This work was supported by intramural grants (2Z06831) from the Korea Institute of Science and Technology (KIST).

Informed Consent Statement

Not applicable.

Data Availability Statement

Not applicable.

Conflicts of Interest

The authors declare no conflict of interest.

References

  1. Schoen, D.J.; Schultz, S.T. Somatic Mutation and Evolution in Plants. Annu. Rev. Ecol. Evol. Syst. 2019, 50, 49–73. [Google Scholar] [CrossRef]
  2. Nashima, K.; Terakami, S.; Nishitani, C.; Yamamoto, T.; Habu, T.; Takahashi, H.; Nakazono, M.; Isuzugawa, K.; Hanada, T.; Takashina, T.; et al. Transcriptome analysis of flower receptacles of the European pear (Pyrus communis L.) ‘La France’ and its giant fruit sport using next-generation sequencing technology. J. Hortic. Sci. Biotechnol. 2014, 89, 293–300. [Google Scholar] [CrossRef]
  3. Huang, J.; Zhang, G.; Li, Y.; Lyu, M.; Zhang, H.; Zhang, N.; Chen, R. Integrative genomic and transcriptomic analyses of a bud sport mutant ‘Jinzao Wuhe’ with the phenotype of large berries in grapevines. PeerJ 2023, 11, e14617. [Google Scholar] [CrossRef] [PubMed]
  4. Kobayashi, S.; Goto-Yamamoto, N.; Hirochika, H. Retrotransposon-Induced Mutations in Grape Skin Color. Science 2004, 304, 982–982. [Google Scholar] [CrossRef]
  5. Xu, Y.; Feng, S.; Jiao, Q.; Liu, C.; Zhang, W.; Chen, W.; Chen, X. Comparison of MdMYB1 sequences and expression of anthocyanin biosynthetic and regulatory genes between Malus domestica Borkh. cultivar ‘Ralls’ and its blushed sport. Euphytica 2011, 185, 157–170. [Google Scholar] [CrossRef]
  6. El-Sharkawy, I.; Liang, D.; Xu, K. Transcriptome analysis of an apple (Malus × domestica) yellow fruit somatic mutation identifies a gene network module highly associated with anthocyanin and epigenetic regulation. J. Exp. Bot. 2015, 66, 7359–7376. [Google Scholar] [CrossRef] [Green Version]
  7. Li, X.; Guo, W.; Li, J.; Yue, P.; Bu, H.; Jiang, J.; Liu, W.; Xu, Y.; Yuan, H.; Li, T.; et al. Histone Acetylation at the Promoter for the Transcription Factor PuWRKY31 Affects Sucrose Accumulation in Pear Fruit. Plant Physiol. 2020, 182, 2035–2046. [Google Scholar] [CrossRef] [Green Version]
  8. Wang, L.; Huang, Y.; Liu, Z.; He, J.; Jiang, X.; He, F.; Lu, Z.; Yang, S.; Chen, P.; Yu, H.; et al. Somatic variations led to the selection of acidic and acidless orange cultivars. Nat. Plants 2021, 7, 954–965. [Google Scholar] [CrossRef]
  9. Foster, T.M.; Aranzana, M.J. Attention sports fans! The far-reaching contributions of bud sport mutants to horticulture and plant biology. Hortic. Res. 2018, 5, 44. [Google Scholar] [CrossRef] [Green Version]
  10. Okie, W.R.; States, U.; Service, A.R. Handbook of Peach and Nectarine Varieties: Performance in the Southeastern United States and Index of Names; USDA: Byron, GA, USA, 1998; Volume 808. [Google Scholar]
  11. Hampson, C.R.; Kemp, H. Characteristics of important commercial apple cultivars. In Apples: Botany, Production and Uses; Ferree, D.C., Warrington, I.J., Eds.; CABI Publishing: Wallingford, UK; Cambridge, MA, USA, 2003. [Google Scholar]
  12. Du, X.; Wang, Y.; Liu, M.; Liu, X.; Jiang, Z.; Zhao, L.; Tang, Y.; Sun, Y.; Zhang, X.; Liu, D.; et al. The assessment of epigenetic diversity, differentiation, and structure in the ‘Fuji’ mutation line implicates roles of epigenetic modification in the occurrence of different mutant groups as well as spontaneous mutants. PLoS ONE 2020, 15, e0235073. [Google Scholar] [CrossRef]
  13. Pathirana, R.; Carimi, F. Management and Utilization of Plant Genetic Resources for a Sustainable Agriculture. Plants 2022, 11, 2038. [Google Scholar] [CrossRef] [PubMed]
  14. Yamamoto, T.; Mochida, K.; Imai, T.; Haji, T.; Yaegaki, H.; Yamaguchi, M.; Matsuta, N.; Ogiwara, I.; Hayashi, T. Parentage Analysis in Japanese Peaches using SSR Markers. Breed. Sci. 2003, 53, 35–40. [Google Scholar] [CrossRef] [Green Version]
  15. Minas, I.S.; i Forcada, C.F.; Dangl, G.S.; Gradziel, T.M.; Dandekar, A.M.; Crisosto, C.H. Discovery of non-climacteric and suppressed climacteric bud sport mutations originating from a climacteric Japanese plum cultivar (Prunus salicina Lindl.). Front. Plant Sci. 2015, 6, 316. [Google Scholar] [CrossRef] [Green Version]
  16. Drake, J.W.; Charlesworth, B.; Charlesworth, D.; Crow, J.F. Rates of Spontaneous Mutation. Genetics 1998, 148, 1667–1686. [Google Scholar] [CrossRef]
