In the wake of the recent UN Food Systems +2 Stocktaking Moment in Rome, the spotlight on global food security has never been more critical. Addressing the challenges of a growing population and changing climate requires innovative solutions, and one area showing remarkable promise is agrigenomics. Notably, the collaboration between Professor Rajeev Varshney and MGI stands as a prime example of how genomics is transforming agriculture.
Advances in genome sequencing over the past decade have significantly benefited agriculture and food security. Through these developments, scientists can better understand crop traits and accelerate the improvement of varieties. By providing cost-effective sequencing, high-quality data and an efficient all-in-one workflow, MGI has contributed to accelerating research on important crops in Australia and other regions, while participating in the advancement of global sustainable food systems.
Agriculture in a drought-hardened Australia
Horticulture is Australia’s third-largest agricultural industry, with most growers being small-scale family farms. Water availability affects horticulture worldwide, meaning growers face not only changing customer demands, but also climate change, food security and other agricultural challenges. In some developing countries, crop productivity is very low due to limited technology and funding, which is further exacerbated in drought-prone areas.
As a key exporter of horticultural products, Australia must remain competitive in global markets by supporting higher production of disease-resistant crops while improving profitability and the livelihoods of growers. Horticultural crop growers are increasingly adapting their practices to become more productive and economically resilient.
Genomics as a solution for crop improvement
Genomics offers a powerful approach to improving crop production and enhancing food security globally. By identifying genes responsible for higher yields, drought tolerance and resilience to abiotic and biotic stresses, breeding programs can become more efficient and sustainable, enabling the development of superior varieties.
Yet some horticultural crops, such as banana, pineapple, papaya, custard apple and passionfruit, either lack basic genomic resources or do not yet utilise them in breeding programs. Cost has been a major barrier to the widespread adoption of genomics in these crops. Leveraging MGI’s highly affordable platform, scientists now have access to cutting-edge sequencing technologies at competitive costs, even in developing countries, unlocking the full potential of agrigenomics.
A fruitful seven-year partnership
Since its inception, MGI has collaborated with Professor Rajeev Varshney, Fellow of the Royal Society and Director of the Centre for Crop and Food Innovation at Murdoch University (MU) in Western Australia. A globally recognized leader in genome sequencing, genomics-assisted breeding, seed systems and capacity building in agriculture, Prof. Varshney has been a longstanding advocate for MGI. During his time at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) in India, he focused on decoding orphan tropical crops and developing relevant genomic resources across Asia and Africa.
As early as 2011, while at ICRISAT, Prof. Varshney led the genome sequencing of pigeon pea, an important crop in many developing countries, and released a high-quality reference genome that has been used to study its genetics and biology. Later, aiming to expand climate-resilient food sources, he identified genes for drought and heat tolerance by sequencing 429 chickpea lines from 45 countries over three years. This work provided insights to develop new varieties with higher yields, enhanced disease and pest resistance, and improved climate resilience.
Continuing his efforts to improve food and nutrition security in India and several African and Asian countries, Prof. Varshney relied on MGI platforms based on DNBSEQ™ sequencing technology, citing advantages such as high accuracy, low duplication rates, and minimal index hopping. In 2021, his team re-sequenced 3,366 chickpea genomes, generating a complete picture of genetic variation and a validated roadmap for using these resources to improve the crop.
More recently, Prof. Varshney collaborated with MGI to sequence 10,225 chickpeas—the largest effort of its kind using the MGI platform—and added stLFR data from 26 individuals using DNBSEQ-T7 in Australia to build a pan-genome. The research has produced more than 17 publications, including seven in the CNS series, such as Nature.
Chickpeas are a vital source of protein and rank third among pulses globally. However, global yields of pulses have stagnated over the last five decades, contributing to low per-capita availability and high malnutrition in developing countries. Drought and rising temperatures have caused over 70% of global yield losses in chickpeas.
Comprehensive genomic maps have facilitated the identification of genetic differences, evolutionary analysis, and candidate gene prediction. These resources have enabled the development of superior lines in India, Ethiopia, Kenya and Tanzania. Following multi-location testing, more than ten improved drought-tolerant and disease-resistant varieties have been released in several developing countries.
For many developing countries, low-cost access to sequencing and genomic information is crucial to improving agricultural productivity. MGI’s cost-effective technology is advancing plant genomics research, creating valuable resources for food crops and supporting global food security.
Latest advances empowered by MGI
This year, led by Prof. Varshney, the Western Australian State Agricultural Biotechnology Centre (SABC) at MU is establishing the SABC Advanced Genomics Platform to further research in crop genomics and keep Australian farmers competitive. Initially, the platform will focus on five fruits: banana, pineapple, papaya, custard apple and passionfruit. Genetic data will be publicly available, allowing breeders to identify relevant traits faster and develop more productive varieties in shorter timeframes. The platform will later extend to other broadacre and horticultural crops.
The platform will use MGI’s MGISP-960 High-throughput Automated Sample Preparation System, DNBSEQ-T7 Ultra-high Throughput Genetic Sequencer, and ZTRON All-in-one Genetic Data Platform. DNBSEQ-T7 offers ultra-high throughput of reliable, high-quality sequencing data at a fraction of the cost, with up to 7TB per day. This will enable Prof. Varshney and his team to analyse more samples, uncover new research possibilities, and accelerate breeding programs at a lower cost.
“Throughout my collaboration with MGI, I have witnessed the continuous evolution of their competitively priced sequencing technology, capable of analysing hundreds of thousands of genomes quickly. Their products are pivotal in accelerating basic science and applying genomics to improve agriculture in both developed and developing countries,” said Prof. Varshney. “MGI is not merely a service provider but a true collaborator, empowering scientists and promoting scientific development.”
Moving forward, MGI will continue to support Prof. Varshney and his team in developing high-quality, sustainable agricultural products, enhancing the competitiveness of Australian agriculture and driving agrigenomics research. Their partnership is helping producers overcome challenges, improve crop performance, and strengthen global food security.
