Identification of quantitative trait loci and candidate genes for cadmium tolerance in Populus

Prime editing in plants and mammalian cells: Mechanism, achievements, limitations, and future prospects

Clustered, regularly interspaced, short palindromic repeat (CRISPR)/CRISPR-associated protein (CRISPR/Cas) system has revolutionized genetic research in the life sciences. Four classes of CRISPR/Cas-derived genome editing agents, such as nuclease, base editor, recombinase, and prime editor have been introduced for engineering the genomes of diverse organisms. The recently introduced prime editing system offers precise editing without many off-target effects than traditional CRISPR-based systems. Many researchers have successfully applied this gene-editing toolbox in diverse systems for various genome-editing applications. This review presents the mechanism of prime editing and summarizes the details of the prime editing system applied in plants and mammalian cells for precise genome editing. We also discuss the advantages, limitations, and potential future applications of prime editing in these systems. This review enables the researcher to gain knowledge on prime editing tools and their potential applications in plants and mammalian cells.

ATP-binding cassette transporters in nonmodel plants

Knowledge about plant ATP-binding cassette (ABC) proteins is of great value for sustainable agriculture, economic yield, and the generation of high-quality products, especially under unfavorable growth conditions. We have learned much about ABC proteins in model organisms, notably Arabidopsis thaliana; however, the importance of research dedicated to these transporters extends far beyond Arabidopsis biology. Recent progress in genomic and transcriptomic approaches for nonmodel and noncanonical model plants allows us to look at ABC transporters from a wider perspective and consider chemodiversity and functionally driven adaptation as distinctive mechanisms during their evolution. Here, by considering several representatives from agriculturally important families and recent progress in functional characterization of nonArabidopsis ABC proteins, we aim to bring attention to understanding the evolutionary background, distribution among lineages and possible mechanisms underlying the adaptation of this versatile transport system for plant needs. Increasing the knowledge of ABC proteins in nonmodel plants will facilitate breeding and development of new varieties based on, for example, genetic variations of endogenous genes and/or genome editing, representing an alternative to transgenic approaches.

Construction of a high-density genetic map using specific-length amplified fragment markers and identification of QTLs for branching angle in poplar

Branching angle is a critical factor that determines the morphological establishment and is a typical quantitative trait controlled by multiple genes. In this study, we used SLAF-seq to construct a high-density genetic map, to investigate the genetic architecture of branching angle in poplar (Populus leucopyramidalis). A total of 240,672 SLAF tags were obtained, including 103,691 polymorphic SLAF tags. After filtering, 53,407 polymorphic markers were sorted into eight segregation types, and 11,162 of them were used to construct the genetic map. 8447 were on the female parent map, 8532 were on the male parent map, and 11,162 were on the integrated map. The marker coverage was 4820.84 and 5044.80 cM for the female and male maps, and 3142.61 cM for the integrated map. The average intervals between two adjacent mapped markers were 0.55, 0.59, and 0.28 cM for the three maps, respectively. Two quantitative trait loci (QTLs) were detected. Seven markers that exceeded the threshold in these two regions were considered as being associated with branching angle and the phenotypic variance explained by each of these marker was 10.64-11.66%. After functional annotation, we identified 15 candidate genes and analyzed the expression of candidate genes in narrow and wide crown progenies by qRT-PCR. These results show that the combination of QTL and SLAF-seq will contribute to future breeding plans in poplar breeding, especially in narrow crown poplar breeding.

Comparative analysis of the stellacyanins (SCs) family and focus on drought resistance of PtSC18 in Populus trichocarpa

Stellacyanin (SC) is a type I (blue) copper protein, which plays a crucial role in plant growth and stress response. However, the comprehensive analysis and functional research of SCs in the woody plant is still lacking. Here, a total of 74 SCs were collected and identified from Arabidopsis, papaya, grape, rice and poplar. Bioinformatics was used to analyze the gene structure, protein structure and evolutionary relationship of 74 genes, especially 19 SCs in Populus trichocarpa. Based on the RNA-seq data, expression pattern of SCs in poplar under cold, high temperature, drought and salt stress were further analyzed. Subsequently, a key candidate gene PtSC18 that strongly responded to drought stress was screened. Subcellular localization experiment exhibited that PtSC18 was localized in the nucleus and plasma membrane. Overexpression of PtSC18 enhanced drought tolerance of transgenic Arabidopsis by improving water retention and reducing oxidative damage. Measurements of physiological indicators, including chlorophyll, H₂O₂, malondialdehyde content, peroxidase and catalase enzyme activities and electrical conductivity, all supported this conclusion. More importantly, PtSC18 enhanced the expression of some stress-related genes in transgenic Arabidopsis. Overall, our results lay a foundation for understanding the structure and function of PtSCs and provide useful gene resources for breeding through genetic engineering.