  17. Krasileva, K.V. The role of transposable elements and DNA damage repair mechanisms in gene duplications and gene fusions in plant genomes. Curr. Opin. Plant Biol. 2019, 48, 18–25. [Google Scholar] [CrossRef] [PubMed]
  18. Golubov, A.; Yao, Y.; Maheshwari, P.; Bilichak, A.; Boyko, A.; Belzile, F.; Kovalchuk, I. Microsatellite Instability in Arabidopsis Increases with Plant Development. Plant Physiol. 2010, 154, 1415–1427. [Google Scholar] [CrossRef] [Green Version]
  19. Shlien, A.; Campbell, B.B.; de Borja, R.; Alexandrov, L.B.; Merico, D.; Wedge, D.; Van Loo, P.; Tarpey, P.S.; Coupland, P.; Behjati, S.; et al. Combined hereditary and somatic mutations of replication error repair genes result in rapid onset of ultra-hypermutated cancers. Nat. Genet. 2015, 47, 257–262. [Google Scholar] [CrossRef]
  20. Robertson, D.S. Mutator Activity in Maize: Timing of Its Activation in Ontogeny. Science 1981, 213, 1515–1517. [Google Scholar] [CrossRef]
  21. Szeverenyi, I.; Ramamoorthy, R.; Teo, Z.W.; Luan, H.F.; Ma, Z.G.; Ramachandran, S. Large-scale Systematic Study on Stability of the Ds Element and Timing of Transposition in Rice. Plant Cell Physiol. 2006, 47, 84–95. [Google Scholar] [CrossRef] [Green Version]
  22. Ban, S.; El-Sharkawy, I.; Zhao, J.; Fei, Z.; Xu, K. An apple somatic mutation of delayed fruit maturation date is primarily caused by a retrotransposon insertion-associated large deletion. Plant J. 2022, 111, 1609–1625. [Google Scholar] [CrossRef]
  23. Jiang, C.; Mithani, A.; Belfield, E.J.; Mott, R.; Hurst, L.D.; Harberd, N.P. Environmentally responsive genome-wide accumulation of de novo Arabidopsis thaliana mutations and epimutations. Genome Res. 2014, 24, 1821–1829. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  24. Molinier, J.; Oakeley, E.J.; Niederhauser, O.; Kovalchuk, I.; Hohn, B. Dynamic response of plant genome to ultraviolet radiation and other genotoxic stresses. Mutat. Res. Mol. Mech. Mutagen. 2005, 571, 235–247. [Google Scholar] [CrossRef] [PubMed]
  25. Kovalchuk, I.; Kovalchuk, O.; Hohn, B. Genome-wide variation of the somatic mutation frequency in transgenic plants. EMBO J. 2000, 19, 4431–4438. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  26. Belfield, E.J.; Brown, C.; Ding, Z.J.; Chapman, L.; Luo, M.; Hinde, E.; van Es, S.W.; Johnson, S.; Ning, Y.; Zheng, S.J.; et al. Thermal stress accelerates Arabidopsis thaliana mutation rate. Genome Res. 2020, 31, 40–50. [Google Scholar] [CrossRef] [PubMed]
  27. Saini, R.; Singh, A.K.; Dhanapal, S.; Saeed, T.H.; Hyde, G.J.; Baskar, R. Brief temperature stress during reproductive stages alters meiotic recombination and somatic mutation rates in the progeny of Arabidopsis. BMC Plant Biol. 2017, 17, 103. [Google Scholar] [CrossRef] [Green Version]
  28. Kiselev, K.V.; Ogneva, Z.V.; Dubrovina, A.S.; Suprun, A.R.; Tyunin, A.P. Altered somatic mutation level and DNA repair gene expression in Arabidopsis thaliana exposed to ultraviolet C, salt, and cadmium stresses. Acta Physiol. Plant. 2018, 40, 21. [Google Scholar] [CrossRef]
  29. Yao, Y.; Kovalchuk, I. Abiotic stress leads to somatic and heritable changes in homologous recombination frequency, point mutation frequency and microsatellite stability in Arabidopsis plants. Mutat. Res. Mol. Mech. Mutagen. 2011, 707, 61–66. [Google Scholar] [CrossRef]
  30. Dubrovina, A.S.; Kiselev, K.V. Age-associated alterations in the somatic mutation and DNA methylation levels in plants. Plant Biol. 2015, 18, 185–196. [Google Scholar] [CrossRef]
  31. Baulcombe, D.; Dean, C. Epigenetic Regulation in Plant Responses to the Environment. Cold Spring Harb. Perspect. Biol. 2014, 6, a019471. [Google Scholar] [CrossRef]
  32. Thiebaut, F.; Hemerly, A.S.; Ferreira, P.C.G. A Role for Epigenetic Regulation in the Adaptation and Stress Responses of Non-model Plants. Front. Plant Sci. 2019, 10, 246. [Google Scholar] [CrossRef] [Green Version]
  33. Monroe, J.G.; Srikant, T.; Carbonell-Bejerano, P.; Becker, C.; Lensink, M.; Exposito-Alonso, M.; Klein, M.; Hildebrandt, J.; Neumann, M.; Kliebenstein, D.; et al. Mutation bias reflects natural selection in Arabidopsis thaliana. Nature 2022, 602, 101–105. [Google Scholar] [CrossRef] [PubMed]
