Wheat Microbiome: Structure, Dynamics, and Role in Improving Performance Under Stress Environments

Wheat is an important cereal crop species consumed globally. The growing global population demands a rapid and sustainable growth of agricultural systems. The development of genetically efficient wheat varieties has solved the global demand for wheat to a greater extent. The use of chemical substances for pathogen control and chemical fertilizers for enhanced agronomic traits also proved advantageous but at the cost of environmental health. An efficient alternative environment-friendly strategy would be the use of beneficial microorganisms growing on plants, which have the potential of controlling plant pathogens as well as enhancing the host plant’s water and mineral availability and absorption along with conferring tolerance to different stresses. Therefore, a thorough understanding of plant-microbe interaction, identification of beneficial microbes and their roles, and finally harnessing their beneficial functions to enhance sustainable agriculture without altering the environmental quality is appealing. The wheat microbiome shows prominent variations with the developmental stage, tissue type, environmental conditions, genotype, and age of the plant. A diverse array of bacterial and fungal classes, genera, and species was found to be associated with stems, leaves, roots, seeds, spikes, and rhizospheres, etc., which play a beneficial role in wheat. Harnessing the beneficial aspect of these microbes is a promising method for enhancing the performance of wheat under different environmental stresses. This review focuses on the microbiomes associated with wheat, their spatio-temporal dynamics, and their involvement in mitigating biotic and abiotic stresses.

Eligible strategies of drought response to improve drought resistance in woody crops: a mini-review

Drought is the main abiotic stress that negatively affects the crop yield. Due to the rapid climate change, actual plant defence mechanisms may be less effective against increased drought stress and other related or co-occurring abiotic stresses such as salt and high temperature. Thus, genetic engineering approaches may be an important tool for improving drought tolerance in crops. This mini-review focuses on the responses to drought stress of the woody crop species Olea europaea and Citrus sp., selecting in particular five main strategies adopted by plants in response to drought stress: aquaporin (AQPs) expression, antioxidant activity, ABA signalling, and trehalose and proline accumulation. Transgenic studies on both the herbaceous Arabidopsis and woody Populus plant models showed an improvement in drought resistance with increasing expression of these drought-inducible genes. Outcomes from the present study suggest the overexpression of the gene families associated with AQPs and ABA biosynthesis, mainly involved in regulating water transport and in preventing water loss, respectively, as candidate targets for improving drought resistance; antioxidants-, trehalose- and proline-related genes remain valid candidates for resistance to a wider spectrum of abiotic stressors, including drought. However, the contribution of an increased stiffness of the modulus elasticity of leaf parenchyma cell walls to the rapid recovery of leaf water potential, delaying by this way the stress onset, is not a secondary aspect of the transgenic optimization, in particular for Olea cultivars.

Pollinator community response to planted pollinator habitat in agroecosystems over time

Pollinators are important both ecologically and economically, with the majority of flowering plants and many of the world’s crop species relying on animal pollination—the majority of which is provided by bees. However, documented pollinator population decline threatens ecosystem functioning and human well-being. As such, conservation methods such as augmented pollinator habitat are becoming popular tools to combat pollinator losses. In our study, we evaluate an initiative to plant pollinator habitat at all North Carolina agricultural research stations to ensure that these efforts result in improved bee communities. From 2016 to 2018, we found significant increases in bee abundance and community diversity. These increases depended on the quality of habitat, with plots with higher cover and more plant diversity supporting larger, more diverse bee communities. Although the habitat positively supported bee communities, we found that overall habitat quality degraded over the course of our study. This points to the need of regular upkeep and maintenance of pollinator habitat in order for it to appropriately support bee communities. Future long-term studies on pollinators will be important as natural fluctuations in bee populations may limit findings and many knowledge gaps on native bees still persist.