Ionomic Approaches for Discovery of Novel Stress-Resilient Genes in Plants

Plants, being sessile, face an array of biotic and abiotic stresses in their lifespan that endanger their survival. Hence, optimized uptake of mineral nutrients creates potential new routes for enhancing plant health and stress resilience. Recently, minerals (both essential and non-essential) have been identified as key players in plant stress biology, owing to their multifaceted functions. However, a realistic understanding of the relationship between different ions and stresses is lacking. In this context, ionomics will provide new platforms for not only understanding the function of the plant ionome during stresses but also identifying the genes and regulatory pathways related to mineral accumulation, transportation, and involvement in different molecular mechanisms under normal or stress conditions. This article provides a general overview of ionomics and the integration of high-throughput ionomic approaches with other "omics" tools. Integrated omics analysis is highly suitable for identification of the genes for various traits that confer biotic and abiotic stress tolerance. Moreover, ionomics advances being used to identify loci using qualitative trait loci and genome-wide association analysis of element uptake and transport within plant tissues, as well as genetic variation within species, are discussed. Furthermore, recent developments in ionomics for the discovery of stress-tolerant genes in plants have also been addressed; these can be used to produce more robust crops with a high nutritional value for sustainable agriculture.

CRISPR-Based Genome Editing Tools: Insights into Technological Breakthroughs and Future Challenges

Genome-editing (GE) is having a tremendous influence around the globe in the life science community. Among its versatile uses, the desired modifications of genes, and more importantly the transgene (DNA)-free approach to develop genetically modified organism (GMO), are of special interest. The recent and rapid developments in genome-editing technology have given rise to hopes to achieve global food security in a sustainable manner. We here discuss recent developments in CRISPR-based genome-editing tools for crop improvement concerning adaptation, opportunities, and challenges. Some of the notable advances highlighted here include the development of transgene (DNA)-free genome plants, the availability of compatible nucleases, and the development of safe and effective CRISPR delivery vehicles for plant genome editing, multi-gene targeting and complex genome editing, base editing and prime editing to achieve more complex genetic engineering. Additionally, new avenues that facilitate fine-tuning plant gene regulation have also been addressed. In spite of the tremendous potential of CRISPR and other gene editing tools, major challenges remain. Some of the challenges are related to the practical advances required for the efficient delivery of CRISPR reagents and for precision genome editing, while others come from government policies and public acceptance. This review will therefore be helpful to gain insights into technological advances, its applications, and future challenges for crop improvement.

The Role of Aquaporin Overexpression in the Modulation of Transcription of Heavy Metal Transporters under Cadmium Treatment in Poplar

Populus alba ‘Villafranca’ clone is well-known for its tolerance to cadmium (Cd). To determine the mechanisms of Cd tolerance of this species, wild-type (wt) plants were compared with transgenic plants over-expressing an aquaporin (aqua1, GenBank GQ918138). Plants were maintained in hydroponic conditions with Hoagland’s solution and treated with 10 µM of Cd, renewed every 5 d. The transcription levels of heavy metal transporter genes (PaHMA2, PaNRAMP1.3, PaNRAMP2, PaNRAMP3.1, PaNRAMP3.2, PaABCC9, and PaABCC13) were analyzed at 1, 7, and 60 d of treatment. Cd application did not induce visible toxicity symptoms in wt and aqua1 plants even after 2 months of treatment confirming the high tolerance of this poplar species to Cd. Most of the analyzed genes showed in wt plants a quick response in transcription at 1 d of treatment and an adaptation at 60 d. On the contrary, a lower transcriptional response was observed in aqua1 plants in concomitance with a higher Cd concentration in medial leaves. Moreover, PaHMA2 showed at 1 d an opposite trend within organs since it was up-regulated in root and stem of wt plants and in leaves of aqua1 plants. In summary, aqua1 overexpression in poplar improved Cd translocation suggesting a lower Cd sensitivity of aqua1 plants. This different response might be due to a different transcription of PaNRAMP3 genes that were more transcribed in wt line because of the importance of this gene in Cd compartmentalization.