  34. Figueroa, D.M.; Bass, H.W. A historical and modern perspective on plant cytogenetics. Briefings Funct. Genom. 2010, 9, 95–102. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  35. Ochatt, S.J. Flow cytometry in plant breeding. Cytom. Part A 2008, 73, 581–598. [Google Scholar] [CrossRef] [PubMed]
  36. Hubbard, M.; Kelly, J.; Rajapakse, S.; Abbott, A.; Ballard, R. Restriction Fragment Length Polymorphisms in Rose and Their Use for Cultivar Identification. Hortscience 1992, 27, 172–173. [Google Scholar] [CrossRef] [Green Version]
  37. Oliveira, E.; Costa, J.L.; Dos Santos, L.F.; De Carvalho, F.M.; Silva, A.D.S.; Dantas, J.L.L. Molecular characterization of papaya genotypes using AFLP markers. Rev. Bras. Frutic. 2011, 33, 849–858. [Google Scholar] [CrossRef]
  38. Aranzana, M.; Carbó, J.; Arús, P. Microsatellite variability in peach [Prunus persica (L.) Batsch]: Cultivar identification, marker mutation, pedigree inferences and population structure. Theor. Appl. Genet. 2003, 106, 1341–1352. [Google Scholar] [CrossRef]
  39. Lee, Y.-P.; Yu, G.-H.; Seo, Y.S.; Han, S.E.; Choi, Y.-O.; Kim, D.; Mok, I.-G.; Kim, W.T.; Sung, S.-K. Microarray analysis of apple gene expression engaged in early fruit development. Plant Cell Rep. 2007, 26, 917–926. [Google Scholar] [CrossRef]
  40. Koia, J.H.; Moyle, R.L.; Botella, J.R. Microarray analysis of gene expression profiles in ripening pineapple fruits. BMC Plant Biol. 2012, 12, 240. [Google Scholar] [CrossRef] [Green Version]
  41. Zhang, Y.; Jiao, F.; Li, J.; Pei, Y.; Zhao, M.; Song, X.; Guo, X. Transcriptomic analysis of the maize inbred line Chang7-2 and a large-grain mutant tc19. BMC Genom. 2022, 23, 4. [Google Scholar] [CrossRef]
  42. Lu, M.; Li, Y.; Jia, H.; Xi, Z.; Gao, Q.; Zhang, Z.-Z.; Deng, W.-W. Integrated proteomics and transcriptome analysis reveal a decreased catechins metabolism in variegated tea leaves. Sci. Hortic. 2021, 295, 110824. [Google Scholar] [CrossRef]
  43. Xu, D.; Xie, Y.; Guo, H.; Zeng, W.; Xiong, H.; Zhao, L.; Gu, J.; Zhao, S.; Ding, Y.; Liu, L. Transcriptome Analysis Reveals a Potential Role of Benzoxazinoid in Regulating Stem Elongation in the Wheat Mutant qd. Front. Genet. 2021, 12, 623861. [Google Scholar] [CrossRef] [PubMed]
  44. Lee, H.; Kim, G.; Kwon, S.; Kim, J.; Kwon, Y.; Choi, C. Analysis of ‘Fuji’ apple somatic variants from next-generation sequencing. Genet. Mol. Res. 2016, 15, 17–36. [Google Scholar] [CrossRef] [PubMed]
  45. Han, M.X.; Sun, Q.B.; Zhou, J.Y.; Qiu, H.R.; Guo, J.; Lu, L.J.; Mu, W.L.; Sun, J. Insertion of a solo LTR retrotransposon associates with spur mutations in ‘Red Delicious’ apple (Malus × domestica). Plant Cell Rep. 2017, 36, 1375–1385. [Google Scholar] [CrossRef]
  46. Sun, C.; Wang, C.; Zhang, W.; Liu, S.; Wang, W.; Yu, X.; Song, T.; Yu, M.; Yu, W.; Qu, S. The R2R3-type MYB transcription factor MdMYB90-like is responsible for the enhanced skin color of an apple bud sport mutant. Hortic. Res. 2021, 8, 156. [Google Scholar] [CrossRef]
  47. Wang, A.; Tan, D.; Tatsuki, M.; Kasai, A.; Li, T.; Saito, H.; Harada, T. Molecular mechanism of distinct ripening profiles in ‘Fuji’ apple fruit and its early maturing sports. Postharvest Biol. Technol. 2009, 52, 38–43. [Google Scholar] [CrossRef]
  48. Sun, T.; Zhang, J.; Zhang, Q.; Li, X.; Li, M.; Yang, Y.; Zhou, J.; Wei, Q.; Zhou, B. Methylome and transcriptome analyses of three different degrees of albinism in apple seedlings. BMC Genom. 2022, 23, 310. [Google Scholar] [CrossRef] [PubMed]
  49. Yao, J.L.; Dong, Y.H.; Morris, B.A.M. Parthenocarpic apple fruit production conferred by transposon insertion mutations in a MADS-box transcription factor. Proc. Natl. Acad. Sci. USA 2001, 98, 1306–1311. [Google Scholar] [CrossRef]
  50. Otto, D.; Petersen, R.; Brauksiepe, B.; Braun, P.; Schmidt, E.R. The columnar mutation (“Co gene”) of apple (Malus × domestica) is associated with an integration of a Gypsy-like retrotransposon. Mol. Breed. 2013, 33, 863–880. [Google Scholar] [CrossRef]
  51. Wolters, P.J.; Schouten, H.J.; Velasco, R.; Si-Ammour, A.; Baldi, P. Evidence for regulation of columnar habit in apple by a putative 2 OG -Fe(II) oxygenase. New Phytol. 2013, 200, 993–999. [Google Scholar] [CrossRef]
