Comparative transcriptomic analysis between 'Summer Black' and its bud sport 'Nantaihutezao' during developmental stages

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

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.

Jasmonic acid negatively regulates branch growth in pear

The quality of seedlings is an important factor for development of the pear industry. A strong seedling with few branches and suitable internodes is ideal material as a rootstock for grafting and breeding. Several branching mutants of pear rootstocks were identified previously. In the present study, 'QAU-D03' (Pyrus communis L.) and it's mutants were used to explore the mechanism that affects branch formation by conducting phenotypic trait assessment, hormone content analysis, and transcriptome analysis. The mutant plant (MP) showed fewer branches, shorter 1-year-old shoots, and longer petiole length, compared to original plants (OP), i.e., wild type. Endogenous hormone analysis revealed that auxin, cytokinin, and jasmonic acid contents in the stem tips of MP were significantly higher than those of the original plants. In particular, the jasmonic acid content of the MP was 1.8 times higher than that of the original plants. Transcriptome analysis revealed that PcCOI1, which is a transcriptional regulatory gene downstream of the jasmonic acid signaling pathway, was expressed more highly in the MP than in the original plants, whereas the expression levels of PcJAZ and PcMYC were reduced in the MP compared with that of the original plants. In response to treatment with exogenous methyl jasmonate, the original plants phenotype was consistent with that of the MP in developing less branches. These results indicate that jasmonic acid negatively regulates branch growth of pear trees and that jasmonic acid downstream regulatory genes play a crucial role in regulating branching.

Integrative genomic and transcriptomic analyses of a bud sport mutant 'Jinzao Wuhe' with the phenotype of large berries in grapevines

Background

Bud sport mutation occurs frequently in fruit plants and acts as an important approach for grapevine improvement and breeding. 'Jinzao Wuhe' is a bud sport of the elite cultivar 'Himord Seedless' with obviously enlarged organs and berries. To date, the molecular mechanisms underlying berry enlargement caused by bud sport in grapevines remain unclear.

Methods

Whole genome resequencing (WGRS) was performed for two pairs of bud sports and their maternal plants with similar phenotype to identify SNPs, InDels and structural variations (SVs) as well as related genes. Furthermore, transcriptomic sequencing at different developmental stages and weighted gene co-expression network analysis (WGCNA) for 'Jinzao Wuhe' and its maternal plant 'Himord Seedless' were carried out to identify the differentially expressed genes (DEGs), which were subsequently analyzed for Gene Ontology (GO) and function annotation.

Results

In two pairs of enlarged berry bud sports, a total of 1,334 SNPs, 272 InDels and 74 SVs, corresponding to 1,022 target genes related to symbiotic microorganisms, cell death and other processes were identified. Meanwhile, 1,149 DEGs associated with cell wall modification, stress-response and cell killing might be responsible for the phenotypic variation were also determined. As a result, 42 DEGs between 'Himord Seedless' and 'Jinzao Wuhe' harboring genetic variations were further investigated, including pectin esterase, cellulase A, cytochromes P450 (CYP), UDP-glycosyltransferase (UGT), zinc finger protein, auxin response factor (ARF), NAC transcription factor (TF), protein kinase, etc. These candidate genes offer important clues for a better understanding of developmental regulations of berry enlargement in grapevine.

Conclusion

Our results provide candidate genes and valuable information for dissecting the underlying mechanisms of berry development and contribute to future improvement of grapevine cultivars.

Insight Into the Multiple Branches Traits of a Mutant in Larix olgensis by Morphological, Cytological, and Transcriptional Analyses

Larix olgensis is a tall deciduous tree species that has many applications in the wood fiber industry. Bud mutations are somatic mutations in plants and are considered an ideal material to identify and describe the molecular mechanism of plant mutation. However, the molecular regulatory mechanisms of bud mutations in L. olgensis remain unknown. In this study, dwarfed (or stunted), short-leaved, and multi-branched mutants of L. olgensis were found and utilized to identify crucial genes and regulatory networks controlling the multiple branch structure of L. olgensis. The physiological data showed that the branch number, bud number, fresh and dry weight, tracheid length, tracheid length-width ratio, inner tracheid diameter, and epidermal cell area of mutant plants were higher than that of wild-type plants. Hormone concentration measurements found that auxin, gibberellin, and abscisic acid in the mutant leaves were higher than that in wild-type plants. Moreover, the transcriptome sequencing of all samples using the Illumina Hiseq sequencing platform. Transcriptome analysis identified, respectively, 632, 157, and 199 differentially expressed genes (DEGs) in buds, leaves, and stems between mutant plants and wild type. DEGs were found to be involved in cell division and differentiation, shoot apical meristem activity, plant hormone biosynthesis, and sugar metabolism. Furthermore, bZIP, WRKY, and AP2/ERF family transcription factors play a role in bud formation. This study provides new insights into the molecular mechanisms of L. olgensis bud and branch formation and establishes a fundamental understanding of the breeding of new varieties in L. olgensis.

Transcriptomic and Weighted Gene Co-expression Correlation Network Analysis Reveal Resveratrol Biosynthesis Mechanisms Caused by Bud Sport in Grape Berry

Resveratrol is a natural polyphenol compound produced in response to biotic and abiotic stresses in grape berries. However, changes in resveratrol caused by bud sport in grapes are scarcely reported. In this study, trans-resveratrol and cis-resveratrol were identified and quantified in the grape berries of 'Summer Black' and its bud sport 'Nantaihutezao' from the veraison to ripening stages using ultra performance liquid chromatography-high resolution tandem mass spectrometry (UPLC-HRMS). We found that bud sport accumulates the trans-resveratrol earlier and increases the contents of cis-resveratrol in the earlier stages but decreases its contents in the later stages. Simultaneously, we used RNA-Seq to identify 51 transcripts involved in the stilbene pathways. In particular, we further identified 124 and 19 transcripts that negatively correlated with the contents of trans-resveratrol and cis-resveratrol, respectively, and four transcripts encoding F3'5'H that positively correlated with the contents of trans-resveratrol by weighted gene co-expression network analysis (WGCNA). These transcripts may play important roles in relation to the synergistic regulation of metabolisms of resveratrol. The results of this study can provide a theoretical basis for the genetic improvement of grapes.