scholarly journals Synthetic directed evolution in plants: unlocking trait engineering and improvement

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Gundra Sivakrishna Rao ◽  
Wenjun Jiang ◽  
Magdy Mahfouz
Keyword(s):  
Directed Evolution ◽  
Selection Pressure ◽  
Gene Sequence ◽  
Plant Traits ◽  
Crop Species ◽  
Base Editing ◽  
Selection Strategies ◽  
Diverse Species ◽  
Plant Genes ◽  
T7 Polymerase

Abstract Genetic variation accelerates adaptation and resilience and enables the survival of species in their changing environment. Increasing the genetic diversity of crop species is essential to improve their yield and enhance food security. Synthetic directed evolution (SDE) employs localized sequence diversification (LSD) of gene sequence and selection pressure to evolve gene variants with better fitness, improved properties and desired phenotypes. Recently, CRISPR–Cas-dependent and -independent technologies have been applied for LSD to mediate synthetic evolution in diverse species, including plants. SDE holds excellent promise to discover, accelerate and expand the range of traits of the value in crop species. Here, we highlight the efficient SDE approaches for the LSD of plant genes, selection strategies and critical traits for targeted improvement. We discuss the potential of emerging technologies, including CRISPR–Cas base editing, retron editing, EvolvR and prime editing, to establish efficient SDE in plants. Moreover, we cover CRISPR–Cas-independent technologies, including T7 polymerase editor for continuous evolution. We highlight the key challenges and potential solutions of applying SDE technologies to improve the plant traits of the value.

scholarly journals Genome Editing in Agriculture: Technical and Practical Considerations

2019 ◽  
Vol 20 (12) ◽  
pp. 2888 ◽  
Author(s):  
Julia Jansing ◽  
Andreas Schiermeyer ◽  
Stefan Schillberg ◽  
Rainer Fischer ◽  
Luisa Bortesi
Keyword(s):  
Genome Editing ◽  
Mechanism Of Action ◽  
High Efficiency ◽  
Public Acceptance ◽  
Crop Species ◽  
Base Editing ◽  
The Public ◽  
Intact Plants ◽  
Efficient Delivery ◽  
Selection Of

The advent of precise genome-editing tools has revolutionized the way we create new plant varieties. Three groups of tools are now available, classified according to their mechanism of action: Programmable sequence-specific nucleases, base-editing enzymes, and oligonucleotides. The corresponding techniques not only lead to different outcomes, but also have implications for the public acceptance and regulatory approval of genome-edited plants. Despite the high efficiency and precision of the tools, there are still major bottlenecks in the generation of new and improved varieties, including the efficient delivery of the genome-editing reagents, the selection of desired events, and the regeneration of intact plants. In this review, we evaluate current delivery and regeneration methods, discuss their suitability for important crop species, and consider the practical aspects of applying the different genome-editing techniques in agriculture.

scholarly journals Progress in plant genome sequencing: research directions

2019 ◽  
Vol 23 (1) ◽  
pp. 38-48 ◽  
Author(s):  
M. K. Bragina ◽  
D. A. Afonnikov ◽  
E. A. Salina
Keyword(s):  
Genome Sequencing ◽  
Plant Traits ◽  
Plant Genome ◽  
Targeted Sequencing ◽  
Genome Sequences ◽  
Crop Species ◽  
High Coverage ◽  
Protein Coding ◽  
Sequencing Technologies ◽  
A Genome

Since the first plant genome of Arabidopsis thaliana has been sequenced and published, genome sequencing technologies have undergone significant changes. New algorithms, sequencing technologies and bioinformatic approaches were adopted to obtain genome, transcriptome and exome sequences for model and crop species, which have permitted deep inferences into plant biology. As a result of an improved genome assembly and analysis methods, genome sequencing costs plummeted and the number of high-quality plant genome sequences is constantly growing. Consequently, more than 300 plant genome sequences have been published over the past twenty years. Although many of the published genomes are considered incomplete, they proved to be a valuable tool for identifying genes involved in the formation of economically valuable plant traits, for marker-assisted and genomic selection and for comparative analysis of plant genomes in order to determine the basic patterns of origin of various plant species. Since a high coverage and resolution of a genome sequence is not enough to detect all changes in complex samples, targeted sequencing, which consists in the isolation and sequencing of a specific region of the genome, has begun to develop. Targeted sequencing has a higher detection power (the ability to identify new differences/variants) and resolution (up to one basis). In addition, exome sequencing (the method of sequencing only protein-coding genes regions) is actively developed, which allows for the sequencing of non-expressed alleles and genes that cannot be found with RNA-seq. In this review, an analysis of sequencing technologies development and the construction of “reference” genomes of plants is performed. A comparison of the methods of targeted sequencing based on the use of the reference DNA sequence is accomplished.

scholarly journals Plant extinction excels plant speciation in the Anthropocene

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Jian-Guo Gao ◽  
Hui Liu ◽  
Ning Wang ◽  
Jing Yang ◽  
Xiao-Ling Zhang
Keyword(s):  
Plant Species ◽  
Plant Traits ◽  
Extinction Risk ◽  
Plant Evolution ◽  
The Arctic ◽  
Polar Regions ◽  
Crop Species ◽  
The Past ◽  
Plant Extinction ◽  
Warming World

