Digital Technologies to Modernize Effective and Efficient use of Plant Genetic Resources Eric Huttner and Miriam McCormack Australian Centre for International Agricultural Research (ACIAR) IAC 2016, New Delhi, India

ACIAR Agricultural Research arm of the Australian Aid program. Broker partnerships between Australian (or International Centres) and Developing Countries Scientists to undertake research for development. 12 Research Programs to target specific areas of agricultural production. About 100 M AUD annual budget. Head office in Canberra, Australia with Country Offices located in Partner Countries and regions. Aligned with partner country priorities and Australian government priorities

ACIAR Priorities Projects are commissioned based on country priorities ©EHuttner2013 Projects are commissioned based on country priorities Australian Aid program priorities: Economic growth, trade, productivity as a way out of poverty Focus on the Asia-Pacific region Empowering women and girls - target of 80% across project portfolio Engage and promote private sector Nutrition Address climate change and its consequences

Crop Improvement and Management Food security through increased productivity Agronomic practices can be improved but they are constrained: Land, Labour, Water, Inputs Sustainability Post-harvest opportunities: markets, products storage Farming systems: Using more productive crops Diversification: crops, varieties Increased productivity through the seeds Better varieties may: give higher yield resist disease and pests, minimise losses have better quality, higher protein, vitamins, cooking Improvement is delivered through seeds easy to adopt limited change required need to produce and distribute the seeds But other improvements contribute too! Improved varieties need genetic resources and exchange

Modernising plant breeding in the 21st century DNA Phenotypic data Information Technologies Modelling Genetic x Environment x Management New breeding approaches Challenges for developing countries Breeding is not enough India 17th Century, National Gallery of Australia

Phenotype to Genotype The age of DNA Low-cost, extensive genetic information Genome sequence as the ultimate indexer for data Whole genome genotyping for breeding Microarrays Sequence based Low density typing High throughput Low cost per sample Outsourcing data production Expand genetic diversity ©Nick Loman

Better phenotyping Breeding effectiveness and efficiency relies on data Electronic data capture Reduce errors (barcodes, sample tracking) Increase throughput New type of data: drones, multispectral images, Near Infra Red analysis, … Digital systems to manage experiments Back up, cloud storage, disaster recovery The end of field books? Not sure! Sorghum Breeding program Ethiopian Institute of Agricultural Research

IT for effective data management Breeding information management system Need to manage Lines, seeds, pedigrees Field experiments Phenotypic data Genotypic data (link with suitable database) Links with Gene Banks Interface with data analysis tools Multiple options: public and private Examples (not an exhaustive list!) IBP: www.integratedbreeding.net/ Agrobase: www.agronomix.com KDDArT: www.kddart.org Dedicated systems from CIMMYT and IRRI

Modelling and Simulation Integrating soil, climate, variety traits and crop management Inform breeding strategies: decide which traits for which context Evaluate climate risks Inform farmers: better decision making at planting time Work in progress! Used by modern plant breeders. Practical application to farm level will require innovation in agriculture extension

New breeding approaches Large amount of reliable data captured and stored electronically Machine learning opportunities (like in other fields of science) Genomic Selection: Build a genotype to phenotype model from a training set Predict the breeding value from high density genotypic profiles in breeding populations Applicable to developing countries, when program are modernized. Using broader genetic diversity Also non crop genomes: symbiont, rhizosphere

International Mung bean Improvement Network (IMIN) Mung bean: an important traditional crop in South Asia Opportunities: short duration crop, high value grain Mini-Core Collection (MCC) from World Vegetable Centre phenotyped by 4 partners: India, Myanmar, Bangladesh and Australia MCC genotyped at high density Partners will adopt a common data management system, electronic data capture. Open network

Sorghum Improvement in Ethiopia Water limitation causes significant crop losses and food insecurity in major dry-land sorghum growing regions Project co-funded by Bill & Melinda Gates Foundation and ACIAR Enhance effectiveness and capacity of the national sorghum breeding program New breeding design, larger experiments, digital data capture, phenotyping for grain quality using NIR. Improve productivity of sorghum in the target rainfall zones of Ethiopia via breeding and agronomic research APSIM to guide breeding and simulate alternative management options Key drought adaptation mechanisms in sorghum

Molecular markers for wheat breeding in India Combined skills of Indian and Australian wheat breeders and researchers Improved wheat varieties for both countries using molecular technologies Germplasm exchange: future varieties will contain traits from both countries Testing Genomic Selection for yield Traits: water use efficiency through deep roots, rust disease resistance, soil toxicity and waterlogging, grain quality Deployment of the Integrated Breeding Platform as a data management system

Challenges to modernizing breeding programs Skills, training Institutional change: rewarding plant breeders for team work, genetic gain, not just for released varieties Access to goods and services, modest amount of foreign currency may be needed Access to expanded genetic diversity

Breeding impact Impact of improved varieties is clear Seed is an effective intervention BUT breeding needs: Responding to demand Seed systems Extension and dissemination Participation of the private sector © Seeds of Life Timor Leste 2004: Sweet potato trials

The power of international science cooperation ©ESA Comet Churyumov-Gerasimenko, 6th of August 2014

©EH(KhulnaBGD02/2013)