Applications of Multi-Omics Technologies for Crop Improvement

Multiple “omics” approaches have emerged as successful technologies for plant systems over the last few decades. Advances in next-generation sequencing (NGS) have paved a way for a new generation of different omics, such as genomics, transcriptomics, and proteomics. However, metabolomics, ionomics, and phenomics have also been well-documented in crop science. Multi-omics approaches with high throughput techniques have played an important role in elucidating growth, senescence, yield, and the responses to biotic and abiotic stress in numerous crops. These omics approaches have been implemented in some important crops including wheat (Triticum aestivum L.), soybean (Glycine max), tomato (Solanum lycopersicum), barley (Hordeum vulgare L.), maize (Zea mays L.), millet (Setaria italica L.), cotton (Gossypium hirsutum L.), Medicago truncatula, and rice (Oryza sativa L.). The integration of functional genomics with other omics highlights the relationships between crop genomes and phenotypes under specific physiological and environmental conditions. The purpose of this review is to dissect the role and integration of multi-omics technologies for crop breeding science. We highlight the applications of various omics approaches, such as genomics, transcriptomics, proteomics, metabolomics, phenomics, and ionomics, and the implementation of robust methods to improve crop genetics and breeding science. Potential challenges that confront the integration of multi-omics with regard to the functional analysis of genes and their networks as well as the development of potential traits for crop improvement are discussed. The panomics platform allows for the integration of complex omics to construct models that can be used to predict complex traits. Systems biology integration with multi-omics datasets can enhance our understanding of molecular regulator networks for crop improvement. In this context, we suggest the integration of entire omics by employing the “phenotype to genotype” and “genotype to phenotype” concept. Hence, top-down (phenotype to genotype) and bottom-up (genotype to phenotype) model through integration of multi-omics with systems biology may be beneficial for crop breeding improvement under conditions of environmental stresses.

Root-lesion Nematodes Affecting Dryland Cereals in the Semiarid Pacific Northwest USA

Root-lesion nematodes (Pratylenchus spp.) are parasites that invade and deteriorate roots, thereby reducing the efficiency of water and nutrient uptake. Pratylenchus neglectus and P. thornei are the two species that are most prevalent and cause reduced yields of rainfed wheat and barley in semiarid regions of the Pacific Northwest. They are particularly damaging where wheat and barley are produced without irrigation in areas receiving less than 450 mm (18 inch) of precipitation annually. This review is focused on the biology and management of P. neglectus and P. thornei in semiarid rainfed agriculture. Characteristics of climates, soils and crop production systems are described as a preface to constraints placed upon management options. Discussions include the economic importance, host ranges, and protocols for sampling and species identification. Discussion of disease management options include crop rotation, genetic resistance and tolerance, planting date, trap and biofumigant crops, crop nutrition, chemical and biological nematicides, and tillage. Predictions for rainfed agriculture in a period of changing climate are presented, as are suggestions for important areas of research including crop genetics, nematode testing and communication of results, Pratylenchus biology, mechanisms of resistance, the phytobiome, and closing the ‘yield gap’ between actual and attainable yields.

Biochemical and Genetic Approaches Improving Nitrogen Use Efficiency in Cereal Crops: A Review

Nitrogen is an essential nutrient required in large quantities for the proper growth and development of plants. Nitrogen is the most limiting macronutrient for crop production in most of the world’s agricultural areas. The dynamic nature of nitrogen and its tendency to lose soil and environment systems create a unique and challenging environment for its proper management. Exploiting genetic diversity, developing nutrient efficient novel varieties with better agronomy and crop management practices combined with improved crop genetics have been significant factors behind increased crop production. In this review, we highlight the various biochemical, genetic factors and the regulatory mechanisms controlling the plant nitrogen economy necessary for reducing fertilizer cost and improving nitrogen use efficiency while maintaining an acceptable grain yield.

