Agriculture and climate change are internally correlated with each other in various aspects, as climate change is the main cause of biotic and abiotic stresses, which have adverse effects on the agriculture of a region. The land and its agriculture are being affected by climate changes in different ways, e.g., variations in annual rainfall, average temperature, heat waves, modifications in weeds, pests or microbes, global change of atmospheric CO2 or ozone level, and fluctuations in sea level. The threat of varying global climate has greatly driven the attention of scientists, as these variations are imparting negative impact on global crop production and compromising food security worldwide. According to some predicted reports, agriculture is considered the most endangered activity adversely affected by climate changes. To date, food security and ecosystem resilience are the most concerning subjects worldwide. Climate-smart agriculture is the only way to lower the negative impact of climate variations on crop adaptation, before it might affect global crop production drastically. In this review paper, we summarize the causes of climate change, stresses produced due to climate change, impacts on crops, modern breeding technologies, and biotechnological strategies to cope with climate change, in order to develop climate resilient crops. Revolutions in genetic engineering techniques can also aid in overcoming food security issues against extreme environmental conditions, by producing transgenic plants.

Impact of Climate Change on Crops Adaptation and Strategies to Tackle Its Outcome: A Review.

The availability of genome sequences for several crops and advances in genome editing approaches has opened up possibilities to breed for almost any given desirable trait. Advancements in genome editing technologies such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) has made it possible for molecular biologists to more precisely target any gene of interest. However, these methodologies are expensive and time-consuming as they involve complicated steps that require protein engineering. Unlike first-generation genome editing tools, CRISPR/Cas9 genome editing involves simple designing and cloning methods, with the same Cas9 being potentially available for use with different guide RNAs targeting multiple sites in the genome. After proof-of-concept demonstrations in crop plants involving the primary CRISPR-Cas9 module, several modified Cas9 cassettes have been utilized in crop plants for improving target specificity and reducing off-target cleavage (eg. Nmcas9, Sacas9, Stcas9). Further, the availability of Cas9 enzymes from additional bacterial species has made available options to enhance specificity and efficiency of gene editing methodologies. This review summarizes the options available to plant biotechnologists to bring about crop improvement using CRISPR/Cas9 based genome editing tools and also presents studies where CRISPR/Cas9 has been used for enhancing biotic and abiotic stress tolerance. Application of these techniques will result in the development of non-genetically modified (Non-GMO) crops with the desired trait that can contribute to increased yield potential under biotic and abiotic stress conditions.

/pdf/crispr-for-crop-improvement-an-update-review-53da0nv2w2.pdf

CRISPR for Crop Improvement: An Update Review.

Plant annexins are Ca2+-dependent phospholipid-binding proteins and exist as multigene families in plants. They are implicated in the regulation of plant development as well as protection from environmental stresses. In this study, the rice annexin gene OsAnn3 knockout was performed via the CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR associated proteins) mediated genome editing. Thus, mutant plantlets were successfully obtained. We identified cold tolerance phenotype of T1 mutant lines from T0 biallelic mutants using the 4∼6°C for 3 days cold treatment. The results showed that REC (the relative electrical conductivity) of T1 mutant lines was increased, and the survival ratio of T1 mutant lines was decreased dramatically compared with the wild type after the exposure to cold treatment. It was suggested that OsAnn3 was involved in cold tolerance of rice.

Knock out of the annexin gene OsAnn3 via CRISPR/Cas9-mediated genome editing decreased cold tolerance in rice

Rhizosphere microbiome: Engineering bacterial competitiveness for enhancing crop production.

Increasing agricultural productivity via modern breeding strategies is of prime interest to attain global food security. An array of biotic and abiotic stressors affect productivity as well as the quality of crop plants, and it is a primary need to develop crops with improved adaptability, high productivity, and resilience against these biotic/abiotic stressors. Conventional approaches to genetic engineering involve tedious procedures. State-of-the-art OMICS approaches reinforced with next-generation sequencing and the latest developments in genome editing tools have paved the way for targeted mutagenesis, opening new horizons for precise genome engineering. Various genome editing tools such as transcription activator-like effector nucleases (TALENs), zinc-finger nucleases (ZFNs), and meganucleases (MNs) have enabled plant scientists to manipulate desired genes in crop plants. However, these approaches are expensive and laborious involving complex procedures for successful editing. Conversely, CRISPR/Cas9 is an entrancing, easy-to-design, cost-effective, and versatile tool for precise and efficient plant genome editing. In recent years, the CRISPR/Cas9 system has emerged as a powerful tool for targeted mutagenesis, including single base substitution, multiplex gene editing, gene knockouts, and regulation of gene transcription in plants. Thus, CRISPR/Cas9-based genome editing has demonstrated great potential for crop improvement but regulation of genome-edited crops is still in its infancy. Here, we extensively reviewed the availability of CRISPR/Cas9 genome editing tools for plant biotechnologists to target desired genes and its vast applications in crop breeding research.