Abstract Background In the past several millenniums, we have domesticated several crop species that are crucial for human civilization, which is a symbol of significant human influence on plant evolution. A pressing question to address is if plant diversity will increase or decrease in this warming world since contradictory pieces of evidence exit of accelerating plant speciation and plant extinction in the Anthropocene. Results Comparison may be made of the Anthropocene with the past geological times characterised by a warming climate, e.g., the Palaeocene-Eocene Thermal Maximum (PETM) 55.8 million years ago (Mya)—a period of “crocodiles in the Arctic”, during which plants saw accelerated speciation through autopolyploid speciation. Three accelerators of plant speciation were reasonably identified in the Anthropocene, including cities, polar regions and botanical gardens where new plant species might be accelerating formed through autopolyploid speciation and hybridization. Conclusions However, this kind of positive effect of climate warming on new plant species formation would be thoroughly offset by direct and indirect intensive human exploitation and human disturbances that cause habitat loss, deforestation, land use change, climate change, and pollution, thus leading to higher extinction risk than speciation in the Anthropocene. At last, four research directions are proposed to deepen our understanding of how plant traits affect speciation and extinction, why we need to make good use of polar regions to study the mechanisms of dispersion and invasion, how to maximize the conservation of plant genetics, species, and diverse landscapes and ecosystems and a holistic perspective on plant speciation and extinction is needed to integrate spatiotemporally.

scholarly journals Linking plant genes to insect communities: Identifying the genetic bases of plant traits and community composition

2019 ◽  
Vol 28 (19) ◽  
pp. 4404-4421 ◽  
Author(s):  
Hilary L. Barker ◽  
Jennifer F. Riehl ◽  
Carolina Bernhardsson ◽  
Kennedy F. Rubert‐Nason ◽  
Liza M. Holeski ◽  
...  
Keyword(s):  
Community Composition ◽  
Plant Traits ◽  
Insect Communities ◽  
Plant Genes ◽  
Genetic Bases

scholarly journals Fusion of Spectral and Structural Information from Aerial Images for Improved Biomass Estimation

2020 ◽  
Vol 12 (19) ◽  
pp. 3164
Author(s):  
Bikram Pratap Banerjee ◽  
German Spangenberg ◽  
Surya Kant
Keyword(s):  
High Throughput ◽  
Plant Traits ◽  
Structural Information ◽  
Vegetation Indices ◽  
Ground Truth ◽  
Breeding Population ◽  
Aerial Images ◽  
Biomass Estimation ◽  
Growth Stages ◽  
Crop Species

Efficient, precise and timely measurement of plant traits is important in the assessment of a breeding population. Estimating crop biomass in breeding trials using high-throughput technologies is difficult, as reproductive and senescence stages do not relate to reflectance spectra, and multiple growth stages occur concurrently in diverse genotypes. Additionally, vegetation indices (VIs) saturate at high canopy coverage, and vertical growth profiles are difficult to capture using VIs. A novel approach was implemented involving a fusion of complementary spectral and structural information, to calculate intermediate metrics such as crop height model (CHM), crop coverage (CC) and crop volume (CV), which were finally used to calculate dry (DW) and fresh (FW) weight of above-ground biomass in wheat. The intermediate metrics, CHM (R2 = 0.81, SEE = 4.19 cm) and CC (OA = 99.2%, Κ = 0.98) were found to be accurate against equivalent ground truth measurements. The metrics CV and CV×VIs were used to develop an effective and accurate linear regression model relationship with DW (R2 = 0.96 and SEE = 69.2 g/m2) and FW (R2 = 0.89 and SEE = 333.54 g/m2). The implemented approach outperformed commonly used VIs for estimation of biomass at all growth stages in wheat. The achieved results strongly support the applicability of the proposed approach for high-throughput phenotyping of germplasm in wheat and other crop species.

scholarly journals Evolutionary insights into plant breeding

2019 ◽  
Author(s):  
Sarah Diane Turner-Hissong ◽  
Makenzie E. Mabry ◽  
Timothy M. Beissinger ◽  
Jeffrey Ross-Ibarra ◽  
J. Chris Pires
Keyword(s):  
Plant Breeding ◽  
Complex Traits ◽  
Life Histories ◽  
Evolutionary Biology ◽  
Genetic Architecture ◽  
Demographic History ◽  
Crop Improvement ◽  
Community Resources ◽  
Crop Species ◽  
Selection Strategies

Crop domestication is a fascinating area of study, as evidenced by a multitude of recent reviews. Coupled with the increasing availability of genomic and phenomic resources in numerous crop species, insights from evolutionary biology will enable a deeper understanding of the genetic architecture and short-term evolution of complex traits, which can be used to inform selection strategies. Future advances in crop improvement will rely on the integration of population genetics with plant breeding methodology, and the development of community resources to support research in a variety of crop life histories and reproductive strategies. We highlight recent advances in the role of selective sweeps and demographic history in shaping genetic architecture, how these breakthroughs can inform selection strategies, and the application of precision gene editing to leverage these connections.

