Bringing high-throughput techniques to orphan crop of Africa: Highlights from the Tef TILLING Project

Orphan- or understudied-crops are mostly staple food crops in developing world. They are broadly classified under cereals, legumes, root crops, fruits and vegetables. These under-researched crops contribute to the diet of a large portion of resource-poor consumers and at the same time generate income for small-holder farmers in developing countries, particularly in Africa. In addition, they perform better than major crops of the world under extreme soil and climatic conditions. However, orphan crops are not without problems. Due to lack of scientific investigation, most of them produce low yields while others have a variety of toxins that affect the health of consumers. Here, we present some highlights on the status and future perspectives of the Tef Biotechnology Project that employs modern improvement technique in order to genetically improve tef (Eragrostis tef), one of the most important orphan crop in Africa. A reverse genetics approach known as TILLING (Targeting Induced Local Lesions IN Genome) is implemented in order to tackle lodging, the major yield limiting factor in tef.Key words: Orphan crops, underresearched crops, Eragrostis tef, TILLING, semi-dwarf.

The prospect of applying chemical elicitors and plant strengtheners to enhance the biological control of crop pests

An imminent food crisis reinforces the need for novel strategies to increase crop yields worldwide. Effective control of pest insects should be part of such strategies, preferentially with reduced negative impact on the environment and optimal protection and utilization of existing biodiversity. Enhancing the presence and efficacy of native biological control agents could be one such strategy. Plant strengthener is a generic term for several commercially available compounds or mixtures of compounds that can be applied to cultivated plants in order to ‘boost their vigour, resilience and performance’. Studies into the consequences of boosting plant resistance against pests and diseases on plant volatiles have found a surprising and dramatic increase in the plants' attractiveness to parasitic wasps. Here, we summarize the results from these studies and present new results from assays that illustrate the great potential of two commercially available resistance elicitors. We argue that plant strengtheners may currently be the best option to enhance the attractiveness of cultivated plants to biological control agents. Other options, such as the genetic manipulation of the release of specific volatiles may offer future solutions, but in most systems, we still miss fundamental knowledge on which key attractants should be targeted for this approach.

Human and ecological risk assessment of a crop protection chemical: a case study with the azole fungicide epoxiconazole.

Conventional risk assessments for crop protection chemicals compare the potential for causing toxicity (hazard identification) to anticipated exposure. New regulatory approaches have been proposed that would exclude exposure assessment and just focus on hazard identification based on endocrine disruption. This review comprises a critical analysis of hazard, focusing on the relative sensitivity of endocrine and non-endocrine endpoints, using a class of crop protection chemicals, the azole fungicides. These were selected because they are widely used on important crops (e.g. grains) and thereby can contact target and non-target plants and enter the food chain of humans and wildlife. Inhibition of lanosterol 14α-demethylase (CYP51) mediates the antifungal effect. Inhibition of other CYPs, such as aromatase (CYP19), can lead to numerous toxicological effects, which are also evident from high dose human exposures to therapeutic azoles. Because of its widespread use and substantial database, epoxiconazole was selected as a representative azole fungicide. Our critical analysis concluded that anticipated human exposure to epoxiconazole would yield a margin of safety of at least three orders of magnitude for reproductive effects observed in laboratory rodent studies that are postulated to be endocrine-driven (i.e. fetal resorptions). The most sensitive ecological species is the aquatic plant Lemna (duckweed), for which the margin of safety is less protective than for human health. For humans and wildlife, endocrine disruption is not the most sensitive endpoint. It is concluded that conventional risk assessment, considering anticipated exposure levels, will be protective of both human and ecological health. Although the toxic mechanisms of other azole compounds may be similar, large differences in potency will require a case-by-case risk assessment.

Role of Crop Research and Development in food Security of Africa

Food security is the main concern in Africa as the production and productivity of crops are under continuous threat. Indigenous crops also known as orphan- or as underutilized- crops provide key contributions to food security under the present scenario of increasing world population and changing climate. Hence, these crops which belong to the major categories of cereals, legumes, fruits and root crops play a key role in the livelihood of the resource-poor farmers and consumers since they perform better than the major world crops under extreme soil and climate conditions prevalent in the continent. These indigenous crops have the major advantage that they fit well into the general socio-economic and ecological context of the region. However, despite their huge importance, African crops have generally received little attention by the global scientific community. With the current production systems, only a fraction of yield potential was achieved for most of these crops. In order to devise strategies towards boosting crop productivity in Africa, the current production constraints should be investigated and properly addressed. Key traits known to increase productivity and/or improve nutrition and diverse conventional and modern crop improvement techniques need to be implemented. Commitments in the value-chain from the research, production, marketing to distribution of improved seeds are required by relevant national and international institutions as well as African governments to promote food security in a sustainable manner. The review also presents major achievements and suggestions for stakeholders interested in African agriculture.

Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef)

Background: Tef (Eragrostis tef), an indigenous cereal critical to food security in the Horn of Africa, is rich in minerals and protein, resistant to many biotic and abiotic stresses and safe for diabetics as well as sufferers of immune reactions to wheat gluten. We present the genome of tef, the first species in the grass subfamily Chloridoideae and the first allotetraploid assembled de novo. We sequenced the tef genome for marker-assisted breeding, to shed light on the molecular mechanisms conferring tef's desirable nutritional and agronomic properties, and to make its genome publicly available as a community resource. Results: The draft genome contains 672 Mbp representing 87% of the genome size estimated from flow cytometry. We also sequenced two transcriptomes, one from a normalized RNA library and another from unnormalized RNASeq data. The normalized RNA library revealed around 38000 transcripts that were then annotated by the SwissProt group. The CoGe comparative genomics platform was used to compare the tef genome to other genomes, notably sorghum. Scaffolds comprising approximately half of the genome size were ordered by syntenic alignment to sorghum producing tef pseudo-chromosomes, which were sorted into A and B genomes as well as compared to the genetic map of tef. The draft genome was used to identify novel SSR markers, investigate target genes for abiotic stress resistance studies, and understand the evolution of the prolamin family of proteins that are responsible for the immune response to gluten. Conclusions: It is highly plausible that breeding targets previously identified in other cereal crops will also be valuable breeding targets in tef. The draft genome and transcriptome will be of great use for identifying these targets for genetic improvement of this orphan crop that is vital for feeding 50 million people in the Horn of Africa.

N budget and NH3 exchange of a grass/clover crop at two levels of N application

Atmospheric ammonia (NH3) exchange during a single growing season was measured over two grass/clover fields managed by cutting and treated with different rates of mineral nitrogen (N) fertilizer. The aim was to quantify the total NH3 exchange of the two systems in relation to their N budget, the latter was split into N derived from symbiotic fixation, from fertilization, and from the soil. The experimental site was located in an intensively managed agricultural area on the Swiss plateau. Two adjacent fields with mixtures of perennial ryegrass (Lolium perenne L.), cocks foot (Dactylis glomerata L.), white clover (Trifolium repens L.) and red clover (Trifolium pratense L.) were used. These were treated with either 80 or 160 kg N ha−1 applied as NH4NO3 fertilizer in equal portions after each of four cuts. Continuous NH3 flux measurements were carried out by micrometeorological techniques. To determine the contribution of each species to the overall NH3 canopy compensation point, stomatal NH3 compensation points of the individual plant species were determined on the basis of NH4+ + NH3 (NHx) concentrations and pH in the apoplast. Symbiotic N2 fixation was measured by the 15N dilution method.

Taking Transgenic Plants with a Pinch of Salt

Making plants resistant to salty environments would be a boon for developing countries where poor land management has rendered large areas of arable land unfit for crop production. In a Perspective, Frommer and colleagues discuss how genetic engineering can be used to confer salt tolerance on plants ( see Apse et al.) and explore the implications of this feat for improving crop production in developing countries.

Dynamic Precision Phenotyping Reveals Mechanism of Crop Tolerance to Root Herbivory

The western corn rootworm (WCR) is a major pest of maize that is well adapted to most crop management strategies. Breeding for tolerance is a promising alternative to combat WCR, but is currently constrained by a lack of physiological understanding and phenotyping tools. We developed dynamic precision phenotyping approaches using carbon-11 with positron emission tomography, root autoradiography and radiometabolite flux analysis to understand maize tolerance to WCR. Our results reveal that WCR attack induces specific patterns of lateral root growth which are associated with a shift in auxin biosynthesis from indole-3-pyruvic acid to indole-3-acetonitrile. WCR attack also increases transport of newly synthesized amino acids to the roots, including the accumulation of glutamine. Finally, the regrowth zones of WCR attacked roots show an increase in glutamine turnover which strongly correlates with the induction of indole-3-acetonitrile-dependent auxin biosynthesis. In summary, our findings identify local changes in the auxin flux network as a promising marker for induced WCR tolerance.