/pdf/modern-trends-in-plant-genome-editing-an-inclusive-review-of-2f495l50w7.pdf

Modern Trends in Plant Genome Editing: An Inclusive Review of the CRISPR/Cas9 Toolbox

Cold stress greatly affects plant growth and crop yield. To identify novel genes and possible mechanisms involved in chilling tolerance responses in rice seedlings, RNA sequencing (RNA-seq) technology was used for genome-wide gene expression profiling analysis to compare three cold-tolerant genotypes and one cold-sensitive genotype under both normal temperature and cold stress treatments. The results showed that in response to cold, a total of 2242 common regulated differentially expressed genes (DEGs) were detected during cold stress in all of the genotypes, and a total of 318 DEGs were detected as common DEGs related to cold tolerance in the three cold-tolerant genotypes. Gene ontology (GO) enrichment analyses were performed for these DEGs. By combining protein function clustering analysis and significantly enriched GO terms analysis, we suggest that calcium signal transduction may play a dominating role in the cold stress response of rice. Further, we suggest that RNA helicases may be directly involved in temperature sensing in rice under cold stress, and that compensation of ATPase activity, alteration of epigenetic processes, and further reduction of functional photosynthesis proteins may serve as mechanisms for cold tolerance regulation in the cold-tolerant rice genotypes. These results expand our understanding of the complex mechanisms involved in chilling tolerance in rice, and provide a foundation for future studies on chilling tolerance in rice and other cereal crops.

Comparative transcriptome analysis of RNA-seq data for cold-tolerant and cold-sensitive rice genotypes under cold stress

Chloroplast is a new hotspot in the field of plant transformation system of plant genetic engineering. Plastid transformation has several advantages: high expression, multiple expressed genes in a single transformation event, absence of gene silencing, et al. A series of elements for construction of dicistronic site-specific integration expression vector of rice chloroplast have been cloned, including trnl-trnA (rice chloroplast homologous recombination fragments), Prrn (16S rRNA operon promotor), PpsbA (the 3' untranslated region of the chloroplastpsbA gene), hptll gene (encoding hygromycin phosphotransferase) and EGFP (encoding enhanced green fluorescence protein). All the elements were constructed into a rice chloroplast dicistronic expression vector pCTE04 (-trnl-Prrn-RBS-hptlI-RBS-EGFP-PpsbA- trnA-). Then pCTE04 was introduced into chloroplasts of Dunaliella salina through particle bombardment. Strong green fluorescence was observed in chloroplasts of some bombarded Dunaliella salina cells under a stereo fluorescence microscope, indicating that pCTE04 could be expressed in Dunaliella salina chloroplasts transiently. It provides a solid foundation for further genetic engineering in rice chloroplast transformation.

Construction of rice site-specific chloroplast transformation vector and transient expression of EGFP gene in Dunaliella salina.

Land subsidence is generally caused by stress concentration of the overlying strata, which may reach the rock failure limit, causing surface collapse. The Liaohe Plain is an important resource producing area in China. Concentrated exploitation of underground resources leads to the generation of underground cavities, and surface subsidence gradually occurs as cavities increase. We used small baseline subsets synthetic aperture radar interferometry to monitor large-scale surface deformation on the Liaohe Plain. Field investigations found that the spatial distribution of land subsidence on the Liaohe Plain is highly correlated with coal mining areas. Taking the interferometric synthetic aperture radar deformation as the real constraint, a nonlinear Bayesian inversion algorithm was used to reconstruct underground reservoir parameters, such as the position and attitude of underground coal seams, based on a multi-source dislocation model. The R2 between observed and modeled deformation in multiple coal mining areas was above 0.9. On this basis, relying on the Coulomb failure stress (CFS) criterion, the elastic model parameters and regional geological data were used to calculate the stress field caused by underground resource exploitation on the ground surface. The results show that the CFS fields of multiple groups of coal seams at close distances have mutual influence, and it is more concentrated at the perimeters than in the central portions of the subsidence area. The proposed dislocation model of closely spaced multiple coal seams improved the inversion accuracy of complex mining conditions, and would provide important information for risk assessment and prevention from the perspective of geodesy. 

Time series interferometric synthetic aperture radar-based modeling and analysis of complex land subsidence caused by multi-seam coal mining on the Liaohe Plain, China

Ronghua He

Papers

Knock out of the annexin gene OsAnn3 via CRISPR/Cas9-mediated genome editing decreased cold tolerance in rice

Comparative transcriptome analysis of RNA-seq data for cold-tolerant and cold-sensitive rice genotypes under cold stress

Construction of rice site-specific chloroplast transformation vector and transient expression of EGFP gene in Dunaliella salina.

Time series interferometric synthetic aperture radar-based modeling and analysis of complex land subsidence caused by multi-seam coal mining on the Liaohe Plain, China