scholarly journals Synthetic evolution of herbicide resistance using a T7 RNAP-based random DNA base editor

2021 ◽  
Author(s):  
Magdy Mahfouz ◽  
Haroon Butt ◽  
Jose Luis Moreno Ramirez
Keyword(s):  
Directed Evolution ◽  
Herbicide Resistance ◽  
Selection Pressure ◽  
High Efficiency ◽  
Rice Genome ◽  
Acetolactate Synthase ◽  
Target Sequence ◽  
T7 Promoter ◽  
Simultaneous Application ◽  
Dna Base

Synthetic directed evolution via localized sequence diversification and the simultaneous application of selection pressure is a promising method for producing new, beneficial alleles that affect traits of interest in diverse species; however, this technique has rarely been applied in plants. Developing systems to induce localized sequence diversification at high efficiency will expand our ability to evolve traits of interest that improve global food security. In this study, we designed, built, and tested a chimeric fusion of T7 RNA Polymerase (RNAP) and deaminase to enable the localized sequence diversification of a target sequence of interest. We tested our T7 RNAP-DNA base editor in Nicotiana benthamiana transient assays to target a transgene expressing GFP under the control of the T7 promoter. More than 7% of C nucleotides were converted to T in long segments of the GFP sequence. We then targeted the T7 promoter-driven ACETOLACTATE SYNTHASE (ALS) sequence that had been stably integrated into the rice (Oryza sativa) genome and generated C-to-T and G-to-A transitions. We used herbicide treatment as a selection pressure for the evolution of the ALS sequence, resulting in the enrichment of herbicide-responsive residues. We then targeted these herbicide-responsive regions in the rice genome using a CRISPR-directed evolution platform and identified herbicide-resistant ALS variants. Thus, our system could be used for the continuous synthetic evolution of gene functions to produce variants with improved herbicide resistance, as well as for other trait engineering applications.

scholarly journals An in vivo selection system with tightly regulated gene expression enables directed evolution of highly efficient enzymes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Parinthon Nearmnala ◽  
Manutsawee Thanaburakorn ◽  
Watanalai Panbangred ◽  
Pimchai Chaiyen ◽  
Narupat Hongdilokkul
Keyword(s):  
Directed Evolution ◽  
Selection Pressure ◽  
Catalytic Efficiency ◽  
Selection System ◽  
In Vivo Selection ◽  
Highly Efficient ◽  
Highly Active ◽  
Wide Range ◽  
Regulated Gene Expression

AbstractIn vivo selection systems are powerful tools for directed evolution of enzymes. The selection pressure of the systems can be tuned by regulating the expression levels of the catalysts. In this work, we engineered a selection system for laboratory evolution of highly active enzymes by incorporating a translationally suppressing cis repressor as well as an inducible promoter to impart stringent and tunable selection pressure. We demonstrated the utility of our selection system by performing directed evolution experiments using TEM β-lactamase as the model enzyme. Five evolutionary rounds afforded a highly active variant exhibiting 440-fold improvement in catalytic efficiency. We also showed that, without the cis repressor, the selection system cannot provide sufficient selection pressure required for evolving highly efficient TEM β-lactamase. The selection system should be applicable for the exploration of catalytic perfection of a wide range of enzymes.

How do seed and seedling traits influence germination and emergence parameters in crop species? A comparative analysis

2016 ◽  
Vol 26 (4) ◽  
pp. 317-331 ◽  
Author(s):  
Antoine Gardarin ◽  
Françoise Coste ◽  
Marie-Hélène Wagner ◽  
Carolyne Dürr
Keyword(s):  
Plant Traits ◽  
Germination Rate ◽  
Seed Mass ◽  
Elongation Rate ◽  
Model Parameters ◽  
Base Temperature ◽  
Plant Establishment ◽  
Crop Species ◽  
Seedling Traits ◽  
Emergence Success

AbstractEarly plant establishment through seed germination and seedling emergence is a crucial process that determines seedling number, emergence time distribution and the early growth of seedlings, all of which are affected by soil climate and soil structure. In the current context of climate change, in which increasing the diversity of cultivated species is considered desirable, and new tillage practices are considerably modifying top-soil surface characteristics, we need to improve our ability to model the effects of the environment on plant establishment. Using a trait-based and model-based framework, we aimed to identify general relationships between seed and seedling traits (e.g. seed mass and lipid content, seedling diameter, base temperature) and germination and emergence model parameters (e.g. time to mid-germination, shoot elongation rate) measured for 18 genotypes belonging to 14 species. Relationships were also investigated among model parameters or traits. Germination rates were faster for species with a high base temperature and for species with seed reserves located principally in the embryo (rather than the endosperm or perisperm). During heterotrophic growth, maximal shoot length and elongation rate increased with seed dry mass. The sensitivity of seedlings to soil obstacles was negatively related to shoot diameter. Thus apart from the known effects of seed mass on seedling establishment, we found that seed reserve location, seedling shoot diameter and shape affected germination rate and emergence success. Such generic rules linking plant traits to germination and emergence parameters enhance our understanding of the determinants of environmental effects on plant establishment success.

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