Occurrence of Macrophomina phaseolina in Israel: Challenges for Disease Management and Crop Germplasm Enhancement

Macrophomina phaseolina is a soil-borne fungal pathogen infecting many important crop plants. The fungus, which can survive on crop debris for a long period of time, causes charcoal rot disease by secreting a diverse array of cell-wall degrading enzymes and toxins. M. phaseolina thrives during periods of high temperatures and arid conditions, as typically occuring in Israel and other countries with a Mediterranean climate. Crop losses due to charcoal rot can be expected to increase and spread to other countries in a warming global climate. Management of this pathogen is challenging, requiring an array of approaches for the various crop hosts. Approaches that have had some success in Israel include grafting of melons and watermelons on resistant squash rootstocks and soil application of fungicide to reduce disease incidence in melons, fumigation and alterations in planting date and mulching of strawberries, and alteration in irrigation regime of cotton. Elsewhere, these approaches as well as soil amendments, and addition of organisms that are antagonistic to M. phaseolina have had success in some crop situations. Management through host resistance would be the most sustainable approach, but requires identifying resistant germplasm for each crop and introgressing the resistance into the leading cultivars. Resistance to charcoal rot is under complex genetic control in most crops, posing a great challenge for its introgression into elite germplasm. Moreover, fast, reliable methods of screening for resistance would have to be developed for each crop. The toothpick-inoculation method used by us holds great promise for selecting resistant germplasm for melons and possibly for sesame, but other methodologies have to be devised for each individual crop.

Assessment of Morphological Mutations and Genetic Components in MMS and EMS Induced Chilli Cultivars, NS 1101 and NS 1701DG

A change in the genetic makeup of a plant is an essential prerequisite for the breeding programs and induce mutagenesis is an important approach to create the variations within crop germplasm. The main objective of this study is to find the mutants in chemically treated M2 chilli plant populations. Since, mutagenesis in chilli plants was induced through EMS and Cd to increase the genetic variability that results in thirteen mutant plants at M2 generation from the genetic background of chilli varieties NS 1101 and NS 1701 DG, respectively. Most of the mutant phenotypes observed felled within qualitative and quantitative characteristics the seven major categories including plant height, leaf shape, leaf color, branch, and flower color, fruits, 1000 seed weight, yield, and root length. The inter-population differences were carried out through analysis of variance of quantitative traits of chemically treated chilli populations. Results reflect increased mean value in quantitative traits that could validate the improvement over the parental lines. Fruit number and seed weight were the main priority traits in the selection of high yield plants and these quantitative traits have a strong association with the yield of the plant. Genetic variability induced by chemical mutagens in chilli can integrate into further chilli breeding programs as new crop germplasm with improved agronomic traits. Mutants selected from 0.2% treated chilli populations can be used to develop an efficient and fast crop variety of chilli with desirable traits. The present study about the genetic variability induced by chemical mutagenesis provides more opportunities to bring diversity in the genetic makeup of chilli plant for improvement of the desirable traits.

Rapid and Accurate Varieties Classification of Different Crop Seeds Under Sample-Limited Condition Based on Hyperspectral Imaging and Deep Transfer Learning

Rapid varieties classification of crop seeds is significant for breeders to screen out seeds with specific traits and market regulators to detect seed purity. However, collecting high-quality, large-scale samples takes high costs in some cases, making it difficult to build an accurate classification model. This study aimed to explore a rapid and accurate method for varieties classification of different crop seeds under the sample-limited condition based on hyperspectral imaging (HSI) and deep transfer learning. Three deep neural networks with typical structures were designed based on a sample-rich Pea dataset. Obtained the highest accuracy of 99.57%, VGG-MODEL was transferred to classify four target datasets (rice, oat, wheat, and cotton) with limited samples. Accuracies of the deep transferred model achieved 95, 99, 80.8, and 83.86% on the four datasets, respectively. Using training sets with different sizes, the deep transferred model could always obtain higher performance than other traditional methods. The visualization of the deep features and classification results confirmed the portability of the shared features of seed spectra, providing an interpreted method for rapid and accurate varieties classification of crop seeds. The overall results showed great superiority of HSI combined with deep transfer learning for seed detection under sample-limited condition. This study provided a new idea for facilitating a crop germplasm screening process under the scenario of sample scarcity and the detection of other qualities of crop seeds under sample-limited condition based on HSI.

Crop Germplasm: Molecular and Physiological Perspective Towards Achieving Global Crop Sustainability

Germplasm is a long-term resource management mission and investment for civilization. For both food and nutritional health, the present changing environmental scenario has become an urgent universal concern. Multiple excellent studies have been previously performed, although the advancement and innovation of practices will require the exploration of the potentiality of crop germplasm. In this study, we emphasized (i) germplasm activates, current challenges and ongoing trends of the crop germplasm, and (ii) how the system biology will be helpful to understand the complex traits such as water use efficiency (WUE), and nitrogen use efficiency (NUE) to mitigate challenges for sustainable development under growing food requirement and climate change conditions. We focused on a vision for transforming PGR into a bio-digital resource system, for the development of climate-smart crops for sustainable food production. Moreover, this review attempted to address current challenges, research gaps and describe the advanced integrated strategies that could provide a platform for future crop improvement research.