Prime Editing Technology and Its Prospects for Future Applications in Plant Biology Research

Many applications in plant biology requires editing genomes accurately including correcting point mutations, incorporation of single-nucleotide polymorphisms (SNPs), and introduction of multinucleotide insertion/deletions (indels) into a predetermined position in the genome. These types of modifications are possible using existing genome-editing technologies such as the CRISPR-Cas systems, which require induction of double-stranded breaks in the target DNA site and the supply of a donor DNA molecule that contains the desired edit sequence. However, low frequency of homologous recombination in plants and difficulty of delivering the donor DNA molecules make this process extremely inefficient. Another kind of technology known as base editing can perform precise editing; however, only certain types of modifications can be obtained, e.g., C/G-to-T/A and A/T-to-G/C. Recently, a new type of genome-editing technology, referred to as "prime editing," has been developed, which can achieve various types of editing such as any base-to-base conversion, including both transitions (C→T, G→A, A→G, and T→C) and transversion mutations (C→A, C→G, G→C, G→T, A→C, A→T, T→A, and T→G), as well as small indels without the requirement for inducing double-stranded break in the DNA. Because prime editing has wide flexibility to achieve different types of edits in the genome, it holds a great potential for developing superior crops for various purposes, such as increasing yield, providing resistance to various abiotic and biotic stresses, and improving quality of plant product. In this review, we describe the prime editing technology and discuss its limitations and potential applications in plant biology research.

Growth and physiological responses of three poplar clones grown on soils artificially contaminated with heavy metals, diesel fuel, and herbicides

We tested the growth and physiological responses of three poplar clones [Populus deltoides Bartr. ex Marsh. 'Bora', 'PE 19/66'; Populus × euramericana (Dode) Guinier 'Pannonia'] grown for 3 years on soils artificially contaminated with heavy metals, diesel fuel, and herbicides at the Experimental Estate of the Institute of Lowland Forestry and Environment (ILFE), University of Novi Sad, Serbia. Within three field blocks, clonal whole-plots were divided into seven subplots containing a non-contaminated control and six artificially-contaminated soil treatments: (1) 10.6 kg Cd ha^-1, (2) 247 kg Cu ha^-1, (3) 183.3 kg Ni ha^-1, (4) 6,667 L diesel fuel ha^-1, (5) 236 g Oxyfluorfen ha^-1, and (6) 1,320 g Pendimethalin ha^-1. Significant clone × treatment interactions governed growth and physiology throughout the study (p < 0.05), and the influence of inorganics versus organics varied with tree age. Heavy metals had a more substantial influence on growth and physiology as the trees matured, while diesel and herbicide treatments were most pronounced during the first growing season (p < 0.0001). Clones 'Bora' and 'PE 19/66' exhibited greater biomass than 'Pannonia', with trees growing in the control soils exhibiting 13.8 and 19.6 times greater biomass than 'Pannonia', respectively.

Genetic analysis of cadmium accumulation in lettuce (Lactuca sativa)

This work characterized mechanisms controlling cadmium (Cd) tolerance and accumulation in lettuce at both the physiological and genetic levels. These traits were evaluated in 18 Lactuca accessions representing a large genetic diversity. Cd tolerance and accumulation in roots and shoots as well as Cd translocation from roots to the shoot varied independently, and with a significant range of variation. Analyses of F1 progenies of crosses between cultivars with contrasted phenotypes showed that high tolerance to Cd, low Cd accumulation and low Cd root-shoot translocation were recessive traits. Results of analyses of F2 progenies of different crosses suggest that root Cd concentration and root-shoot Cd translocation were under a complex genetic determinism involving at least two loci. This work thus revealed that limiting both Cd accumulation and Cd root-shoot translocation in lettuce is possible and depends on recessive loci. Differences in the ability to accumulate Cd in roots in the long term could not be linked to differences in short-term 109Cd uptake into, or efflux from, roots. In contrast, the cultivar with the highest root-shoot Cd translocation was the same in the long term and in the short term, which suggests that this trait relies on processes that are implemented quickly (i.e. in less than three days) after the start of Cd exposure.

