Comparative and phylogenetic analysis of complete chloroplast genome sequences of Salvia regarding its worldwide distribution.

Salvia is widely used as medicine, food, and ornamental plants all over the world, with three main distribution centers, the Central and western Asia/Mediterranean (CAM), the East Aisa (EA), and the Central and South America (CASA). Along with its large number of species and world-wide distribution, Salvia is paraphyletic with multiple diversity. Chloroplast genomes (CPs) are useful tools for analyzing the phylogeny of plants at lower taxonomic levels. In this study, we reported chloroplast genomes of five species of Salvia and performed phylogenetic analysis with current available CPs of Salvia. Repeated sequence analysis and comparative analysis of Salvia CPs were also performed with representative species from different distribution centers. The results showed that the genetic characters of the CPs are related to the geographic distribution of plants. Species from CAM diverged first to form a separate group, followed by species from EA, and finally species from CASA. Larger variations of CPs were observed in species from CAM, whereas more deficient sequences and less repeated sequences in the CPs were observed in species from CASA. These results provide valuable information on the development and utilization of the worldwide genetic resources of Salvia.

A non-destructive testing method for early detection of ginseng root diseases using machine learning technologies based on leaf hyperspectral reflectance.

Ginseng is an important medicinal plant benefiting human health for thousands of years. Root disease is the main cause of ginseng yield loss. It is difficult to detect ginseng root disease by manual observation on the changes of leaves, as it takes a long time until symptoms appear on leaves after the infection on roots. In order to detect root diseases at early stages and limit their further spread, an efficient and non-destructive testing (NDT) method is urgently needed. Hyperspectral remote sensing technology was performed in this study to discern whether ginseng roots were diseased. Hyperspectral reflectance of leaves at 325-1,075 nm were collected from the ginsengs with no symptoms on leaves at visual. These spectra were divided into healthy and diseased groups according to the symptoms on roots after harvest. The hyperspectral data were used to construct machine learning classification models including random forest, extreme random tree (ET), adaptive boosting and gradient boosting decision tree respectively to identify diseased ginsengs, while calculating the vegetation indices and analyzing the region of specific spectral bands. The precision rates of the ET model preprocessed by savitzky golay method for the identification of healthy and diseased ginsengs reached 99% and 98%, respectively. Combined with the preliminary analysis of band importance, vegetation indices and physiological characteristics, 690-726 nm was screened out as a specific band for early detection of ginseng root diseases. Therefore, underground root diseases can be effectively detected at an early stage by leaf hyperspectral reflectance. The NDT method for early detection of ginsengs root diseases is proposed in this study. The method is helpful in the prevention and control of root diseases of ginsengs to prevent the reduction of ginseng yield.

The complete chloroplast genome and phylogenetic analysis of Salvia karwinskii (Lamiaceae).

Salvia karwinskii Benth. 1835 is a perennial herb in the Lamiaceae family native in Mexico and Central America. The complete chloroplast (cp) genome of S. karwinskii was sequenced using the Illumina platform and assembled for the first time. The complete plastid genome of S. karwinskii was 150,907 bp in length including a large single-copy (LSC) region of 82,205 bp, a small single-copy (SSC) region of 17,538 bp, and a pair of inverted repeat (IR) regions of 25,582 bp. The total GC content of this genome was 38.05%, and that of LSC, SSC, and IR regions was 36.22%, 31.77%, and 43.14%, respectively. The cp genome contained 114 unique genes, including 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. The maximum-likelihood phylogenetic tree was constructed with 38 complete cp genomes, supporting a close relationship between S. karwinskii and a 10 species lineage, all of which belong to the subg. Calosphace of Salvia. The cp genome of S. karwinskii provides a foundation for further studies on genetic diversity and improving the classification system of Salvia.

The complete chloroplast genome and phylogenetic analysis of Salvia oxyphora Briq. 1896 (Nepetoideae, Lamiaceae).

Salvia oxyphora Briq. 1896 is a perennial herb in the family Lamiaceae native to Central Bolivia. In this study, the chloroplast genome of S. oxyphora was sequenced using the Illumina platform and was assembled for the first time. The complete plastid genome of S. oxyphora was 151,014 bp in length including a large single-copy (LSC) region of 82,293 bp, a small single-copy (SSC) region of 17,531 bp, and a pair of inverted repeats (IR) regions of 25,595 bp. The total GC content of this genome was 38.04%, and that of LSC, SSC and IR regions was 36.21%, 31.80% and 43.13%, respectively. A total of 114 unique genes of this genome have been annotated, including 80 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. The maximum likelihood phylogenetic tree was constructed with 51 complete chloroplast genomes, illustrating the close relationship of S. oxyphora to the Brazil's native medicinal species S. splendens. The chloroplast genome of S. oxyphora provides a foundation for further studies on the adaptive evolution and genetic diversity of the genus Salvia.