  52. Okada, K.; Wada, M.; Moriya, S.; Katayose, Y.; Fujisawa, H.; Wu, J.Z.; Kanamori, H.; Kurita, K.; Sasaki, H.; Fujii, H.; et al. Expression of a putative dioxygenase gene adjacent to an insertion mutation is involved in the short internodes of columnar apples (Malus × domestica). J. Plant Res. 2016, 129, 1109–1126. [Google Scholar] [CrossRef]
  53. Dougherty, L.; Bai, T.; Brown, S.; Xu, K. Exploring DNA Variant Segregation Types Enables Mapping Loci for Recessive Phenotypic Suppression of Columnar Growth in Apple. Front. Plant Sci. 2020, 11, 692. [Google Scholar] [CrossRef] [PubMed]
  54. Alós, E.; Roca, M.; Iglesias, D.J.; Mínguez-Mosquera, M.I.; Damasceno, C.M.B.; Thannhauser, T.W.; Rose, J.K.C.; Talón, M.; Cercós, M. An Evaluation of the Basis and Consequences of a Stay-Green Mutation in the navel negra Citrus Mutant Using Transcriptomic and Proteomic Profiling and Metabolite Analysis. Plant Physiol. 2008, 147, 1300–1315. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  55. Mesejo, C.; Marzal, A.; Martínez-Fuentes, A.; Reig, C.; Lucas, M.; Iglesias, D.J.; Primo-Millo, E.; Blázquez, M.A.; Agustí, M. Reversion of fruit-dependent inhibition of flowering in Citrus requires sprouting of buds with epigenetically silenced CcMADS19. New Phytol. 2021, 233, 526–533. [Google Scholar] [CrossRef] [PubMed]
  56. Liu, Y.; Liu, Q.; Xiong, J.; Deng, X. Difference of a citrus late-ripening mutant (Citrus sinensis) from its parental line in sugar and acid metabolism at the fruit ripening stage. Sci. China Life Sci. 2007, 50, 511–517. [Google Scholar] [CrossRef]
  57. Ríos, G.; Naranjo, M.A.; Rodrigo, M.-J.; Alós, E.; Zacarías, L.; Cercós, M.; Talón, M. Identification of a GCC transcription factor responding to fruit colour change events in citrus through the transcriptomic analyses of two mutants. BMC Plant Biol. 2010, 10, 276. [Google Scholar] [CrossRef] [Green Version]
  58. Walker, A.R.; Lee, E.; Robinson, S. Two new grape cultivars, bud sports of Cabernet Sauvignon bearing pale-coloured berries, are the result of deletion of two regulatory genes of the berry colour locus. Plant Mol. Biol. 2006, 62, 623–635. [Google Scholar] [CrossRef]
  59. Azuma, A.; Kobayashi, S.; Goto-Yamamoto, N.; Shiraishi, M.; Mitani, N.; Yakushiji, H.; Koshita, Y. Color recovery in berries of grape (Vitis vinifera L.) ‘Benitaka’, a bud sport of ‘Italia’, is caused by a novel allele at the VvmybA1 locus. Plant Sci. 2009, 176, 470–478. [Google Scholar] [CrossRef]
  60. Xu, Y.; Jiang, N.; Zhang, Y.; Wang, M.; Ren, J.; Tao, J. A SNP in the promoter region of theVvmybA1 gene is responsible for differences in grape berry color between two related bud sports of grape. Plant Growth Regul. 2017, 82, 457–465. [Google Scholar] [CrossRef]
  61. Wei, L.; Cao, Y.; Cheng, J.; Xiang, J.; Shen, B.; Wu, J. Comparative transcriptome analyses of a table grape ‘Summer Black’ and its early-ripening mutant ‘Tiangong Moyu’ identify candidate genes potentially involved in berry development and ripening. J. Plant Interactions 2020, 15, 213–222. [Google Scholar] [CrossRef]
  62. Leng, F.; Ye, Y.; Zhu, X.; Zhang, Y.; Shi, J.; Shen, N.; Jia, H.; Wang, L. Comparative transcriptomic analysis between ‘Summer Black’ and its bud sport ‘Nantaihutezao’ during developmental stages. Planta 2021, 253, 23. [Google Scholar] [CrossRef]
  63. Nwafor, C.C.; Gribaudo, I.; Schneider, A.; Wehrens, R.; Grando, M.S.; Costantini, L. Transcriptome analysis during berry development provides insights into co-regulated and altered gene expression between a seeded wine grape variety and its seedless somatic variant. BMC Genom. 2014, 15, 1030. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  64. Royo, C.; Torres-Pérez, R.; Mauri, N.; Diestro, N.; Cabezas, J.A.; Marchal, C.; Lacombe, T.; Ibáñez, J.; Tornel, M.; Carreño, J.; et al. The Major Origin of Seedless Grapes Is Associated with a Missense Mutation in the MADS-Box Gene VviAGL11. Plant Physiol. 2018, 177, 1234–1253. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  65. Liu, Q.; Zhu, A.; Chai, L.; Zhou, W.; Yu, K.; Ding, J.; Xu, J.; Deng, X. Transcriptome analysis of a spontaneous mutant in sweet orange [Citrus sinensis (L.) Osbeck] during fruit development. J. Exp. Bot. 2009, 60, 801–813. [Google Scholar] [CrossRef] [PubMed]
  66. Zhang, M.; Du, T.; Yin, Y.; Cao, H.; Song, Z.; Ye, M.; Liu, Y.; Shen, Y.; Zhang, L.; Yang, Q.; et al. Synergistic effects of plant hormones on spontaneous late-ripening mutant of ‘Jinghong’ peach detected by transcriptome analysis. Food Qual. Saf. 2022, 6, fyac010. [Google Scholar] [CrossRef]