Construction of a high-density genetic map and its application for leaf shape QTL mapping in poplar

High-quality and dense genetic maps were constructed, and leaf shape variation was dissected by QTL mapping in poplar. Species in the genus Populus, also known as poplars, are important woody species and considered model plants for perennial trees. High-density genetic maps are valuable genomic resources for population genetics. Here, we generated a high-quality and dense genetic map for an F1 poplar population using high-throughput NGS-based genotyping. A total of 92,097 high-quality SNP markers were developed by stringent filtering and identification. In total, 889 and 1650 SNPs formed the female and male genetic maps, respectively. To test the application of the genetic maps, QTL mapping of leaf shape was conducted for this F1 population. A total of nine parameters were scored for leaf shape variation in three different environments. Combining genetic maps and measurements of the nine leaf shape parameters, we mapped a total of 42 significant QTLs. The highest LOD score of all QTLs was 9.2, and that QTL explained the most (15.13%) trait variation. A total of nine QTLs could be detected in at least two environments, and they were located in two genomic regions. Within these two QTL regions, some candidate genes for regulating leaf shape were predicted through functional annotation. The successful mapping of leaf shape QTLs demonstrated the utility of our genetic maps. According to the performance of this study, we were able to provide high-quality and dense genetic maps and dissect the leaf shape variation in poplar.

Sexual competition affects biomass partitioning, carbon-nutrient balance, Cd allocation and ultrastructure of Populus cathayana females and males exposed to Cd stress

Although increasing attention has been paid to plant adaptation to soil heavy metal contamination, competition and neighbor effects have been largely overlooked, especially in dioecious plants. In this study, we investigated growth as well as biochemical and ultrastructural responses of Populus cathayana Rehder females and males to cadmium (Cd) stress under different sexual competition patterns. The results showed that competition significantly affects biomass partitioning, photosynthetic capacity, leaf and root ultrastructure, Cd accumulation, the contents of polyphenols, and structural and nonstructural carbohydrates. Compared with single-sex cultivation, plants of opposite sexes exposed to sexual competition accumulated more Cd in tissues and their growth was more strongly inhibited, indicating enhanced Cd toxicity under sexual competition. Under intrasexual competition, females showed greater Cd accumulation, more serious damage at the ultrastructural level and greater reduction in physiological activity than under intersexual competition, while males performed better under intrasexual competition than under intersexual competition. Males improved the female microenvironment by greater Cd uptake and lower resource consumption under intersexual competition. These results demonstrate that the sex of neighbor plants and competition affect sexual differences in growth and in key physiological processes under Cd stress. The asymmetry of sexual competition highlighted here might regulate population structure, and spatial segregation and phytoremediation potential of both sexes in P. cathayana growing in heavy metal-contaminated soils.

Genotypic variations in the dynamics of metal concentrations in poplar leaves: a field study with a perspective on phytoremediation

Poplar is commonly used for phytoremediation of metal polluted soils. However, the high concentrations of trace elements present in leaves may return to soil upon leaf abscission. To investigate the mechanisms controlling leaf metal content, metal concentrations and expression levels of genes involved in metal transport were monitored at different developmental stages on leaves from different poplar genotypes growing on a contaminated field. Large differences in leaf metal concentrations were observed among genotypes. Whereas Mg was remobilized during senescence, Zn and Cd accumulation continued until leaf abscission in all genotypes. A positive correlation between Natural Resistance Associated Macrophage Protein 1 (NRAMP1) expression levels and Zn bio-concentration factors was observed. Principal component analyses of metal concentrations and gene expression levels clearly discriminated poplar genotypes. This study highlights a general absence of trace element remobilization from poplar leaves despite genotype specificities in the control of leaf metal homeostasis.