The Influence of Physical Treatments on Phytochemical Changes in Fresh Produce after Storage and Marketing

More food with high nutritional content will be needed to feed the growing global human population, which is expected to reach 10 billion by 2050. Fruits and vegetables contain most of the minerals, micronutrients, and phytonutrients essential for human nutrition and health. The quantity of these phytochemicals depends on crop genetics, weather and environmental factors, growth conditions, and pre-harvest and post-harvest treatments. These phytochemicals are known to have anti-cancer properties and to regulate immunity, in addition to hypolipidemic, antioxidant, anti-aging, hypotensive, hypoglycemic, and other pharmacological properties. Physical treatments have been reported to be effective for managing several post-harvest diseases and physiological disorders. These treatments may affect the external, internal, and nutritional qualities of fruits and vegetables. Therefore, the aim of this review is to summarize the information recently reported regarding the use of physical treatments applied either directly or in combination with other means to maximize and maintain the phytochemical content of fresh and fresh-cut or processed fruits and vegetables.

Nitrogen and Stem Development: A Puzzle Still to Be Solved

High crop yields are generally associated with high nitrogen (N) fertilizer rates. A growing tendency that is urgently demanding the adoption of precision technologies that manage N more efficiently, combined with the advances of crop genetics to meet the needs of sustainable farm systems. Among the plant traits, stem architecture has been of paramount importance to enhance harvest index in the cereal crops. Nonetheless, the reduced stature also brought undesirable effect, such as poor N-uptake, which has led to the overuse of N fertilizer. Therefore, a better understanding of how N signals modulate the initial and late stages of stem development might uncover novel semi-dwarf alleles without pleiotropic effects. Our attempt here is to review the most recent advances on this topic.

Open Innovation and Value Creation in Crop Genetics

The development of cultivars exhibiting improved climate resilience and containing effective input and agronomic traits and their adoption by growers and acceptance by supply chains, consumers, and society remain essential drivers of a successful agricultural strategy directed to feed the world and overcome the challenges brought by nature, an increasingly stringent regulatory environment, and an ever-growing population. In order to deliver on the daunting challenge of providing affordable, nutritious food to humankind, while reducing agriculture’s environmental footprint, new innovation models are needed. Open innovation is being adopted by seed companies in order to tap into the vast pool of human talent available beyond their boundaries and increase their ability to generate, adopt, develop, and bring to market novel technologies while building upon the increasing global community of innovators and harnessing the resources of venture capitalists. In addition, open innovation can help streamline product development processes, as well as lead to the exploration of novel markets which would otherwise go unexploited. At the same time, open innovation provides the means for other firms and entrepreneurs to gain access to technologies which would be beyond the scope of their development abilities but which can be leveraged to create significant value for their own customers and markets. This chapter provides an updated perspective on the most salient aspects of open innovation. Though its main focus is crop genetics and the development of improved cultivars, the general principles discussed also apply to other activities associated with the value chains linking agriculture and customers.

Michael Denis Gale. 25 August 1943—18 July 2009

Michael (Mike) Gale was an internationally well-known crop geneticist with a career devoted mostly to wheat genetics. However, he also studied rice, maize, pearl millet and fox millet for the benefit of agriculture in developing countries. He brought new knowledge and techniques into plant breeding that made a difference to crop improvement worldwide. Noteworthy is his team's leadership in (i) defining the genetic basis of dwarfism in wheat, the major genetic innovation underlying the previously achieved ‘green revolution’ in wheat production; (ii) expanding knowledge of ‘pre-harvest sprouting’, which occurs in many wheat varieties growing in temperate climates, which reduces their flour quality and value; (iii) developing the first comprehensive genetic maps of wheat based on isozymic and DNA-based molecular markers; and (iv) developing the comparative genetics of grasses based on the conserved order of genes on chromosome segments, consistent with the evolution of the species from a common ancestor. These discoveries had a major impact in plant genetics. His team also provided the worldwide cereal geneticists and breeding communities with technologies and genetic markers that accelerated the development of cereal genetics and facilitated more efficient plant breeding. He made major and influential contributions to international agricultural research, particularly targeted at developing countries, through his participation on international and national committees, including those of the Consultative Group for International Agricultural Research. His contribution helped to drive the international research agenda for crop genetics, plant breeding and plant science generally.