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Ficus carica Linn. is an important economic tree species with high developmental prospects and scientific research for edible and medicinal value. The F. carica chloroplast genome has recently been reported; however, the mitochondrial genome is still unexplored. We assembled the complete mitogenome of F. carica using reads from PacBio Biosciences sequencing platforms. The circular mitogenome F. carica has a length of 480,902 base pairs (bp), which contain 46 genes, including 27 protein-coding genes, 16 transfer RNA (tRNA) genes, and three ribosomal RNA (rRNA) genes. The base composition, codon usage, sequence repeats, RNA editing, and selective pressure were examined. We also conducted the phylogenetic analysis based on the mitogenomes of F. carica and 21 other taxa to know the evolutionary and taxonomic status of F. carica. Our analyses provided comprehensive information on the F. carica mitochondrial genome, which would facilitate evolutionary research in other fruit trees in the future.
Rubber dandelion (Taraxacum kok-saghyz) is a natural rubber-producing dandelion that has the potential to become an industrial crop. Inulin is a storage carbohydrate in rubber dandelion, and its synthesis competes with rubber production for assimilated carbon. We used the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) system to simultaneously target two sites in the gene that encodes 1-fructan:fructan-1-fructosyl transferase gene (1-FFT), a key enzyme in inulin biosynthesis. Agrobacterium rhizogenes and Agrobacterium tumefaciens-mediated plant transformation methods were used to generate transgenic plants with CRISPR/Cas9 elements. Transformation rates were 71% and 64% via A. rhizogenes and A. tumefaciens-mediated transformations, respectively. Mutagenesis was confirmed by the loss of restriction site method and Sanger sequencing. Of 13 transgenic plants obtained via A. rhizogenes, six showed editing of both target sites within the 1-FFT gene. Transgenic rubber dandelion plants were obtained within 10 weeks using A. rhizogenes-mediated transformation, which was much faster than the 6 months required for A. tumafaciens transformants. Of 11 transgenic plants obtained via A. tumefaciens, five showed mutations in both target sites. Reverse-transcription polymerase chain reaction confirmed Cas9 expression in all edited transformants. Both A. rhizogenes-mediated double-mutant transformants and A. tumefaciens-mediated double mutant transformants had lower levels of inulin than wild-type plants. Moreover, A. rhizogenes-mediated transformants had a higher rubber content than wild-type plants. Therefore, the present study validates the use of CRISPR/Cas9 gene editing as an efficient tool for the generation of useful mutations in rubber dandelion and could be implemented in future crop improvement approaches.
Far-red photons (700–750 nm) can accelerate crop growth during indoor production through both physiological and morphological processes. A previous study showed that far-red photons can drive photosynthesis with efficiency similar to that of traditionally defined photosynthetically active photons (400–700 nm) if they are provided together with shorter-wavelength photons. Far-red photons also promote leaf and canopy expansion, which can increase light interception and growth. This study aimed to distinguish the contribution of morphological and physiological changes to crop growth induced by substituting red photons with far-red photons. We studied the long-term effects of substituting red photons with far-red photons on canopy light interception and whole-plant photosynthesis. ‘Little Gem’ lettuce (Lactuca sativa) seedlings were grown under four light spectrums of the same total photon flux density (400–750 nm). In addition to a background of a mixture of white and blue photons of 150 μmol⋅m−2⋅s−1, we provided 51 μmol⋅m−2⋅s−1 red photons, far-red photons, or mixtures of red and far-red photons. In the first run, plants were harvested twice. The first harvest was at canopy closure, and the second harvest was when plants reached full size. In the second run, we harvested lettuce plants more frequently to minimize leaf overlap and interplant competition. We found that far-red photon substitution promoted leaf and canopy expansion and increased light interception. The effect of far-red photon substitution on leaf and canopy expansion was stronger in the second run than in the first run, likely because of lower plant density in the second run when plants were harvested more frequently. Far-red photon substitution of red photons decreased the amount of extended photosynthetically active radiation (ePAR) photons (400–750 nm) absorbed by leaves because of the lower leaf absorptance of far-red photons. The greater effect on canopy expansion in the second run of far-red photons substitution was able to exceed the reduction of ePAR photon absorption by leaves; therefore, we observed an increased crop gross photosynthetic rate (Pg) between the second and third harvests during the second run. However, during the first run, lower absorptance of ePAR completely offset the effect of the greater canopy size and light interception, and crop Pg was decreased in the first run before the first harvest. The changes in light interception and crop Pg resulting from far-red photon substitution did not affect dry weight. Far-red photons had photosynthetic activity when applied with a blue and white light mixture, but their efficiency was approximately half that of red photons, potentially because of the lower absorptance of far-red photons. In conclusion, far-red photon substitution of red photons increased canopy size but decreased ePAR photons absorbed by leaves and did not increase the final dry weight. Because far-red light-emitting diodes (LEDs) have higher efficacy for converting electricity into photons, including far-red LEDs in fixtures for sole-source lighting can reduce energy costs without decreasing lettuce yields.
The branch number of plants is an important agronomic trait that directly influences the ornamental characters and production costs of ornamental plants. Shoot branching has always been a hot topic for Petunia hybrida. During our research, we isolated the homologous gene of narrow-leaf 1 (NAL1), denoted as PhNAL1. The expression level of PhNAL1 was higher in leaves and axils than in roots, stems, and flowers. Pertinent to shoot apex removal and 6-benzyladenine treatments, both interventions demonstrated a suppressive effect on the expression of PhNAL1. Through subcellular localization analysis, we found that PhNAL1 predominantly localized in the nucleus. By using RNA interference targeting PhNAL1, we induced a noticeable increase in branch number while concurrently reducing plant height of petunia. These findings demonstrate that PhNAL1 is involved in regulating branch development within petunia. This study provides genetic resources for the subsequent cultivation of new cultivars of petunia endowed with distinct branching characteristics.