Generation of expressed sequence tags under cadmium stress for gene discovery and development of molecular markers in chickpea

Chickpea is the world's third most important legume crop and belongs to Fabaceae family but suffered from severe yield loss due to various biotic and abiotic stresses. Development of modern genomic tools such as molecular markers and identification of resistant genes associated with these stresses facilitate improvement in chickpea breeding towards abiotic stress tolerance. In this study, 1597 high-quality expressed sequence tags (ESTs) were generated from a cDNA library of variety Pusa 1105 root tissue after cadmium (Cd) treatment. Assembly of ESTs resulted in a total of 914 unigenes of which putative homology was obtained for 38.8 % of unigenes after BLASTX search. In terms of species distribution, majority of sequences found similarity with Medicago truncatula followed by Glycine max, Vitis vinifera and Populus trichocarpa and Pisum sativum sequences. Functional annotation was assigned using Blast2Go, and the Gene Ontology (GO) terms were categorized into biological process, molecular function and cellular component. Approximately 10.83 % of unigenes were assigned at least one GO term. Moreover, in the distribution of transcripts into various biological pathways, 20 of the annotated transcripts were assigned to ten pathways in KEGG database. A majority of the genes were found to be involved in sulphur and nitrogen metabolism. In the quantitative real-time PCR analysis, five of the transcription factors and three of the transporter genes were found to be highly expressed after Cd treatment. Besides, the utility of ESTs was demonstrated by exploiting them for the development of 83 genic molecular markers including EST-simple sequence repeats and intron targeted polymorphism that would assist in tagging of genes related to metal stress for future prospects.

Adaptive response of poplar (Populus nigra L.) after prolonged Cd exposure period

An outdoor pot experiment was designed to study the changes of growth parameters, accumulation, and distribution of Cd in poplar (Populus nigra L.) during a prolonged exposure period (growing period of 17 months including three harvest points), allowing the consideration of time effects and prolonged adaptation to Cd stress. Simultaneously, changes to the antioxidant system in roots and leaves were monitored. It was demonstrated that poplar could adapt to the Cd-contaminated soils after prolonged exposure. Total Cd accumulation in the aerial parts of poplar, due to high biomass production and acceptable Cd accumulation parameters, implies that the tested poplar species could be a good candidate for Cd phytoextraction application as well as could be used as phytostabilizer of Cd in heavily polluted soil. Furthermore, the activity of the antioxidant machinery displays both a tissue- and exposure-specific response pattern to different Cd treatments, indicating that strict regulation of the antioxidant defense system is required for the adaptive response of poplar. In addition, this report highlights the importance of prolonged exposure studies of physiological responses of plants, especially for long-life-cycle woody species under heavy metal stress, since some misleading conclusions could be reached after shorter time periods.

Effect of environmental stress factors on ecophysiological traits and susceptibility to pathogens of five Populus clones throughout the growing season

The variability of ecophysiological traits associated with productivity (e.g., water relations, leaf structure, photosynthesis and nitrogen (N) content) and susceptibility to fungal and insect infection were investigated in five poplar clones (Populus deltoides Batr.-Lux clone; Populus nigra L.-58-861 clone and Populus × canadensis Mönch.-Luisa Avanzo, I-214 and Adige clones) during their growing season. The objective of the study was to determine their physiological responses under summer constraints (characteristic of the Mediterranean climate) and to propose clone candidates for environmental restoration activities such as phytoremediation. Relative water content, the radiometric water index and (13)C isotope discrimination (Δ(13)C) results reflected improved water relations in Adige and Lux during summer drought. Leaf structural parameters such as leaf area, leaf mass per area, density (D) and thickness (T) indicated poorer structural adaptations to summer drought in clone 58-861. Nitrogen content and Δ(13)C results pointed to a stomatal component as the main limitant of photosynthesis in all clones. Adige and Lux showed enhanced photoprotection as indicated by the size and the de-epoxidation index of the xanthophyll-cycle pool, and also improved antioxidant defence displayed by higher ascorbate, reduced glutathione, total phenolics and α-tocopherol levels. Photoprotective and antioxidative responses allowed all clones to maintain a high maximum quantum yield of PSII (Fv/Fm) with the exception of Luisa Avanzo and 58-861 which experienced slight photoinhibition in late spring. The study of susceptibility to rust (Melampsora sp.) and lace bug (Monosteira unicostata Muls. and Rey) infections showed Adige and Lux to be the most tolerant. Overall, these two clones presented high adaptability to summer conditions and improved resistance to abiotic and biotic stress, thereby making them highly commendable clones for use in environmental remediation programmes.