Field-omics—understanding large-scale molecular data from field crops

Abstract

The recent advances in gene expression analysis as well as protein and metabolite quantification enable genome-scale capturing of complex biological processes at the molecular level in crop field trials. This opens up new possibilities for understanding the molecular and environmental complexity of field-based systems and thus shedding light on the black box between genotype and environment, which in agriculture always is influenced by a multi-stress environment and includes management interventions. Nevertheless, combining different types of data obtained from the field and making biological sense out of large datasets remain challenging. Here we highlight the need to create a cross-disciplinary platform for innovative experimental design, sampling and subsequent analysis of large-scale molecular data obtained in field trials. For these reasons we put forward the term field-omics: “Field-omics strives to couple information from genomes, transcriptomes, proteomes, metabolomes and metagenomes to the long-established practice in crop science of conducting field trials as well as to adapt current strategies for recording and analysing field data to facilitate integration with ‘-omics’ data.”

Metabolite profiles of maize leaves in drought, heat and combined stress field trials reveal the relationship between metabolism and grain yield

“…This is likely due to the progressive nature of field stress treatments and needs to be considered as a general trend under field conditions. In contrast to the phenotypic and transcriptomic profiles monitored in previous studies (Witt et al, 2012;Alexandersson et al, 2014), some typical stress responses of primary metabolism in field-grown plants are fairly similar to those of greenhouse-grown plants and seem well conserved between growth conditions and even among species. This robustness of metabolic change renders it a good candidate for marker-assisted breeding.…”

“…HS was applied by altering the planting date to ensure that the reproductive phase coincided with high temperatures (Craufurd et al, 2013). Despite limitations in fine climate control, large-scale field trials are still valuable, since it is often reported that important agronomical traits are masked in greenhouse-grown crops (Alexandersson et al, 2014). In our previous study in controlled greenhouse conditions, genotypes chosen to cover a wide range of DS tolerance based on field results did not display differential effects of DS on physiological traits (Witt et al, 2012).…”

Plant Resistance Inducers against Pathogens in Solanaceae Species—From Molecular Mechanisms to Field Application

“…This is a key issue in a field setting, which represents a multi-stress environment with many classes of pathogens and pests, as exemplified by the established distinction between biotrophs inducing SA-related pathways and necrotrophs and insect herbivores inducing mainly JA/ET-related pathways. In general, there is a need to move molecular studies from laboratory to field settings and also try to incorporate as much knowledge as possible from model species into crops [158]. For example, in a field experiment by Thaler et al [36] tomato plants treated with BTH exhibited reduced symptoms of bacterial speck caused by P. syringae compared to non-treated plants.…”

Improved Representation of Biological Information by Using Correlation as Distance Function for Heatmap Cluster Analysis

“…Raw data from the omic experiments need to be analysed and converted into figures, models, and other visual representations to be shared among the scientific community. The holistic measurement of the phenotype of a crop plant such as maize or rice is the main objective of agricultural phenomics, also called field-omics [13]. Currently, yield and phenotypic data obtained by public breeding institutions such as Centro Internacional de Mejoramiento de Maiz y Trigo (CIMMYT) and the International Rice Research Institute (IRRI) are mostly provided as numbers within large tables in spreadsheet format.…”