Improving root system architecture for enhanced drought tolerance and nutrient use efficiency in semi-arid agriculture of chickpea

Lead Research Organisation: University of Edinburgh
Department Name: Sch of Biological Sciences

Abstract

This project will focus on chickpea in Ethiopia. Agriculture in Ethiopia and a further 19 of 31 "least developed" countries in Africa is constrained by arid, infertile and marginal soil conditions. Climate change, altered precipitation patterns, prolonged droughts and the soil loss that ensues, adds to the challenges. Ethiopia's population has risen 2.6% annually over the last 50 years, but crop production grew by only 2% annually. Solutions are required to increase crop productivity, quantity and quality, for food security and climate resilience.
Legumes such as chickpea and grains such as sorghum, millet and maize are the major crops here. We will focus on chickpea, a key crop in developing nations. Pulses such as chickpea are crucial for protein nutrition to provide income and support livelihoods in rural areas of the least developed countries. Most chickpea growers in semi-arid agrosystems are subsistence farmers who lack resources and knowledge for crop improvement, thus, in the long-term, will benefit most from the improvements we aim for.
The crucial role of root systems in limiting crop productivity was not previously addressed in breeding. Root system size and distribution sets the capacity for water and nutrient acquisition and therefore is key for climate stress resilience, contributing to drought tolerance, water and nutrient use efficiency. We will focus on developing advanced but cheap and cost-effective tools for root growth characterisation. This will subsequently allow researchers and breeders in Ethiopia to identify suitable germplasm for chickpea breeding. Plant resilience depends on appropriate root system architecture adapted to local soils; our low-cost but powerful tools will enable location-adapted breeding programs in Ethiopia for the first time. This will be the most direct path to innovation for increased and sustainable chickpea production by subsistence farmers.
We are working closely with international scientists from Ethiopia and USA, with their project: "Climate resistant chickpea" (CRC). This initiative has support by several international programs, e.g. the USAID "Feed the Future", CGIAR "Consortium Research Program on Grain Legumes", and is key for success in our project. CRC generates a huge amount of information and resources for crop improvement. These include: a pre-breeding population consisting of >7000 unique lines and a collection of >600 landrace accessions in Ethiopia. Ethiopia has developed networks of agricultural advice services throughout the country that are critical for uptake of novel technologies and germplasm. We will work closely with these networks through our Ethiopian and international partners to provide pathways for innovation.
We have three main aims at the Foundation Project stage:
First, to develop, complement and enhance the existing network of Ethiopian and international efforts by using our multidisciplinary expertise to develop tools to enhance breeding for good yields even in drought conditions. For this to succeed in the longer term, we will develop collaborations, workshops and site visits to Ethiopia and through regular communication;
Second, we will develop powerful, low-cost technologies and equipment for root phenotyping in Edinburgh and Ethiopia; and in close coordination with Ethiopian colleagues. The project's Foundation phase will advance technology development in concert with evaluation in Ethiopia, to make the equipment fit for purpose under local conditions and in the hands of local breeders.
Third, to identify how our expertise in innovation financing and soil quality enhancement can serve to accelerate uptake of the technological innovations we will develop and how to increase soil fertility and soil nutrient recycling, potentially by biochar amendment. We will, in collaboration with Ethiopian colleagues, contribute to long-term planning for sustainable enhancement of food security in Ethiopia and other countries with an arid climate.

Technical Summary

This project focuses on increasing climate resilience of chickpea in Ethiopia, where it is planted in semi-arid cropping systems. Eight Edinburgh and Ethiopian academics and chickpea breeders joined up to co-develop this proposal to develop technology necessary to measure chickpea root traits. This will inform breeding strategies that desire to introduce genetic determinants found in deep-rooting varieties and combine these traits with varieties that produce small shoot canopies that transpire less water, for water efficient varieties that specifically resist 'terminal drought': low water availability at the time of flowering and seed set; a major factor limiting yields. This has previously not been possible due to the complexity and prohibitive cost of systems that can measure root system growth and distribution in soil several times during the life cycle of the crop.
The disruptive technology we propose to develop, is powerful, yet affordable, and takes advantage of the large size and ease of visibility of the chickpea root. Using mesocosms assembled from material readily available locally, and commodity electronic components to build camera arrays that are >2 orders of magnitude cheaper than conventional solutions, powerful and sophisticated machine-learning algorithms and distributed computing software; we aim to provide data to inform breeding efforts by phenotypic analysis of large numbers of natural accessions and landraces grown in soil. The low cost of each imaging array, and the rapid image capture, will allow the phenotyping platform to be replicated many times at breeding stations, further contributing to the high analytical throughput and allowing, for the first time, for whole breeding populations to be characterised for root traits.
These efforts will be complemented by case studies to address financial incentives for technological innovation and the improvement of soil quality for long-term sustainability of the projected agronomic gains.

