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CRISPR Crops: Plant Genome Editing Toward Disease Resistance.
Langner, T, Kamoun, S, Belhaj, K
Annual review of phytopathology. 2018;:479-512
Abstract
Genome editing by sequence-specific nucleases (SSNs) has revolutionized biology by enabling targeted modifications of genomes. Although routine plant genome editing emerged only a few years ago, we are already witnessing the first applications to improve disease resistance. In particular, CRISPR-Cas9 has democratized the use of genome editing in plants thanks to the ease and robustness of this method. Here, we review the recent developments in plant genome editing and its application to enhancing disease resistance against plant pathogens. In the future, bioedited disease resistant crops will become a standard tool in plant breeding.
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2.
Advancing Agrobacterium-Based Crop Transformation and Genome Modification Technology for Agricultural Biotechnology.
Anand, A, Jones, TJ
Current topics in microbiology and immunology. 2018;:489-507
Abstract
The last decade has seen significant strides in Agrobacterium-mediated plant transformation technology. This has not only expanded the number of crop species that can be transformed by Agrobacterium, but has also made it possible to routinely transform several recalcitrant crop species including cereals (e.g., maize, sorghum, and wheat). However, the technology is limited by the random nature of DNA insertions, genotype dependency, low frequency of quality events, and variation in gene expression arising from genomic insertion sites. A majority of these deficiencies have now been addressed by improving the frequency of quality events, developing genotype-independent transformation capability in maize, developing an Agrobacterium-based site-specific integration technology for precise gene targeting, and adopting Agrobacterium-delivered CRISPR-Cas genes for gene editing. These improved transformation technologies are discussed in detail in this chapter.
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3.
Genome encode analyses reveal the basis of convergent evolution of fleshy fruit ripening.
Lü, P, Yu, S, Zhu, N, Chen, YR, Zhou, B, Pan, Y, Tzeng, D, Fabi, JP, Argyris, J, Garcia-Mas, J, et al
Nature plants. 2018;(10):784-791
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Abstract
Fleshy fruits using ethylene to regulate ripening have developed multiple times in the history of angiosperms, presenting a clear case of convergent evolution whose molecular basis remains largely unknown. Analysis of the fruitENCODE data consisting of 361 transcriptome, 71 accessible chromatin, 147 histone and 45 DNA methylation profiles reveals three types of transcriptional feedback circuits controlling ethylene-dependent fruit ripening. These circuits are evolved from senescence or floral organ identity pathways in the ancestral angiosperms either by neofunctionalisation or repurposing pre-existing genes. The epigenome, H3K27me3 in particular, has played a conserved role in restricting ripening genes and their orthologues in dry and ethylene-independent fleshy fruits. Our findings suggest that evolution of ripening is constrained by limited hormone molecules and genetic and epigenetic materials, and whole-genome duplications have provided opportunities for plants to successfully circumvent these limitations.
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4.
Camelina sativa, an oilseed at the nexus between model system and commercial crop.
Malik, MR, Tang, J, Sharma, N, Burkitt, C, Ji, Y, Mykytyshyn, M, Bohmert-Tatarev, K, Peoples, O, Snell, KD
Plant cell reports. 2018;(10):1367-1381
Abstract
The rapid assessment of metabolic engineering strategies in plants is aided by crops that provide simple, high throughput transformation systems, a sequenced genome, and the ability to evaluate the resulting plants in field trials. Camelina sativa provides all of these attributes in a robust oilseed platform. The ability to perform field evaluation of Camelina is a useful, and in some studies essential benefit that allows researchers to evaluate how traits perform outside the strictly controlled conditions of a greenhouse. In the field the plants are subjected to higher light intensities, seasonal diurnal variations in temperature and light, competition for nutrients, and watering regimes dictated by natural weather patterns, all which may affect trait performance. There are difficulties associated with the use of Camelina. The current genetic resources available for Camelina pale in comparison to those developed for the model plant Arabidopsis thaliana; however, the sequence similarity of the Arabidopsis and Camelina genomes often allows the use of Arabidopsis as a reference when additional information is needed. Camelina's genome, an allohexaploid, is more complex than other model crops, but the diploid inheritance of its three subgenomes is straightforward. The need to navigate three copies of each gene in genome editing or mutagenesis experiments adds some complexity but also provides advantages for gene dosage experiments. The ability to quickly engineer Camelina with novel traits, advance generations, and bulk up homozygous lines for small-scale field tests in less than a year, in our opinion, far outweighs the complexities associated with the crop.
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5.
On the Road to Breeding 4.0: Unraveling the Good, the Bad, and the Boring of Crop Quantitative Genomics.
Wallace, JG, Rodgers-Melnick, E, Buckler, ES
Annual review of genetics. 2018;:421-444
Abstract
Understanding the quantitative genetics of crops has been and will continue to be central to maintaining and improving global food security. We outline four stages that plant breeding either has already achieved or will probably soon achieve. Top-of-the-line breeding programs are currently in Breeding 3.0, where inexpensive, genome-wide data coupled with powerful algorithms allow us to start breeding on predicted instead of measured phenotypes. We focus on three major questions that must be answered to move from current Breeding 3.0 practices to Breeding 4.0: ( a) How do we adapt crops to better fit agricultural environments? ( b) What is the nature of the diversity upon which breeding can act? ( c) How do we deal with deleterious variants? Answering these questions and then translating them to actual gains for farmers will be a significant part of achieving global food security in the twenty-first century.
