Search Results (3)

Whole-genome multi-omics profiles contain valuable information for the characterization and prediction of complex traits in plants. In this study, we evaluate multi-omics models to predict four complex traits in barley (Hordeum vulgare); grain yield, thousand kernel weight, protein content, and nitrogen uptake. Genomic, transcriptomic, and DNA methylation data were obtained from 75 spring barley lines tested in the RadiMax semi-field phenomics facility under control and water-scarce treatment. By integrating multi-omics data at genomic, transcriptomic, and DNA methylation regulatory levels, a higher proportion of phenotypic variance was explained (0.72–0.91) than with genomic models alone (0.55–0.86). The correlation between predictions and phenotypes varied from 0.17–0.28 for control plants and 0.23–0.37 for water-scarce plants, and the increase in accuracy was significant for nitrogen uptake and protein content compared to models using genomic information alone. Adding transcriptomic and DNA methylation information to the prediction models explained more of the phenotypic variance attributed to the environment in grain yield and nitrogen uptake. It furthermore explained more of the non-additive genetic effects for thousand kernel weight and protein content. Our results show the feasibility of multi-omics prediction for complex traits in barley. Full article

The cultivation of nutritionally and economically important crops like tomato are often threatened by dry spells due to drought as these crops largely depend on an assured water supply. The magnitude and intensity of drought is predicted to intensify under climate change scenarios, particularly in semi-arid regions, where water is already a scarce resource. Hence, it is imperative to devise strategies to mitigate the adverse effects of drought on tomato through improvement in the plant’s efficiency to utilise the moisture in the growth medium. Since the root is the entry point for water, its intrinsic structure and functions play a crucial role in maintaining the soil–water–plant continuum during moisture deficit at the rhizosphere. Grafting offers a great opportunity to replace the root system of the cultivated tomato plants with that of wild species and hence provide a rapid solution to modulate root system architecture in contrast to the time-consuming conventional breeding approach. However, the success in developing the best graft combination of cultivated tomato and rootstock depends on the source of rootstock and selection methods. In this study, we used a high throughput phenomics facility to assess the efficiency of tomato, grafted on the rootstocks of different genetic backgrounds, at different levels of moisture in the soil. Rootstocks included tomato cultivars and the hybrids, derived from the crosses involving wild relatives, as donor parents. Among the rootstocks, an interspecific (Solanum lycopersicum × S. pennellii) derivative RF4A was highly efficient in terms of productive use of water. The RF4A rootstock-grafted plants were more conservative in water use with higher plant water status through relatively better stomatal regulation and hence were more efficient in generating greater biomass under water stress conditions. These plants could maintain a higher level of PSII efficiency, signifying better photosynthetic efficiency even under water stress. The distinct response of interspecific rootstock, RF4A, to water stress can be ascribed to the effective root system acquired from a wild parent (S. pennellii), and hence efficient water uptake. Overall, we demonstrated the efficient use of a phenomics platform and developed a protocol to identify promising rootstock–scion combinations of tomato for optimization of water use. Full article

Stress in forest ecosystems (FES) occurs as a result of land-use intensification, disturbances, resource limitations or unsustainable management, causing changes in forest health (FH) at various scales from the local to the global scale. Reactions to such stress depend on the phylogeny of forest species or communities and the characteristics of their impacting drivers and processes. There are many approaches to monitor indicators of FH using in-situ forest inventory and experimental studies, but they are generally limited to sample points or small areas, as well as being time- and labour-intensive. Long-term monitoring based on forest inventories provides valuable information about changes and trends of FH. However, abrupt short-term changes cannot sufficiently be assessed through in-situ forest inventories as they usually have repetition periods of multiple years. Furthermore, numerous FH indicators monitored in in-situ surveys are based on expert judgement. Remote sensing (RS) technologies offer means to monitor FH indicators in an effective, repetitive and comparative way. This paper reviews techniques that are currently used for monitoring, including close-range RS, airborne and satellite approaches. The implementation of optical, RADAR and LiDAR RS-techniques to assess spectral traits/spectral trait variations (ST/STV) is described in detail. We found that ST/STV can be used to record indicators of FH based on RS. Therefore, the ST/STV approach provides a framework to develop a standardized monitoring concept for FH indicators using RS techniques that is applicable to future monitoring programs. It is only through linking in-situ and RS approaches that we will be able to improve our understanding of the relationship between stressors, and the associated spectral responses in order to develop robust FH indicators. Full article