Planned Impact

The immediate beneficiaries of this project are Ethiopian researchers and plant breeders working on improving chickpea yields and its climate resilience. Chickpea is a crop of the semi-arid tropics, planted by subsistence and smallholder farmers, which has low resource requirements and is nutritious (high protein and mineral content in seed). It is a key source of protein for the rural population in Ethiopia, East Africa, the Middle East, India and Pakistan. More than 90% of the world's crop of chickpea is produced in these ODA-eligible countries, with no production in the UK. The proposed project will ultimately benefit the main producers, subsistence and smallholder farmers, social and economic progress in less-developed, ODA eligible countries the most.
This project is a joint effort by four investigators each in Edinburgh and Ethiopia and one investigator in the USA, a leader of global efforts for chickpea improvement. A key objective of our project to establish a long-term collaboration with these investigators to promote the dissemination of knowledge, the co-development and uptake of innovative technologies for chickpea germplasm improvement by breeding and to promote the future introduction of efficient and sustainable agricultural practice. The best approach for insuring food security is to strengthen Ethiopia's national efforts at breeding and improved agronomic practice by collaborating with the key 'movers' at the national level that will implement the innovative technologies in their breeding programs. The involvement of our Ethiopian partners is best to robustly build and enhance the country's capacities for self-sustainable crop improvement. Technology and knowledge transfer are part of this project and will start at the beginning of the project.
Our Ethiopian project partners are directly placed within and are leaders of the Ethiopian chickpea crop improvement and breeding efforts. Therefore, they are providing a direct path to impact by implementing the innovations into their on-going breeding programs, sharing their experience and innovative approaches with other breeders and researchers in Ethiopia and beyond.
A significant part of the proposed research activities will occur at EIAR, under the direction of Dr. Fikre and the involvement of the other Ethiopian project partners. Therefore, technology and knowledge transfer will occur throughout the project and this itself is impactful, as through experience and training in the use of the new technology for imaging and analysing plant phenotypes (traits), a wide range of opportunities to apply these to the crop improvement efforts for other Ethiopian crops opens up. To further ensure an impactful outcome of the project, 3-week training visits of two Ethiopian collaborators of Dr. Fikre in Edinburgh (planned for Q1/2018 and Q1/2019) will ensure that the technology is firmly in Ethiopian hands at the end of the project and can be implemented in a large scale for the local breeding efforts.
Our Ethiopian collaborators are also linked to international crop improvement and breeding efforts that operate in other ODA-eligible countries such as India. A key measure for success in our project would be the dissemination and uptake of the technology we propose to develop also by international chickpea breeders in countries with semi-arid agriculture.
Ultimately poor farmers in Ethiopia will only benefit the adoption of this technology in breeding programs is funded. Therefore, one WP of the project focuses on the financial tools and incentives necessary to fund technological innovation.
In summary, there are three main efforts we will undertake to promote and achieve long-term impact: collaboration with Ethiopian breeders and researchers; outreach to international organisations involved in chickpea breeding in ODA eligible countries, and developing funding models to approach potential funders for breeding programs with our Ethiopian and American collaborators.
 
Description We can demonstrate that growing chickpea plants in the rhizobox system can provide a substrate for vigorous growth and flowering of the plants subjected to these tests. This is significant, because we now have specific evidence that the hypothesis underlying the proposal (that plants can be properly grown in soil and their root systems visualised) is valid and we can progress now to develop and optimise the machine learning approaches to recognition and pattern analysis of root system architecture. Further work in characterising different soil and environmental conditions has revealed that root system architecture in rhizoboxes responds in patterns expected from soil or field grown plants. This further exemplifies the power of the approach we are establishing to generate a system and toolkit for high-throughput screening of plants for root system based traits.
Exploitation Route We have been communicating our results to our Ethiopian collaborators for implementation, and the PI recently met with them in Ethiopia for discussions.
Sectors Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Education,Environment,Government, Democracy and Justice

URL http://chickpearoots.org/home
 
Description The work in progress has attracted much interest from students here in Edinburgh. Several students have now been integrated into the project in the form of projects, volunteer work and extracurricular research projects. We have held two workshops in Ethiopia, which involved investigators within and outside of the project, and which are leading to collaborations with other research projects for other crops.
Sector Agriculture, Food and Drink
Impact Types Cultural,Societal

 
Title Growth of large root systems in low-cost mesocosms 
Description We have developed a reproducible method to grow chickpea plants in large mesocosms, which can potentially be used for other large crops with extensive root systems. 
Type Of Material Technology assay or reagent 
Year Produced 2018 
Provided To Others? No  
Impact The methodology will be made available this year. 
 
Title Software for image-stitching, distortion-free image assembly and segmentation 
Description This software is being developed to perform the first of a multi-step process to utilise the images generated by Raspberry PI cameras 
Type Of Technology New/Improved Technique/Technology 
Year Produced 2018 
Impact The software is currently being validated 
 
Description Engagement with chickpea researchers at international conference and with other Ethiopian chickpea researchers (not partners in the current award) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This refers mainly to the participation at an annual chickpea conference, where our project was introduced in discussion groups. Secondly it also refers to presentations given by the PI at various institutions in Ethiopia which has significantly broadened awareness and interest in the project.
Year(s) Of Engagement Activity 2017,2018
 
Description Training workshop in Ethiopia 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Training workshop in Derbe Zeit Ethiopia on machine learning and plant growth techniques. The participants learned how to integrate biological research aims with sophisticated analysis by computer vision.
Year(s) Of Engagement Activity 2019
 
Description Workshop in Ethiopia 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The Edinburgh research team held a workshop in Ethiopia. Stakeholders of all kind participated: students, employees of the Ethiopian Agricultural Research Agency, from other Ethiopian Universities, from national organisations such as the Ethiopian Biotechnology Institute and the Ethiopian Soil Agency.
We presented our novel system to phenotype root system architecture which attracted a lot of interest from people working on chickpea and those working on other crops such as tef.
Year(s) Of Engagement Activity 2018