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6.
Rice Genomics: over the Past Two Decades and into the Future.
Song, S, Tian, D, Zhang, Z, Hu, S, Yu, J
Genomics, proteomics & bioinformatics. 2018;(6):397-404
Abstract
Domestic rice (Oryza sativa L.) is one of the most important cereal crops, feeding a large number of worldwide populations. Along with various high-throughput genome sequencing projects, rice genomics has been making great headway toward direct field applications of basic research advances in understanding the molecular mechanisms of agronomical traits and utilizing diverse germplasm resources. Here, we briefly review its achievements over the past two decades and present the potential for its bright future.
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7.
The long and short of doubling down: polyploidy, epigenetics, and the temporal dynamics of genome fractionation.
Wendel, JF, Lisch, D, Hu, G, Mason, AS
Current opinion in genetics & development. 2018;:1-7
Abstract
We consider the rapidly advancing discipline of plant evolutionary genomics, with a focus on the evolution of polyploid genomes. In many lineages, polyploidy is followed by 'biased fractionation', the unequal loss of genes from ancestral progenitor genomes. Mechanistically, it has been proposed that biased fractionation results from changes in the epigenetic landscape near genes, likely mediated by transposable elements. These epigenetic changes result in unequal gene expression between duplicates, establishing differential fitness that leads to biased gene loss with respect to ancestral genomes. We propose a unifying conceptual framework and a set of testable hypotheses based on this model, relating genome size, the proximity of transposable elements to genes, epigenetic reprogramming, chromatin accessibility, and gene expression.
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8.
Plant STAND P-loop NTPases: a current perspective of genome distribution, evolution, and function : Plant STAND P-loop NTPases: genomic organization, evolution, and molecular mechanism models contribute broadly to plant pathogen defense.
Arya, P, Acharya, V
Molecular genetics and genomics : MGG. 2018;(1):17-31
Abstract
STAND P-loop NTPase is the common weapon used by plant and other organisms from all three kingdoms of life to defend themselves against pathogen invasion. The purpose of this study is to review comprehensively the latest finding of plant STAND P-loop NTPase related to their genomic distribution, evolution, and their mechanism of action. Earlier, the plant STAND P-loop NTPase known to be comprised of only NBS-LRRs/AP-ATPase/NB-ARC ATPase. However, recent finding suggests that genome of early green plants comprised of two types of STAND P-loop NTPases: (1) mammalian NACHT NTPases and (2) NBS-LRRs. Moreover, YchF (unconventional G protein and members of P-loop NTPase) subfamily has been reported to be exceptionally involved in biotic stress (in case of Oryza sativa), thereby a novel member of STAND P-loop NTPase in green plants. The lineage-specific expansion and genome duplication events are responsible for abundance of plant STAND P-loop NTPases; where "moderate tandem and low segmental duplication" trajectory followed in majority of plant species with few exception (equal contribution of tandem and segmental duplication). Since the past decades, systematic research is being investigated into NBS-LRR function supported the direct recognition of pathogen or pathogen effectors by the latest models proposed via 'integrated decoy' or 'sensor domains' model. Here, we integrate the recently published findings together with the previous literature on the genomic distribution, evolution, and distinct models proposed for functional molecular mechanism of plant STAND P-loop NTPases.
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9.
Towards a more predictable plant breeding pipeline with CRISPR/Cas-induced allelic series to optimize quantitative and qualitative traits.
Scheben, A, Edwards, D
Current opinion in plant biology. 2018;(Pt B):218-225
Abstract
The rate of crop improvement must increase to meet rising global demand for food. Crop breeding pipelines can be hampered by the imprecision and multi-generational timeframe of methods such as intercrossing and stochastic mutagenesis used to generate variation. Genome editing can generate targeted allelic series of trait-related genes and regulatory elements, creating a series of variable phenotypes for breeding within a single generation. Disrupting genic and regulatory regions is particularly effective for engineering quantitative traits. Although qualitative traits can be more difficult to engineer using disruption, precise base editing may allow an efficient path to rationally improve qualitative traits if protein function can be accurately modelled. As functional understanding of genes and regulatory elements increases, genome editing can enhance the predictability of plant breeding outcomes and will ensure food security.
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10.
Characteristics of Genome Editing Mutations in Cereal Crops.
Zhu, C, Bortesi, L, Baysal, C, Twyman, RM, Fischer, R, Capell, T, Schillberg, S, Christou, P
Trends in plant science. 2017;(1):38-52
Abstract
Designer nucleases allow the creation of new plant genotypes by introducing precisely-targeted double-strand breaks that are resolved by endogenous repair pathways. The major nuclease technologies are meganucleases, zinc-finger nucleases, transcription activator-like effector nucleases, and the CRISPR/Cas9 system. Each comprises a promiscuous endonuclease guided by protein-DNA or RNA-DNA interactions. A great deal is known about the principles of designer nucleases but much remains to be learned about their detailed behavioral characteristics in different plant species. The outcome of genome engineering reflects the intrinsic properties of each nuclease and target genome, causing variations in efficiency, accuracy, and mutation structure. In this article, we critically discuss the activities of designer nucleases in different cereals representing a broad range of genome characteristics.