  67. López-Girona, E.; Zhang, Y.; Eduardo, I.; Mora, J.R.H.; Alexiou, K.G.; Arús, P.; Aranzana, M.J. A deletion affecting an LRR-RLK gene co-segregates with the fruit flat shape trait in peach. Sci. Rep. 2017, 7, 6714. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  68. Tan, Q.; Liu, X.; Gao, H.; Xiao, W.; Chen, X.; Fu, X.; Li, L.; Li, D.; Gao, D. Comparison Between Flat and Round Peaches, Genomic Evidences of Heterozygosity Events. Front. Plant Sci. 2019, 10, 592. [Google Scholar] [CrossRef]
  69. Li, X.; Guo, W.; Xu, M.; Zhao, J.; Wang, G.; Yuan, H.; Wang, A. PuWRKY31 Affects Ethylene Production in Response to Sucrose Signal in Pear Fruit. Hortic. Res. 2022, 9, uhac156. [Google Scholar] [CrossRef]
  70. Wang, Z.; Meng, D.; Wang, A.; Li, T.; Jiang, S.; Cong, P.; Li, T. The Methylation of the PcMYB10 Promoter Is Associated with Green-Skinned Sport in Max Red Bartlett Pear. Plant Physiol. 2013, 162, 885–896. [Google Scholar] [CrossRef] [Green Version]
  71. Qian, M.; Sun, Y.; Allan, A.C.; Teng, Y.; Zhang, D. The red sport of ‘Zaosu’ pear and its red-striped pigmentation pattern are associated with demethylation of the PyMYB10 promoter. Phytochemistry 2014, 107, 16–23. [Google Scholar] [CrossRef]
  72. i Marti, A.F.; Saski, C.A.; Manganaris, G.A.; Gasic, K.; Crisosto, C.H. Genomic Sequencing of Japanese Plum (Prunus salicina Lindl.) Mutants Provides a New Model for Rosaceae Fruit Ripening Studies. Front. Plant Sci. 2018, 9, 21. [Google Scholar] [CrossRef] [Green Version]
  73. Crisosto, C.H.; Crisosto, G.M.; Metheney, P. Consumer acceptance of ‘Brooks’ and ‘Bing’ cherries is mainly dependent on fruit SSC and visual skin color. Postharvest Biol. Technol. 2003, 28, 159–167. [Google Scholar] [CrossRef]
  74. Turner, J.; Seavert, C.; Colonna, A.; Long, L. Consumer sensory evaluation of sweet cherry cultivars in oregon, USA. Acta Hortic. 2008, 795, 781–786. [Google Scholar] [CrossRef]
  75. Normann, A.; Röding, M.; Wendin, K. Sustainable Fruit Consumption: The Influence of Color, Shape and Damage on Consumer Sensory Perception and Liking of Different Apples. Sustainability 2019, 11, 4626. [Google Scholar] [CrossRef] [Green Version]
  76. Zhou, J.; Cao, L.; Chen, S.; Perl, A.; Ma, H. Consumer-assisted selection: The preference for new tablegrape cultivars in China. Aust. J. Grape Wine Res. 2015, 21, 351–360. [Google Scholar] [CrossRef]
  77. Lapins, K.O. Segregation of compact growth types in certain apple seedling progenies. Can. J. Plant Sci. 1969, 49, 765–768. [Google Scholar] [CrossRef]
  78. Dirlewanger, E.; Pronier, V.; Parvery, C.; Rothan, C.; Guye, A.; Monet, R. Genetic linkage map of peach [Prunus persica (L.) Batsch] using morphological and molecular markers. Theor. Appl. Genet. 1998, 97, 888–895. [Google Scholar] [CrossRef]
  79. Lesley, J. A genetic study of saucer fruit shape and other characters in the peach. Proc. Am. Soc. Hortic. Sci. 1940, 37, 218–222. [Google Scholar]
  80. Guo, J.; Cao, K.; Li, Y.; Yao, J.-L.; Deng, C.; Wang, Q.; Zhu, G.; Fang, W.; Chen, C.; Wang, X.; et al. Comparative Transcriptome and Microscopy Analyses Provide Insights into Flat Shape Formation in Peach (Prunus persica). Front. Plant Sci. 2018, 8, 2215. [Google Scholar] [CrossRef] [Green Version]
Plants 12 01316 g001 550
Figure 1. Overview of factors, inducing somatic mutations and methods for analysis in fruit crops.
Figure 1. Overview of factors, inducing somatic mutations and methods for analysis in fruit crops.
Plants 12 01316 g001
Table
Table 1. Molecular techniques for detecting somatic mutation.
Table 1. Molecular techniques for detecting somatic mutation.
TechniqueDescriptionUse
Cytogenetic techniquesAnalysis of chromosome number, structure, and behavior.Detection of chromosomal abnormalities, such as aneuploidy, polyploidy, deletions, and translocations.
Flow cytometryMeasurement of DNA content of individual cells.Detection of aneuploidy and polyploidy, as well as changes in the DNA content of individual cells.
DNA fingerprintingAnalysis of DNA fragments to identify genetic differences between individuals.Detection of somatic mutations by comparing the DNA fingerprint of a mutated cell to that of a normal cell.
