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.

/pdf/somatic-mutations-in-fruit-trees-causes-detection-methods-1zqv546t.pdf

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

Abstract Phytohormones, epigenetic regulation and environmental factors regulate fruit ripening but their interplay during strawberry fruit ripening remains to be determined. In this study, bagged strawberry fruit exhibited delayed ripening compared with fruit grown in normal light, correlating with reduced abscisic acid (ABA) accumulation. Transcription of the key ABA catabolism gene, ABA 8′‐hydroxylase FaCYP707A4 , was induced in bagged fruit. With light exclusion whole genome DNA methylation levels were up‐regulated, corresponding to a delayed ripening process, while DNA methylation levels in the promoter of FaCYP707A4 were suppressed, correlating with increases in transcript and decreased ABA content. Experiments indicated FaCRY1, a blue light receptor repressed in bagged fruit and FaAGO4, a key protein involved in RNA‐directed DNA methylation, could bind to the promoter of FaCYP707A4 . The interaction between FaCRY1 and FaAGO4, and an increased enrichment of FaAGO4 directed to the FaCYP707A4 promoter in fruit grown under light suggests FaCRY1 may influence FaAGO4 to modulate the DNA methylation status of the FaCYP707A4 promoter. Furthermore, transient overexpression of FaCRY1 , or an increase in FaCRY1 transcription by blue light treatment, increases the methylation level of the FaCYP707A4 promoter, while transient RNA interference of FaCRY1 displayed opposite phenotypes. These findings reveal a mechanism by which DNA methylation influences ABA catabolism, and participates in light‐mediated strawberry ripening. 

DNA methylation controlling abscisic acid catabolism responds to light to mediate strawberry fruit ripening


 As global climate change progresses and the demand for nutritional value in food increases, new challenges have been posed for the cultivation of grains, fruits, and vegetables and the functionality of food. Traditional breeding combined with hybridization enhances grain yield, boosts fruit and vegetable production, and augments the beneficial components of food. However, these approaches fail to satisfy the diverse requirements. The gene editing technology offers new tools like clustered regularly interspaced short palindromic repeats- (CRISPR)- CRISPR associated protein 9 (Cas9), transcription activator-like effector nucleases (TALENs), and zinc finger nucleases (ZFNs), enabling precise modifications of plant or animal genes to enhance their characteristics. Gene-edited foods offer numerous advantages, such as increased crop yields, improved nutritional value, enhanced stress resistance, and disease resistance. However, promoting genetically edited food faces several challenges, such as safety research, international regulatory differences, and public perception and acceptance. To achieve widespread application of gene-edited food, strengthening safety research, harmonizing international regulations, and raising public awareness are essential. This review highlights the development of gene editing technology and its application in fruits and vegetables, reviews the legal regulations and attitudes of different countries towards gene-edited food, and provides perspectives on the future of gene-edited food.

Development and prospect of gene edited fruits and vegetables

Long non-coding RNAs (lncRNAs), a class of important regulatory factors for many biological processes in plants, have received much attention in recent years. To explore the molecular roles of lncRNAs in sweet cherry fruit ripening, we conducted widely targeted metabolome, transcriptome and lncRNA analyses of sweet cherry fruit at three ripening stages (yellow stage, pink stage, and dark red stage). The results show that the ripening of sweet cherry fruit involves substantial metabolic changes, and the rapid accumulation of anthocyanins (cyanidin 3-rutinoside, cyanidin 3-O-galactoside, and cyanidin 3-O-glucoside) is the main cause of fruit coloration. These ripening-related alterations in the metabolic profile are driven by specific enzyme genes related to the synthesis and decomposition of abscisic acid (ABA), cell wall disintegration, and anthocyanin biosynthesis, as well as transcription factor genes, such as 

Integrated Metabolome, Transcriptome and Long Non-Coding RNA Analysis Reveals Potential Molecular Mechanisms of Sweet Cherry Fruit Ripening