Populus euphratica Phospholipase Dδ Increases Salt Tolerance by Regulating K+/Na+ and ROS Homeostasis in Arabidopsis.

Phospholipase Dα (PLDα), which produces signaling molecules phosphatidic acid (PA), has been shown to play a critical role in plants adapting to salt environments. However, it is unclear whether phospholipase Dδ (PLDδ) can mediate the salt response in higher plants. PePLDδ was isolated from salt-resistant Populus euphratica and transferred to Arabidopsis thaliana to testify the salt tolerance of transgenic plants. The NaCl treatment (130 mM) reduced the root growth and whole-plant fresh weight of wild-type (WT) A. thaliana, vector controls (VC) and PePLDδ-overexpressed lines, although a less pronounced effect was observed in transgenic plants. Under salt treatment, PePLDδ-transgenic Arabidopsis exhibited lower electrolyte leakage, malondialdehyde content and H2O2 levels than WT and VC, resulting from the activated antioxidant enzymes and upregulated transcripts of genes encoding superoxide dismutase, ascorbic acid peroxidase and peroxidase. In addition, PePLDδ-overexpressed plants increased the transcription of genes encoding the plasma membrane Na+/H+ antiporter (AtSOS1) and H+-ATPase (AtAHA2), which enabled transgenic plants to proceed with Na+ extrusion and reduce K+ loss under salinity. The capacity to regulate reactive oxygen species (ROS) and K+/Na+ homeostasis was associated with the abundance of specific PA species in plants overexpressing PePLDδ. PePLDδ-transgenic plants retained a typically higher abundance of PA species, 34:2 (16:0-18:2), 34:3 (16:0-18:3), 36:4 (18:2-18:2), 36:5 (18:2-18:3) and 36:6 (18:3-18:3), under control and saline conditions. It is noteworthy that PA species 34:2 (16:0-18:2), 34:3 (16:0-18:3), 36:4 (18:2-18:2) and 36:5 (18:2-18:3) markedly increased in response to NaCl in transgenic plants. In conclusion, we suppose that PePLDδ-derived PA enhanced the salinity tolerance by regulating ROS and K+/Na+ homeostasis in Arabidopsis.

Ectomycorrhizal Fungal Strains Facilitate Cd2+ Enrichment in a Woody Hyperaccumulator under Co-Existing Stress of Cadmium and Salt.

Cadmium (Cd2+) pollution occurring in salt-affected soils has become an increasing environmental concern in the world. Fast-growing poplars have been widely utilized for phytoremediation of soil contaminating heavy metals (HMs). However, the woody Cd2+-hyperaccumulator, Populus × canescens, is relatively salt-sensitive and therefore cannot be directly used to remediate HMs from salt-affected soils. The aim of the present study was to testify whether colonization of P. × canescens with ectomycorrhizal (EM) fungi, a strategy known to enhance salt tolerance, provides an opportunity for affordable remediation of Cd2+-polluted saline soils. Ectomycorrhization with Paxillus involutus strains facilitated Cd2+ enrichment in P. × canescens upon CdCl2 exposures (50 µM, 30 min to 24 h). The fungus-stimulated Cd2+ in roots was significantly restricted by inhibitors of plasmalemma H+-ATPases and Ca2+-permeable channels (CaPCs), but stimulated by an activator of plasmalemma H+-ATPases. NaCl (100 mM) lowered the transient and steady-state Cd2+ influx in roots and fungal mycelia. Noteworthy, P. involutus colonization partly reverted the salt suppression of Cd2+ uptake in poplar roots. EM fungus colonization upregulated transcription of plasmalemma H+-ATPases (PcHA4, 8, 11) and annexins (PcANN1, 2, 4), which might mediate Cd2+ conductance through CaPCs. EM roots retained relatively highly expressed PcHAs and PcANNs, thus facilitating Cd2+ enrichment under co-occurring stress of cadmium and salinity. We conclude that ectomycorrhization of woody hyperaccumulator species such as poplar could improve phytoremediation of Cd2+ in salt-affected areas.

Wood Formation under Severe Drought Invokes Adjustment of the Hormonal and Transcriptional Landscape in Poplar.

Drought is a severe environmental stress that exerts negative effects on plant growth. In trees, drought leads to reduced secondary growth and altered wood anatomy. The mechanisms underlying wood stress adaptation are not well understood. Here, we investigated the physiological, anatomical, hormonal, and transcriptional responses of poplar to strong drought. Drought-stressed xylem was characterized by higher vessel frequencies, smaller vessel lumina, and thicker secondary fiber cell walls. These changes were accompanied by strong increases in abscisic acid (ABA) and antagonistic changes in salicylic acid in wood. Transcriptional evidence supported ABA biosynthesis and signaling in wood. Since ABA signaling activates the fiber-thickening factor NST1, we expected upregulation of the secondary cell wall (SCW) cascade under stress. By contrast, transcription factors and biosynthesis genes for SCW formation were down-regulated, whereas a small set of cellulose synthase-like genes and a huge array of genes involved in cell wall modification were up-regulated in drought-stressed wood. Therefore, we suggest that ABA signaling monitors normal SCW biosynthesis and that drought causes a switch from normal to "stress wood" formation recruiting a dedicated set of genes for cell wall biosynthesis and remodeling. This proposition implies that drought-induced changes in cell wall properties underlie regulatory mechanisms distinct from those of normal wood.