Microarray analysisHybridization of DNA fragments to a chip containing thousands of probes.Detection of differences in gene expression between mutated and normal cells.
Next-generation sequencingRapid generation of large amounts of DNA sequence data.(1) Comparison of DNA sequence between mutated and normal tissues.
(2) Through RNA-Seq, differences in gene expression or isoforms of expressed genes can also be detected.
Table
Table 2. Case studies of somatic mutations in different fruit crops.
Table 2. Case studies of somatic mutations in different fruit crops.
PlantMutant PhenotypeMajor FindingsRef.
AppleFruit-bearing type (spur)A novel 2190 bp insertion associated with a preexisting Gypsy-50 retrotransposon was identified in the genome of ‘Red Delicious’ spur mutants using inter-retrotransposon amplified polymorphism (IRAP) and genome walking. The insertion is a spur-specific solo long-terminal repeat (sLTR).[45]
AppleFruit colorThe aim of the study was to investigate the genetic basis of the blushed coloring pattern in the fruit skin of a bud sport of Malus domestica Borkh. cultivar ‘Ralls’ by comparing it with ‘Ralls’ (striped red). The study found that the DNA methylation in the promoter region of MdMYB1 played a significant role in regulating MdMYB1 expression and affecting the color pattern of the apples.[5]
AppleFruit colorA module consisting of 34 genes that were highly correlated with anthocyanin content was identified using RNA-Seq and weighted gene co-expression network analysis (WGCNA). The researchers found that methylation in the promoter region of MdMYB10 was likely responsible for the yellow color fruit.[6]
AppleFruit colorRNA-seq analysis was used to identify the genetic basis of enhanced coloration in a red ‘Fuji’ apple mutant. A novel R2R3-MYB transcription factor, MdMYB90-like, was discovered to regulate anthocyanin biosynthesis by interacting with other transcription factors. The upregulation of MdMYB90-like in the mutant is due to decreased DNA methylation in its promoter region. Transgenic analysis validated that upregulation of MdMYB90-like increases the expression of genes associated with anthocyanin production.[46]
AppleFruit maturation dateUsing next-generation sequencing, single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) were detected in the ‘Fuji’ apple and its bud mutant cultivars, and unique genetic variations were identified for each bud mutant.[44]
AppleFruit maturation dateDifferential gene expression of ethylene biosynthesis and signaling genes, along with a cell-wall degradation enzyme, was observed between the mutant and its parental variety.[47]
AppleFruit maturation dateThrough a combination of RNA-Seq and genomic sequencing, a hemizygous deletion of 2.8 Mb on chromosome 6 was identified in a late-maturing mutant. The 2.8 Mb hemizygous deletion found on chromosome 6 in the late-maturing mutant was replaced by a 10.7 kb retrotransposon insertion from chromosome 7, resulting in the loss of the functional MdACT7 allele that may be responsible for early fruit maturation.[22]
AppleLeaf albinismThis study utilized bisulfite sequencing and RNA sequencing to examine diverse types of albinism in apple seedlings, leading to the discovery of differentially methylated regions (DMRs) and differentially expressed genes. Nine genes involved in the pathways of carotenoid metabolism and flavonoid biosynthesis were found to be associated with the identified DMRs.[48]
AppleParthenocarpyThe apple PI homolog (MdPI) was cloned and a retrotransposon insertion causing loss of function was identified. This resulted in parthenocarpy fruit development in apple.[49]
AppleTree-growth habit (columnar growth)Researchers used classical and NGS analysis to explore the genetic basis of columnar growth in apple trees, discovering a Ty3/Gypsy retrotransposon insertion at 18.8 Mb as the only genomic difference between columnar and non-columnar trees. RNA-seq data show that the columnar growth habit in ‘McIntosh’ and ‘McIntosh Wijcik’ is linked to the retrotransposon transcript’s differential expression, which alters the expression of numerous protein-coding genes.[50]
