Genetic Architecture of Heterophylly: Single and Multi-Leaf Genome-Wide Association Mapping in Populus euphratica.

Heterophylly is an adaptive strategy used by some plants in response to environmental changes. Due to the lack of representative plants with typical heteromorphic leaves, little is known about the genetic architecture of heterophylly in plants and the genes underlying its control. Here, we investigated the genetic characteristics underlying changes in leaf shape based on the model species, Populus euphratica, which exhibits typical heterophylly. A set of 401,571 single-nucleotide polymorphisms (SNPs) derived from whole-genome sequencing of 860 genotypes were associated with nine leaf traits, which were related to descriptive and shape data using single- and multi-leaf genome-wide association studies (GWAS). Multi-leaf GWAS allows for a more comprehensive understanding of the genetic architecture of heterophylly by considering multiple leaves simultaneously. The single-leaf GWAS detected 140 significant SNPs, whereas the multi-leaf GWAS detected 200 SNP-trait associations. Markers were found across 19 chromosomes, and 21 unique genes were implicated in traits and serve as potential targets for selection. Our results provide novel insights into the genomic architecture of heterophylly, and provide candidate genes for breeding or engineering P. euphratica. Our observations also improve understanding of the intrinsic mechanisms of plant growth, evolution, and adaptation in response to climate change.

Selective thermotherapy of tumor by self-regulating photothermal conversion system.

One major challenge of photothermal therapy (PTT) is achieving thermal ablation of the tumor without damaging the normal cells and tissues. Here, we designed a self-regulating photothermal conversion system for selective thermotherapy based on self-assembling gold nanoparticles (S-AuNPs) and investigated the selectivity effect using a novel home-made in vitro selective photothermal transformation model and an in vivo skin damaging assessment model. In the in vitro selective photothermal transformation model, laser irradiation selectively increased the temperature of the internal microenvironment (pH 5.5) and resulted in an obvious temperature difference (ΔT ≥ 5 °C) with that of the external environment (pH 7.4). More importantly, in the in vivo skin damaging assessment model, S-AuNPs achieved good tumor inhibition without damaging the normal skin tissue compared with the conventional photothermal material. This work provides not only a novel validation protocol for tumor thermotherapy to achieve the biosafety of specifically killing tumor cells and normal tissue but also an evaluation methodology for other precise therapy for cancers.

Functional mapping of gravitropism and phototropism for a desert tree, Populus euphratica.

Background: Plants have evolved the dual capacity for maximizing light assimilation through stem growth (phototropism) and maximizing water and nutrient absorption through root growth (gravitropism). Previous studies have revealed the physiological and molecular mechanisms of these two processes, but the genetic basis for how gravitropism and phototropism interact and coordinate with one another to determine plant growth remains poorly understood. Methods: We designed a seed germination experiment using a full-sib F1 family of Populus euphratica to simultaneously monitor the gravitropic growth of the radicle and the phototropic growth of the plumule throughout seedling ontogeny. We implemented three functional mapping models to identify quantitative trait loci (QTLs) that regulate gravitropic and phototropic growth. Univariate functional mapping dissected each growth trait separately, bivariate functional mapping mapped two growth traits simultaneously, and composite functional mapping mapped the sum of gravitropic and phototropic growth as a main axis. Results: Bivariate model detected 8 QTLs for gravitropism and phototropism (QWRF, GLUR, F-box, PCFS4, UBQ, TAF12, BHLH95, TMN8), composite model detected 7 QTLs for growth of main axis (ATL8, NEFH, PCFS4, UBQ, SOT16, MOR1, PCMP-H), of which, PCFS4 and UBQ were pleiotropically detected with the both model. Many of these QTLs are situated within the genomic regions of candidate genes. Conclusions: The results from our models provide new insight into the mechanisms of genetic control of gravitropism and phototropism in a desert tree, and will stimulate our understanding of the relationships between gravity and light signal transduction pathways and tree adaptation to arid soil.

Dual Modal Imaging-Guided Drug Delivery System for Combined Chemo-Photothermal Melanoma Therapy.

PURPOSE: Malignant melanoma is one of the most devastating types of cancer with rapid relapse and low survival rate. Novel strategies for melanoma treatment are currently needed to enhance therapeutic efficiency for this disease. In this study, we fabricated a multifunctional drug delivery system that incorporates dacarbazine (DTIC) and indocyanine green (ICG) into manganese-doped mesoporous silica nanoparticles (MSN(Mn)) coupled with magnetic resonance imaging (MRI) and photothermal imaging (PI), for achieving the superior antitumor effect of combined chemo-photothermal therapy. MATERIALS AND METHODS: MSN(Mn) were characterized in terms of size and structural properties, and drug loading and release efficiency MSN(Mn)-ICG/DTIC were analyzed by UV spectra. Photothermal imaging effect and MR imaging effect of MSN(Mn)-ICG/DTIC were detected by thermal imaging system and 3.0 T MRI scanner, respectively. Then, the combined chemo-phototherapy was verified in vitro and in vivo by morphological evaluation, ultrasonic and pathological evaluation. RESULTS: The as-synthesized MSN(Mn) were characterized as mesoporous spherical nanoparticles with 125.57±5.96 nm. MSN(Mn)-ICG/DTIC have the function of drug loading-release which loading ratio of ICG and DTIC could reach to 34.25±2.20% and 50.00±3.24%, and 32.68±2.10% of DTIC was released, respectively. Manganese doping content could reach up to 65.09±2.55 wt%, providing excellent imaging capability in vivo which the corresponding relaxation efficiency was 14.33 mM-1s-1. And outstanding photothermal heating ability and stability highlighted the potential biomedical applicability of MSN(Mn)-ICG/DTIC to kill cancer cells. Experiments by A375 melanoma cells and tumor-bearing mice demonstrated that the compound MSN(Mn)-ICG/DTIC have excellent biocompatibility and our combined therapy platform delivered a superior antitumor effect compared to standalone treatment in vivo and in vitro. CONCLUSION: Our findings demonstrate that composite MSN(Mn)-ICG/DTIC could serve as a multifunctional platform to achieve a highly effective chemo-photothermal combined therapy for melanoma treatment.