Functionally diverse flax-based rotations improve wild oat (Avena fatua) and cleavers (Galium spurium) management

Wild oat (Avena fatua L.) and false cleavers (Galium spurium) are currently a challenge to manage in less competitive crops such as flax (Linum usitatissimum L.). Increasing the functional diversity in crop rotations can be an option to improve weed management. Nonetheless, this strategy is not tested in flax in Western Canada. A 5-yr (2015-2019) crop rotation study was carried at three locations in western Canada to determine the effect of diverse flax-based crop rotations with differences in crop species, crop life cycles, harvesting time and reduced herbicides on managing A. fatua and G. spurium. The perennial rotation (flax-alfalfa (Medicago sativa L.)-alfalfa-alfalfa-flax) under reduced herbicide use was found to be the most consistent cropping system, providing similar A. fatua and G. spurium control to the conventional annual flax crop rotation[flax-barley (Hordium vulgare L.)-flax-oat (Avena sativa L.)-flax] with standard herbicides. At Carman, this alfalfa rotation provided even better weed control (80% A. fatua, 75% G. spurium) than the conventional rotation. Furthermore, a greater A. fatua control was identified compared to conventional rotation where two consecutive winter cereal crops were grown successfully in rotation (flax-barley-winter triticale (x Triticosecale ex A. Camus)-winter wheat (Triticum aestivum L.)-flax), greater A. fatua control was observed compared to the conventional crop rotation under standard herbicides. Incorporation of silage oat crops did not show consistent management benefits compared to the perennial alfalfa rotation but were generally similar to the conventional rotation with standard herbicides. The results showed that perennial alfalfa in the rotation minimized G. spurium and A. fatua in flax cropping systems, followed by rotations with two consecutive winter cereal crops.

Genome-Wide Association Study of Leaf Chlorophyll Content Using High-Density SNP Array in Peanuts (Arachis hypogaea L.)

The content of chlorophyll, a fundamental component required for photosynthesis in plants, has been widely studied across crop species. In this study, we aimed to evaluate the genetic diversity of 453 peanut accessions. We evaluated the evolutionary relationships using a genome-wide association study (GWAS) of leaf color data based on chlorophyll content analysis using the Axiom_Arachis array containing 58K single-nucleotide polymorphisms (SNPs). We identified seven SNPs as being significantly associated with leaf chlorophyll content on the chromosomes Aradu.A02, Aradu.A08, Araip.B02, Araip.B05, Araip.B06, and Araip.B08 in a GAPIT analysis. The SNP AX-176820297 on Araip.B05 was significantly linked with leaf chlorophyll content across the seasons. The Arahy.SDG4EV gene was detected to be in linkage disequilibrium (LD) with the significant SNPs, and its expression was significantly correlated with leaf chlorophyll content. The results of the current study provide useful and fundamental information with which to assess genetic variations in chlorophyll content and can be utilized for further genetic and genomic studies and breeding programs in peanuts.

Chromosome-scale assembly of the highly heterozygous genome of red clover (Trifolium pratense L.), an allogamous forage crop species

Red clover (Trifolium pratense L.) is used as a forage crop due to a variety of favorable traits relative to other crops. Improved varieties have been developed through conventional breeding approaches, but progress could be accelerated and gene discovery facilitated using modern genomic methods. Existing short-read based genome assemblies of the ~420 Megabase (Mb) genome are fragmented into >135,000 contigs with numerous errors in order and orientation within scaffolds, likely due to the biology of the plant which displays gametophytic self-incompatibility resulting in inherent high heterozygosity. A high-quality long-read based assembly of red clover is presented that reduces the number of contigs by more than 500-fold, improves the per-base quality, and increases the contig N50 statistic by three orders of magnitude. The 413.5 Mb assembly is nearly 20% longer than the 350 Mb short read assembly, closer to the predicted genome size. Quality measures are presented and full-length isoform sequence of RNA transcripts reported for use in assessing accuracy and for future annotation of the genome. The assembly accurately represents the seven main linkage groups present in the genome of an allogamous (outcrossing), highly heterozygous plant species.

CRISPR/Cas9 Mediated Genome Editing in Crop Plants

Recently, most genomic research has focused on genome editing methods to develop new technologies that could be easy, reliable, and feasible to edit plant genomes for highly productive agriculture. Genome editing is based on alternating a specific target DNA sequence by adding, replacing, and removing DNA bases. This newest technology called CRISPR/Cas9 seems to be less time-consuming, more effective and used in many research areas of plant genetic research. CRISPR/Cas9 systems have many advantages in comparison with ZFNs and TALENs and has been extensively used for genome editing to many crop plant species. Around 20 crop species are successfully worked out for trait improvements, for example, yield improvement, disease resistance, herbicide tolerance, and biotic and abiotic stress management. This review paper will overview recent advances in CRISPR/Cas genome editing research in detail. The main focus will be on the use of CRISPR/Cas9 technology in plant genome research.