AppleTree-growth habit (columnar growth)A 1956 bp non-coding DNA element unique to Pyreae was identified in the Co region of ‘Wijcik’ when compared to its wild-type ‘McIntosh’. Among the candidate genes found in the Co region, the MdCo31 was up-regulated in axillary buds of ‘Wijcik’. Constitutive expression of MdCo31 in Arabidopsis thaliana resulted in plants exhibiting a columnar growth phenotype.[51]
AppleTree-growth habit (columnar growth)A single dominant gene, Co, controls the phenotype that was fine mapped to a 101 kb region. The study found an 8202 bp LTR retroposon insertion mutation in the Co region, which was closely linked to the columnar growth phenotype. The 91071 gene, located near the insertion mutation, was identified as a possible candidate gene responsible for the phenotype. Overexpressing the 91071 gene in transgenic apples produced a similar phenotype to columnar apples.[52]
AppleTree-growth habit (columnar growth)This study utilized pooled-genomic sequencing between columnar and standard seedlings for a genetic mapping. Two loci of recessive suppressors (c2 and c3) were discovered to be linked to the repression of the Co gene expression, which is induced by retroposon and associated with the columnar phenotype in apple trees.[53]
CitrusFruit colorThe researchers utilized a citrus microarray to perform transcript profiling and discovered that the mutant exhibited reduced expression levels of a citrus ortholog of STAY-GREEN genes.[54]
CitrusFloweringThe researchers stimulated early growth of lateral buds in fruit-bearing shoots and observed that the absence of the repressive H3K27me3 marks of CcMADS19 locus in old leaves was linked to the phenomenon. Conversely, young leaves still retained the H3K27me3 marks.[55]
CitrusFruit maturation dateThis study aimed to compare the sugar and acid content and the expression of metabolic enzymes during fruit ripening of a late-ripening mutant and its parental line. The mutant exhibited delayed expression of citrus sucrose synthase (CitSS1) and higher expression of citrus acid invertase (CitAI) compared to the parental cultivars.[56]
CitrusFruit ripeningThe researchers used two Citrus clementina mutants with delayed color break. The study showed that when the CcGCC1 gene was down-regulated, the color break was delayed due to genetic, developmental, and hormonal factors.[57]
GrapeFruit colorThe loss of color in white varieties of Vitis vinifera is attributed to the insertion of a retrotransposon in the VvmybA1 gene[4]
GrapeFruit colorThe researchers discovered that the presence or absence of the red-colored allele at the berry-colored locus is responsible for determining the color.[58]
GrapeFruit colorThe study unveiled that the recovered color mutant harbors a heterozygous VvmybA1 locus, consisting of a non-functional VvmybA1a allele and a novel VvmybA1BEN allele. The presence of VvmybA1BEN restored VvmybA1 transcripts.[59]
GrapeFruit colorThis study discovered that an SNP mutation in the promoter region of the VvmybA1 gene caused the color change from red to black. The color difference caused by the SNP was verified by producing red cells through Agrobacterium-mediated transformation.[60]
GrapeFruit development and ripeningRNA-seq was used to identify differentially expressed genes between a mutant and its parent, with a focus on genes involved in berry development and ripening.[61]
GrapeFruit quality (taste and color)In this study, RNA sequencing was conducted to compare two cultivars, and a total of 5388 genes were identified to be associated with changes in total soluble solid and anthocyanin contents. Two significant genes, namely 4-coumarate-CoA ligase and copper amine oxidase, were found to play a crucial role in the changes in total soluble solid and anthocyanin levels caused by bud sport.[62]
GrapeFruit sizeWhole genome resequencing and transcriptomic sequencing were conducted. Genetic variations related to cell death, symbiotic microorganisms, and other processes, as well as differentially expressed genes related to cell-wall modification, stress response, and cell killing, were identified.[3]
GrapeSeedlessDifferential-gene-expression analysis was conducted between a seeded wine grape and its seedless somatic mutant at three developmental stages. A total of 1075 differentially expressed genes were identified, highlighting significant coordination and enrichment of pollen and ovule developmental pathways.[63]