Long non-coding RNAs: a promising tool to improve horticultural quality traits

Blood flesh is a key fruit trait in peaches (Prunus persica) and can be attributed to the accumulation of anthocyanins. The roles of long non-coding RNAs (lncRNAs) have been highlighted by multiple studies in regulating fruit ripening, anthocyanin accumulation, and abiotic stress responses in many flowering plants. Such regulatory functions of lncRNAs in Prunus persica, nonetheless, have not been reported. In this research, we sequenced and analyzed the complete transcriptome of C3-20 (a blood-fleshed peach) fruit at four developmental stages. Analyses of the correlated genes and differentially expressed lncRNA target genes helped to forecast lncRNAs’ possible functions. The RNA-seq data were generated using high-throughput sequencing. In total, 17,456 putative lncRNAs, including 4,800 intergenic lncRNAs, 2,199 antisense lncRNAs, and 10,439 intronic lncRNAs were discovered, of which 4,871 differentially expressed lncRNAs (DE-lncRNAs) were annotated in the fruit developmental processes. The target genes of these DE-lncRNAs and their regulatory relationship identifying 21,795 cis-regulated and 18,271 trans-regulated targets of the DE-lncRNAs were in a similar way predicted by us. The enriched GO terms for the target genes included anthocyanin biosynthesis. Flavonoid biosynthesis and plant hormone signal transduction were also included in the enriched KEGG pathways. Co-expression network construction demonstrated that the highly expressed genes might co-regulate multiple other genes associated with auxin signal transduction and take effect in equal pathways. We discovered that lncRNAs, including LNC_000987, LNC_000693, LNC_001323, LNC_003610, LNC_001263, and LNC_003380, correlated with fruit that ripened and could take part in ethylene biosynthesis and metabolism and the ABA signaling pathway. Several essential transcription factors, such as ERFs, WRKY70, NAC56, and NAC72, may in a similar way regulate fruit ripening. Three DE-lncRNAs, XLOC_011933, XLOC_001865, and XLOC_042291, are involved in UV-B-induced anthocyanin biosynthesis and positively regulating UVR8 and COP10, were identified and characterized. Our discovery and characterization of XLOC_011933, XLOC_001865, and XLOC_042291 provide a more precise understanding and preliminarily establishes a theoretical framework for UV-B-induced flesh anthocyanin biosynthesis. This phenomenon might encourage more in-depth investigations to study the molecular mechanisms underlying peach flesh coloring.

Identification and Analysis of Long Non-Coding RNAs Related to UV-B-Induced Anthocyanin Biosynthesis During Blood-Fleshed Peach (Prunus persica) Ripening


 
 
 Peach (Prunus persica L.) is an ancient fruit tree that originated from China. It is the climacteric fruit which belongs to genus Prunus in family Rosaceae. Ethylene, which is produced during ripening, accelerates fruit softening, and therefore peaches cannot be stored for a long time.
 
 
 
 To study the mechanism of fruit late ripening, transcriptome analysis of the fruit of a late-ripening mutant of ‘Jinghong’ peach was performed to identify genes and pathways involved in fruit late ripening.
 
 
 
 A total of 1,805, 1,511, and 2,309 genes were found to be differentially expressed in W2_vs_M1, W3_vs_M2, and W3_vs_M3, respectively. Functional enrichment analysis of the differentially expressed genes showed they were related to carotenoid biosynthesis, starch and sucrose metabolism plant hormone signal transduction, flavonoid biosynthesis, and photosynthesis. The expression trends of ripening-related genes that encode transcription factors and plant hormone signal transduction-related genes that encode enzymes were similar.
 
 
 
 It will help to elucidate the transcriptional regulatory network of fruit development in the spontaneous late-ripening mutant of ‘Jinghong’ peach and provide a theoretical basis for understanding the molecular regulatory mechanism of fruit ripening.


/pdf/synergistic-effects-of-plant-hormones-on-spontaneous-late-185ad9rf.pdf

Synergistic Effects of Plant Hormones on Spontaneous Late-ripening Mutant of ‘Jinghong’ Peach Detected by Transcriptome Analysis

Comparative Cytological and Transcriptome Analysis Reveals Differential Gene Expression in Pollen Development in Sterile and Fertile Peach Varieties

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Identification and Analysis of Long Non-Coding RNAs Related to UV-B-Induced Anthocyanin Biosynthesis During Blood-Fleshed Peach (Prunus persica) Ripening

Synergistic Effects of Plant Hormones on Spontaneous Late-ripening Mutant of ‘Jinghong’ Peach Detected by Transcriptome Analysis

Comparative Cytological and Transcriptome Analysis Reveals Differential Gene Expression in Pollen Development in Sterile and Fertile Peach Varieties