Exploring Plant Genetic Variations with Morphometric and Molecular Markers

For centuries, crop improvement has served as the basis of food security of ever increasing human population. Though vast germplasm collections are available; their exploitation for crop improvement still depends upon efficient assessment of genetic diversity. Genetic variability is the key element in adaptation of plants to varying climates. While crops with narrow genetic diversity are vulnerable to stresses. The estimation of extent and pattern of genetic variability is a prerequisite for generating superior varieties. Genetic diversity analysis generates key information to dissect genetic variations in crop germplasm with the help of morphometrical, biochemical and molecular tools. Among these, DNA markers provide a reliable and detailed insight into the similarities and differences among crops. In this chapter, we discuss the applications of phenotypic and molecular markers to probe genetic divergence in crops and present case studies that describe the significance of these tools to characterize sorghum germplasm. Furthermore, we spotlight sorghum biodiversity exploration efforts worldwide and propose future directions.

Advances in the generation of insertion-based genome edits in plants

Tremendous progress has been achieved in the field of gene editing in plants, such as with the use of zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR). Because of the potential advantages associated with mutant creation and crop germplasm innovation, genome editing technology has been rapidly developed and widely used in crop improvement in recent years. In this review, we aim to document some of the important recent developments and applications of genome-editing tools, especially with respect to gene knock-ins. We introduce the mechanism underlying knock-ins and different outcomes of insertion. We also discuss genome editing tools and methods developed to improve insertion efficiencies. Additionally, we review the recent trends in genetic editing biotechnologies; several strategies are being developed to further improve the efficiency of plant gene knock-ins. Undoubtedly, CRISPR/Cas technology will boost the development of new plant breeding techniques tremendously.

Using wild relatives and related species to build climate resilience in Brassica crops

Climate change will have major impacts on crop production: not just increasing drought and heat stress, but also increasing insect and disease loads and the chance of extreme weather events and further adverse conditions. Often, wild relatives show increased tolerances to biotic and abiotic stresses, due to reduced stringency of selection for yield and yield-related traits under optimum conditions. One possible strategy to improve resilience in our modern-day crop cultivars is to utilize wild relative germplasm in breeding, and attempt to introgress genetic factors contributing to greater environmental tolerances from these wild relatives into elite crop types. However, this approach can be difficult, as it relies on factors such as ease of hybridization and genetic distance between the source and target, crossover frequencies and distributions in the hybrid, and ability to select for desirable introgressions while minimizing linkage drag. In this review, we outline the possible effects that climate change may have on crop production, introduce the Brassica crop species and their wild relatives, and provide an index of useful traits that are known to be present in each of these species that may be exploitable through interspecific hybridization-based approaches. Subsequently, we outline how introgression breeding works, what factors affect the success of this approach, and how this approach can be optimized so as to increase the chance of recovering the desired introgression lines. Our review provides a working guide to the use of wild relatives and related crop germplasm to improve biotic and abiotic resistances in Brassica crop species.

Precision agriculture and geospatial techniques for sustainable disease control

The agricultural community is confronted with dual challenges; increasing production of nutritionally dense food and decreasing the impacts of these crop production systems on the land, water, and climate. Control of plant pathogens will figure prominently in meeting these challenges as plant diseases cause significant yield and economic losses to crops responsible for feeding a large portion of the world population. New approaches and technologies to enhance sustainability of crop production systems and, importantly, plant disease control need to be developed and adopted. By leveraging advanced geoinformatic techniques, advances in computing and sensing infrastructure (e.g., cloud-based, big data-driven applications) will aid in the monitoring and management of pesticides and biologicals, such as cover crops and beneficial microbes, to reduce the impact of plant disease control and cropping systems on the environment. This includes geospatial tools being developed to aid the farmer in managing cropping system and disease management strategies that are more sustainable but increasingly complex. Geoinformatics and cloud-based, big data-driven applications are also being enlisted to speed up crop germplasm improvement; crop germplasm that has enhanced tolerance to pathogens and abiotic stress and is in tune with different cropping systems and environmental conditions is needed. Finally, advanced geoinformatic techniques and advances in computing infrastructure allow a more collaborative framework amongst scientists, policymakers, and the agricultural community to speed the development, transfer, and adoption of these sustainable technologies.

Proline, Total Antioxidant Capacity, and OsP5CS Gene Activity in Radical and Plumule of Rice are Efficient Drought Tolerance Indicator Traits

The success of a plant breeding program is linked with the rapid screening of crop germplasm. In the following study, the germination stage of rice seeds has been examined for the rapid screening of drought-tolerant genotypes. The rice genotypes (10 drought tolerant, 5 moderately drought tolerant, and 5 drought susceptible) were sown in Petri dishes under control and osmotic stress of 15% PEG6000. Data were recorded after four days of sowing for the osmotic stress-induced change in imbibition rate, speed of germination, radical and plumule length, radical and plumule total fresh and dry weight, proline contents, total antioxidant capacity, and malondialdehyde level in radical and plumule of seeds. Moreover, the change in expression of OsP5CS gene was also recorded in one of each drought tolerant, moderately drought tolerant, and drought susceptible genotypes. Under osmotic stress, the level of proline, total antioxidant capacity, and the expression of OsP5CS were increased in drought-tolerant genotypes as compared to moderately drought tolerant and drought susceptible genotypes. While, the change in imbibition rate, speed of germination, radical and plumule length, and fresh and dry weight were not symmetrical in drought tolerant, moderately drought tolerant, and drought susceptible genotypes. In short, the symmetrical change in proline, total antioxidant capacity, and expression of OsP5CS gene within radical and plumule of drought tolerant, moderately drought tolerant, and drought susceptible genotypes can help rapid screening of drought-tolerant rice genotypes.