Abscisic acid signalling mediates biomass trade-off and allocation in poplar.

Abscisic acid (ABA) is a well known stress hormone regulating drought adaptation of plants. Here, we hypothesised that genetic engineering of genes involved in ABA stress signalling and photoperiodic regulation affected drought resistance by trade-off with biomass production in perennial poplar trees. We grew Populus tremula × tremuloides wild-type (T89) and various transgenic lines (two transformation events of 35S::abi1-1, 35S::RCAR, RCAR:RNAi, 35S::ABI3, 35S::AREB3, 35S::FDL1, FDL1:RNAi, 35S::FDL2 and FDL2:RNAi) outdoors and exposed them to drought in the second growth period. After the winter, the surviving lines showed a huge variation in stomatal conductance, leaf size, whole-plant leaf area, tree height, stem diameter, and biomass. Whole-plant leaf area was a strong predictor for woody biomass production. The 35S::AREB3 lines were compromised in biomass production under well irrigated conditions compared with wild-type poplars but were resilient to drought. ABA signalling regulated FDL1 and FDL2 expression under stress. Poplar lines overexpressing FDL1 or FDL2 were drought-sensitive; they shed leaves and lost root biomass, whereas the FDL RNAi lines showed higher biomass allocation to roots under drought. These results assign a new function in drought acclimation to FDL genes aside from photoperiodic regulation. Our results imply a critical role for ABA-mediated processes in balancing biomass production and climate adaptation.

Evaluation of efficiency of controlled pollination based parentage analysis in a Larix gmelinii var. principis-rupprechtii Mayr. seed orchard.

Controlled pollination (CP) is an important tool for breeding programs to improve seed quality, as it rapidly generates desirable genotypes and maximizes genetic gains. However, few studies have evaluated the success rate of CP, especially in Larix gmelinii var. principis-rupprechtii Mayr. seed orchards. In this study, we estimated the rate of correct parentage in 257 CP progeny in an L. gmelinii var. principis-rupprechtii seed orchard from ten candidate parents using 13 microsatellites. The parentage exclusion probabilities of all combined loci in the single parent and parent pair tests were > 0.99, which was sufficient to distinguish the relatedness of the sampled individuals. Comparing the maximum likelihood-based parentage analysis results with breeding records revealed that the percentages of correctly identified maternal and paternal parents were 22.6% and 35.0% at 95% CL, respectively, suggestive of parent mislabeling and pollen contamination in the CP population. We conducted a pedigree reconstruction by identifying the expected parents and assigned maternity, paternity, and parent pairs to 176 (68.5%), 199 (77.4%), and 132 (51.4%) progeny, respectively. This study provides a reference for future selection of elite genotypes for commercial production. To increase the efficiency of CP, molecular markers should be used to correctly identify individuals in seed orchards before conducting CP.

[Teaching design and practice of human blood type traits in genetics comprehensive laboratory course].

Comprehensive laboratory courses, which enable students to aptly apply theoretic knowledge and master experiment skills, play an important role in the present educational reform of laboratory courses. We utilized human ABO blood type as the experimental subject, and designed the experiment--"Molecular Genotyping of Human ABO Blood Type and Analysis of Population Genetic Equilibrium". In the experiment, DNA in mucosal cells is extracted from students' saliva, and each student's genotype is identified using a series of molecular genetics technologies, including PCR amplification of target fragments, enzymatic digestion, and electrophoretic separation. Then, taking the whole class as an analogous Mendel population, a survey of genotype frequency of ABO blood type is conducted, followed with analyses of various population genetic parameters using Popgene. Through the open laboratory course, students can not only master molecular genetic experimental skills, but also improve their understanding of theoretic knowledge through independent design and optimization of molecular techniques. After five years of research and practice, a stable experimental system of molecular genetics has been established to identify six genotypes of ABO blood types, namely I(A)I(A), I(A)i, I(B)I(B), I(B)i, I(A)I(B) and ii. Laboratory courses of molecular and population genetics have been integrated by calculating the frequencies of the six genotypes and three multiple alleles and testing population genetic equilibrium. The goal of the open laboratory course with independent design and implementation by the students has been achieved. This laboratory course has proved effective and received good reviews from the students. It could be applied as a genetics laboratory course for the biology majors directly, and its ideas and methods could be promoted and applied to other biological laboratory courses.