GrapeSeedlessIn this study, researchers used quantitative genetics, fine-mapping, and RNA-sequencing to identify the primary causal factor of seedlessness in grapes as the AGAMOUS-LIKE11 (VviAGL11) gene. Specifically, they discovered that a single-point variation in VviAGL11 resulting in an arginine-197-to-leucine substitution was fully associated with stenospermocarpy.[64]
OrangeFruit acidityA reference genome of sweet orange and six diploid genomes of somatic mutants were assembled de novo. Subsequently, 114 somatic mutants were sequenced, revealing somatic mutations, structural variations, and transposable-element transpositions, including transporter or regulatory gene insertions linked to fruit acidity variation.[8]
OrangeFruit qualityBy searching for differentially expressed genes using subtractive hybridization and microarray analysis, 13 signal transduction- or transcription-factor genes were identified.[65]
PeachFruit maturation dateDifferentially expressed genes (DEGs) identified during fruit development stages using RNA-Seq are associated with carotenoid biosynthesis, starch and sucrose metabolism, plant hormone signal transduction, flavonoid biosynthesis, and photosynthesis.[66]
PeachFruit shape (flat shape)It was discovered that a deletion of approximately 10 kb was present and affecting a gene that co-segregates with the trait. This gene was identified as being orthologous to leucine-rich repeat receptor-like kinase (LRR-RLK).[67]
PeachFruit shape (round shape)Loss of heterozygosity event was identified by NGS in bud sport as the potential cause for alteration in fruit shape. Furthermore, a genome-wide association study involving 127 peach accessions was performed and a single nucleotide polymorphism associated with variations in fruit shape was identified.[68]
PearFruit quality (sucrose)In this study, the expression levels of the SWEET gene, PuSWEET15, were compared between a somatic-mutant high-sucrose pear variety (BNG) and its parent (NG) using RNA-Seq data. The study discovered that PuSWEET15 was expressed at higher levels in BNG; overexpression of this gene in NG increased the sucrose content, whereas silencing it in BNG decreased it. The study also revealed that the WRKY transcription factor PuWRKY31 was expressed to greater levels in BNG fruit and was found to bind to the PuSWEET15 promoter and induce its transcription. Additionally, PuWRKY31 was found to upregulate the transcription of ethylene-biosynthetic genes.[7,69]
PearFruit skin colorThe study found a correlation between hypermethylation of the PcMYB10 promoter and the green-skin phenotype. Infiltrating red-skin fruits with a plasmid to silence endogenous PcMYB10 resulted in blocked anthocyanin biosynthesis.[70]
PearFruit skin colorA high correlation was found between the accumulation of anthocyanin and the expression of genes PpUFGT2 and PyMYB10. The red bud sport of ‘Zaosu’ pear and the striped pigmentation pattern of ‘Zaosu Red’ pear were found to be related to the demethylation of the PyMYB10 promoter. [71]
PearLarge fruitThis study identified 61 core cell-cycle genes by transcriptome analysis.[2]
PlumFruit-ripening typeThe genomic DNA of six plum cultivars were sequenced using genomic sequencing. Potential genes related to ethylene perception and signal transduction were identified as potential candidate genes.[72]
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content.

Share and Cite

MDPI and ACS Style

Ban, S.; Jung, J.H. Somatic Mutations in Fruit Trees: Causes, Detection Methods, and Molecular Mechanisms. Plants 2023, 12, 1316. https://doi.org/10.3390/plants12061316

AMA Style

Ban S, Jung JH. Somatic Mutations in Fruit Trees: Causes, Detection Methods, and Molecular Mechanisms. Plants. 2023; 12(6):1316. https://doi.org/10.3390/plants12061316

Chicago/Turabian Style

Ban, Seunghyun, and Je Hyeong Jung. 2023. "Somatic Mutations in Fruit Trees: Causes, Detection Methods, and Molecular Mechanisms" Plants 12, no. 6: 1316. https://doi.org/10.3390/plants12061316

APA Style

Ban, S., & Jung, J. H. (2023). Somatic Mutations in Fruit Trees: Causes, Detection Methods, and Molecular Mechanisms. Plants, 12(6), 1316. https://doi.org/10.3390/plants12061316

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Back to TopTop