Long-read genome assembly and genetic architecture of fruit shape in the bottle gourd.

The bottle gourd (Lagenaria siceraria, Cucurbitaceae) is an important horticultural crop exhibiting tremendous diversity in fruit shape. The genetic architecture of fruit shape variation in this species remains unknown. We assembled a long-read-based, high-quality reference genome (ZAAS_Lsic_2.0) with a contig N50 value over 390-fold greater than the existing reference genomes. We then focused on dissection of fruit shape using a one-step geometric morphometrics-based functional mapping approach. We identified 11 quantitative trait loci (QTLs) responsible for fruit shape (fsQTLs), reconstructed their visible effects and revealed syntenic relationships of bottle gourd fsQTLs with 12 fsQTLs previously reported in cucumber, melon or watermelon. Homologs of several well-known and newly identified fruit shape genes, including SUN, OFP, AP2 and auxin transporters, were comapped with bottle gourd QTLs.

Preparation of mitochondria to measure superoxide flashes in angiosperm flowers.

BACKGROUND: Mitochondria are the center of energy metabolism and the production of reactive oxygen species (ROS). ROS production results in a burst of "superoxide flashes", which is always accompanied by depolarization of mitochondrial membrane potential. Superoxide flashes have only been studied in the model plant Arabidopsis thaliana using a complex method to isolate mitochondria. In this study, we present an efficient, easier method to isolate functional mitochondria from floral tissues to measure superoxide flashes. METHOD: We used 0.5 g samples to isolate mitochondria within <1.5 h from flowers of two non-transgenic plants (Magnolia denudata and Nelumbo nucifera) to measure superoxide flashes. Superoxide flashes were visualized by the pH-insensitive indicator MitoSOX Red, while the mitochondrial membrane potential (ΔΨ m) was labelled with TMRM. RESULTS: Mitochondria isolated using our method showed a high respiration ratio. Our results indicate that the location of ROS and mitochondria was in a good coincidence. Increased ROS together with a higher frequency of superoxide flashes was found in mitochondria isolated from the flower pistil. Furthermore, a higher rate of depolarization of the ΔΨ m was observed in the pistil. Taken together, these results demonstrate that the frequency of superoxide flashes is closely related to depolarization of the ΔΨ m in petals and pistils of flowers.

Differential profiling analysis of miRNAs reveals a regulatory role in low N stress response of Populus.

Nitrogen (N) is an essential mineral element for plant growth processes, and its availability severely affects the productivity of plants, especially trees. MicroRNAs (miRNAs) are a class of non-coding RNAs approximately 21 nucleotides in length that play important roles in plant growth, development and stress responses. To identify Populus miRNAs and their functions in response to nutrition stress, high-throughput sequencing was performed using Populus tomentosa plantlets treated with or without low concentrations of N. We identified 160 conserved miRNAs, 15 known but non-conserved miRNAs, 2 candidate novel miRNAs and 71 corresponding miRNA*s. Differential expression analysis showed that expression of the 21 conserved miRNA families was significantly altered. Real-time quantitative PCR (qPCR) was used to further validate and analyze the dynamic expression of the identified miRNAs. A total of 218 target genes from the low-N-responsive miRNAs were predicted, and their functions were further annotated in combination with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. These results suggest that miRNAs play important roles in the response of Populus to low N stress. Furthermore, this study provides the first identification and profiles of N stress-responsive miRNAs from trees.

Genome-wide identification and expression analysis of heat-responsive and novel microRNAs in Populus tomentosa.

Plant microRNAs have a vital role in various abiotic stress responses by regulating gene expression. Heat stress is one of the most severe abiotic stresses, and affects plant growth and development, even leading to death. To identify heat-responsive miRNAs at the genome-wide level in Populus, Solexa sequencing was employed to sequence two libraries from Populus tomentosa, treated and untreated by heat stress. Sequence analysis identified 134 conserved miRNAs belonging to 30 miRNA families, and 16 novel miRNAs belonging to 14 families. Among these miRNAs, 52 miRNAs from 15 families were responsive to heat stress and most of them were down-regulated. qRT-PCR analysis confirmed that the conserved and novel miRNAs were expressed in P. tomentosa, and revealed similar expression trends to the Solexa sequencing results obtained under heat stress. One hundred and nine targets of the novel miRNAs were predicted. This study opens up a new avenue for understanding the regulatory mechanisms of miRNAs involvement in the heat stress response of trees.