A fully split shell in pistachio (Pistacia vera) is a trait that is preferred by consumers and is a criterion in evaluating the grade of the pistachio nut. However, although the expanding kernel has been hypothesized to provide the physical force needed for shell split, the mechanisms that control shell split remain unknown. Furthermore, it is intriguing how the shell, or endocarp, splits at the suture ridge when there is no clear dehiscence zone. The objectives of this study were 1) to identify traits associated with dehiscence in fruit in the high-split rate cultivar Golden Hills when compared with the lower split rate cultivar Kerman and determine the anatomic features associated with endocarp dehiscence at the suture region, and 2) to examine the effect of kernel shape on endocarp dehiscence. We determined that, despite the fact that the pistachio endocarp is composed primarily of a single type of polylobate sclerenchyma cell, specialization of cell shape and size at the suture site results in smaller, more flattened cells. We report there is a furrowing of the shell at the dorsal and apical suture sites, where dehiscence initiates. This furrowing is not observed at the ventral suture site or in the indehiscent fruit of Pistacia atlantica, a species that has been used as rootstock for P. vera. In addition, the size of the kernel in the sagittal axis (the width) is strongly associated with a greater split rate. Based on our results, a tentative model emerges in which, in the absence of specialized cell types, cell shape modification can create an anatomically distinct region that is mechanically weak in the endocarp for the initiation of dehiscence, whereas the force from the width of the kernel is necessary for the shell split rate difference as observed in cultivars.
We evaluated the genetic diversity of a newly available collection of 94 almond [Prunus dulcis (Mill.) D.A. Webb] accessions from the former Improving Perennial Plants for Food and Bioenergy (IPPFBE) Foundation. Most of the collection (87 accessions) were collected as seeds from trees growing in the central Asian nations of Kyrgyzstan, Tajikistan, and Uzbekistan, and included several examples of Prunus bucharica (Korsh.) Hand.-Mazz, and related wild species. Of the remaining accessions, six were sourced from a nursery in northern Utah in the United States, and one was a seedling of ‘Nonpareil’, a major commercial cultivar. DNA fingerprints were generated from 10 simple sequence repeat markers. To evaluate the comparative diversity of these new accessions, 66 accessions from the US Department of Agriculture, National Plant Germplasm System (NPGS) almond germplasm collection near Davis, CA, USA, were also included. These NPGS accessions were chosen to represent those collected in similar regions of Central Asia and the Caucasus. The fingerprints were analyzed via hierarchical clustering, principal components analysis (PCA), and discriminant analysis of principal components (DAPC). Hierarchical clustering suggested that half of the Utah-sourced accessions are closely related to each other and to the ‘Nonpareil’ seedling. Additional close relationships were detected (including at least one duplication or mislabeling), and two P. bucharica accessions from the IPPFBE collection were separated from the rest of the collection. A plot of the first two principal components clearly separated wild almond relatives (P. bucharica and Prunus fenzliana Fritsch) from the remaining accessions. PCA after removal of the wild species separated the ‘Nonpareil’ seedling, the Utah-sourced accessions, and many of the IPPFBE accessions (mostly from Uzbekistan) from nearly all other individuals. The third principal component identified an additional population structure that separated groups of predominantly IPPFBE or NPGS accessions. DAPC showed a considerable admixture of accessions from Azerbaijan, and a little to no admixture of accessions from Georgia and Tajikistan. These results suggest that central Asian/Caucasian almond germplasm is generally distinct from ‘Nonpareil’ and its relatives, and that although there is overlap between the NPGS and IPPFBE collections from this region, the IPPFBE collection does enhance the diversity of available almond germplasm.
The Oomycete plant pathogen, Phytophthora capsici, causes root, crown, and fruit rot of winter squash (Cucurbita moschata) and limits production. Some C. moschata cultivars develop age-related resistance (ARR), whereby fruit develop resistance to P. capsici 14 to 21 days postpollination (DPP) because of thickened exocarp; however, wounding negates ARR. We uncovered the genetic mechanisms of ARR of two C. moschata cultivars, Chieftain and Dickenson Field, that exhibit ARR at 14 and 21 DPP, respectively, using RNA sequencing. The sequencing was conducted using RNA samples from ‘Chieftain’ and ‘Dickenson Field’ fruit at 7, 10, 14, and 21 DPP. A differential expression and subsequent gene set enrichment analysis revealed an overrepresentation of upregulated genes in functional categories relevant to cell wall structure biosynthesis, cell wall modification/organization, transcription regulation, and metabolic processes. A pathway enrichment analysis detected upregulated genes in cutin, suberin monomer, and phenylpropanoid biosynthetic pathways. A further analysis of the expression profile of genes in those pathways revealed upregulation of genes in monolignol biosynthesis and lignin polymerization in the resistant fruit peel. Our findings suggest a shift in gene expression toward the physical strengthening of the cell wall associated with ARR to P. capsici. These findings provide candidate genes for developing Cucurbita cultivars with resistance to P. capsici and improve fruit rot management in Cucurbita species.