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Background Understanding the molecular basis of sport mutations in fruit trees has the potential to accelerate generation of improved cultivars. Results For this, we analyzed the genome of the apple tree that developed the RubyMac phenotype through a sport mutation that led to the characteristic fruit coloring of this variety. Overall, we found 46 somatic mutations that distinguished the mutant and wild-type branches of the tree. In addition, we found 54 somatic gene conversions (i.e., loss-of-heterozygosity mutations) that also distinguished the two parts of the tree. Approximately 20% of the mutations were specific to individual cell lineages, suggesting that they originated from the corresponding meristematic layers. Interestingly, the de novo mutations were enriched for GC =  > AT transitions while the gene conversions showed the opposite bias for AT =  > GC transitions, suggesting that GC-biased gene conversions have the potential to counteract the AT-bias of de novo mutations. By comparing the gene expression patterns in fruit skins from mutant and wild-type branches, we found 56 differentially expressed genes including 18 involved in anthocyanin biosynthesis. While none of the differently expressed genes harbored a somatic mutation, we found that some of them in regions of the genome that were recently associated with natural variation in fruit coloration. Conclusion Our analysis revealed insights in the characteristics of somatic change, which not only included de novo mutations but also gene conversions. Some of these somatic changes displayed strong candidate mutations for the change in fruit coloration in RubyMac .

Root system architecture (RSA) is critical for improving nutrient and water uptake and maintaining crop yield under both optimal and drought conditions. The meristematic zone of root tips is ideal for studying RSA, because of its high mitotic rate. miRNAs are important post-transcriptional regulators and play a crucial role in plant response to drought stress. To decipher the changes in miRNA expression patterns under drought stress, sequencing of small RNAs in the meristematic root tips of the highly tolerant genotypes Azucena and the susceptible IR64 was performed. Prediction of target genes of differentially expressed miRNAs (DEMs) in drought-stressed Azucena compared with normal conditions revealed that these genes mainly encode aquaporin, AP2, DELLA protein, ERF, and OsIAA18-auxin responsive. Most of these genes are involved in the regulation of response to stress, meristem growth, ethylene-activated signaling pathway, post-transcriptional regulation, and lipid metabolism. Whereas, the predicted target genes in IR64 under the same conditions were mainly involved in controlling carbohydrate biosynthesis, lignin catabolism, primary metabolic processes, cell death, and RNAi. This result shows that IR64 promotes thickening of cell walls to cope with stress, while lateral root system expansion and root length are used as a strategy to cope with drought stress in Azucena. Azucena-specific down-regulation of miR164-NAC5, miR1857-MADX-box5, miR1861-EXP1, and miR169-NF-YA may be the main reason for root elongation, root system development, and stress adaptation of this genotype. Moreover, miR528 and miR398, which serve as hub regulators, and target redox-related enzymes such as SOD and peroxidase (POX) to control cellular homeostasis in response to drought stress, were down-regulated in Azucena. Furthermore, our histochemical assay also confirmed the fact that the cell wall thickness of the root tips was increased in the drought-sensitive IR64 for insulation purposes to cope with stress. However, this may substantially reduce its ability to extend roots to obtain water from deeper soil layers. Our results shed light on drought-related miRNA regulatory networks as well as important miRNAs that have the potential to further improve drought tolerance in rice.

Organisms are increasingly exposed to ultraviolet (UV) rays of sunlight, due to the thinning of the ozone layer and its widespread use in sterilization processes, especially against the SARS-CoV-2 virus. The present study was conducted with the purpose of evaluating the damages of UV-A and UV-C radiations in Allium cepa L. roots. The effects of two different types of UV on some physiological, biochemical, cytogenotoxic, and anatomical parameters were investigated in a multifaceted study. Three groups were formed from Allium bulbs, one of which was the control group. One of the other groups was exposed to 254 nm (UV-C) and the other to 365 nm (UV-A) UV. Growth retardation effect of UV was investigated with respect to germination percentage, total weight gain, and root elongation, while cytogenotoxicity arisen from UV exposure was analyzed using mitotic index (MI) and chromosomal aberration (CA) and micronucleus (MN) frequency. Oxidative stress due to UV application was investigated based on the accumulation of malondialdehyde (MDA) and the total activities of superoxide dismutase (SOD) and catalase (CAT) enzymes. Also, anatomical changes induced by UV-A and UV-C were analyzed in root meristematic cells. UV treatments caused significant reductions in growth-related parameters. Both UV treatments caused a significant increase in MDA levels and induction of SOD and CAT enzymes in root meristematic cells. A decrease in MI and an increase in the frequency of MN and CAs were observed in root tip cells, indicating the cytogenotoxic effect of UV application. Anatomical damages such as epidermis cell damage, cortex cell damage, necrotic zones, giant cell nucleus, and indistinct transmission tissue occurred in cells exposed to UV. All of the physiological, biochemical, cytogenetic, and anatomical damages observed in this study were more severe in cells treated with UV-C compared to UV-A. This study suggested that UV exposure triggered growth inhibition, cytogenotoxicity, oxidative stress, and meristematic cell damages in A. cepa roots depending on the wavelength.

When thin cell layers (TCLn), isolated from the nodalregion of the hypocotyl of 5 day old seedlings, werecultured in medium M1 with IAA and BA, entire plantswere obtained from L. mutabilis explants andprolific shoots from L. albus explants.Histological studies carried out on L. mutabilisTCLn showed that meristematic cells, present in theexplants at the time of inoculation, gave rise to theformation of a primary meristem resulting inorganogenesis. In TCLn where apical or axillarymeristematic cells were absent, we observed theformation of a nodular structure with a cambium-likelayer at its periphery which divided to form a primarymeristem leading to organogenesis. Plant regenerationfrom TCLn may be useful in genetic transformationassays.[PUBLICATION ABSTRACT]