How MGI boosts agrigenomics and food sustainability with sequencing technology: An Australian case study

Date:07-31-2023

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 burgeoning 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 shining example of how genomics is revolutionizing agriculture.

Advances in genome sequencing in the past decade have significantly benefited agriculture and food security. Through these genomics advances, scientists are not just able to better understand crop traits, but also enjoy a more rapid process for improving varieties. By providing cost-effective sequencing, high quality data and a truly efficient all-in-one workflow, MGI has contributed to accelerating and elevating the research of important crops in Australia and other regions and participating 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. With water availability affecting horticulture in almost all areas of the world, growers not only face changing customer demands, but are also dealing with climate change, food security and other agricultural challenges. In some developing countries, crop productivity is very low due to a lack of technology and funds and can be further exacerbated in drought areas.

As a key exporter of horticultural products, Australia needs to remain competitive among global markets by supporting a higher production and cultivation of crops that are resistant to diseases while also improving the profitability and livelihood for growers. Also, horticultural crop growers are learning how to adapt their own agriculture practices to become more productive and economically resilient.

Genomics is a vital solution to improving crop production and facilitating better food security on a global level. By using genomics, we can identify the genes that are responsible for a higher yield, and to be tolerant to drought and resilience to different abiotic and biotech stresses. In addition, breeding programs can become more efficient and sustainable with the help of genetic solutions, and more superior varieties can be developed based on genetic information.

Yet, the truth is that some horticultural crops like banana, pineapple, papaya, custard apple and passionfruit either lack basic genomic resources or they are not being used in breeding programs. Until now, cost has been a main barrier for the widespread adoption of genomics in such crops. Thus, leveraging MGI's highly affordable platform, scientists today can have access to highly efficient, cutting-edge sequencing technologies at a competitive cost, even for those in developing countries, and tap into the full potential of agrigenomics.

A fruitful partnership spanning over seven years

Since its inception, MGI has been working with Professor Rajeev Varshney, Fellow of the Royal Society and Director of Centre for Crop and Food Innovation at Murdoch University (MU) in Western Australia. A globally recognized leader in genome sequencing, cataloguing and utilizing genetic diversity, genomics-assisted breeding, seed system and capacity building in agriculture, Prof. Varshney has been a formidable advocate for MGI since his time at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) in India, devoting himself to decoding major orphan tropical crops and creating relevant genomic resources across Asia and Africa.

As early as 2011, Prof. Varshney, while at ICRISAT, he led the genome sequencing of pigeon pea, an important crop in many developing countries, and released a high-quality reference genome for the crop, which has since been used by researchers to study its genetics and biology. Later, with the goal to expand the world's climate change-resilient food sources, he identified genes for tolerance to drought and heat by sequencing 429 chickpea lines from 45 countries over three years, yielding insights that would allow newer varieties of chickpea with higher yields to be developed, along with varieties which are disease and pest-resistant and better able to withstand the vagaries of weather.

In his continuous work on improving food and nutrition security in India and several other countries in Africa and Asia, Prof. Varshney relied on MGI platforms based on its proprietary DNBSEQ™ sequencing technology, citing its core advantages of accuracy, decreased levels of duplication, and an impressively low index hopping rate. In 2021, the team conducted a large-scale re-sequencing of 3,366 chickpea genomes and generated a complete picture of the genetic variation within chickpeas, along with a validated roadmap for using the knowledge and genomic resources to improve the crop.

More recently, Prof. Varshney joined hands with MGI to sequence 10,225 chickpeas, representing the largest effort of its kind for crops utilizing the MGI platform, and in last year, Prof. Varshney added stLFR data from 26 individuals based on DNBSEQ-T7* in Australia to build the pan-genome for analyzing 10,225 individuals, and the data demonstrated was impressive. The joint research effort between Prof. Varshney and MGI has generated more than 17 publications to date, among which seven articles were published on CNS series, including Nature.

The research on chickpeas is particularly significant as the crop represents an important source of protein, and its production ranks third among pulses globally. However, global yields of pulses have stagnated over the last five decades, contributing to low per-capita availability of such foods, and high levels of malnutrition in developing countries. In addition, drought and rising temperatures have caused over 70% global yield losses in chickpeas.

The comprehensive maps generated have facilitated the identification of a large number of genetic differences, genetic evolution analysis and the prediction of candidate genes. Scientists are able to develop high-quality genomic resources in so-called orphan legume crops, which is highly effective in identifying the genes related to drought tolerance. These genes have also been used to develop superior lines in India, Ethiopia, Kenya and Tanzania, and after multi-location testing of these lines, more than 10  improved drought-tolerant and disease-registered varieties have been released in several developing countries.

For many developing countries, the ability to utilize and sequence information for crop improvement at a relatively low cost is crucial in addressing the many factors affecting agricultural productivity. On that front, MGI's cost-effective sequencing technology is helping to advance our understanding of plant genetics and genomics, contributing to the development of valuable genomic resources for important food crops and putting an end to world hunger.

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 to keep Australian farmers competitive in the global marketplace. The initiative aims initially to study the genetic material in plant cells to improve the quality and resilience of five fruits: banana, pineapple, papaya, custard apple and passionfruit. The genetic data and information produced will be available to breeders and growers through a publicly available database, allowing breeders to pinpoint the relevant traits more quickly and ultimately benefit growers through the development of more productive varieties in shorter timeframes. SABC-Advanced Genomics Platform will later be available for use on other broadacre and horticultural crops.

The up-and-coming platform will be facilitated by an end-to-end workflow consisting of 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. For the purpose of assembling whole genome sequencing (WGS) data and undertaking WGS of Australian germplasm collection for all these five crops, DNBSEQ-T7* offers the capacity to deliver ultra-high throughput of high-quality, reliable sequencing data at a fraction of the cost with a quick turnaround time (up to 7TB per daily). Through deeper, faster and more accurate sequencing, Prof. Varshney and his team look forward to significantly boosting the number of samples they can analyze and uncovering new research possibilities at a much lower cost.

"Throughout my collaboration with MGI, I have witnessed the continuous evolution of their competitively priced sequencing technology that can be used on hundreds of thousands of genomes in a relatively short amount of time. Their products are pivotal in playing an important role in accelerating basic science as well as the practical application of genomics for improving agriculture, in both developed and developing countries," explained Prof. Varshney. "MGI is not merely a service provider, but a true collaborator in empowering scientists and promoting scientific development."

Moving forward, MGI will continue to empower the work of Prof. Varshney and his team at MU in developing high-quality, safe, and sustainable agricultural products and increasing the competitiveness of the Australian agriculture industry (both broadacre and horticultural crops) with its state-of-the-art life science tools. As a trusted partner in life science innovations, MGI will keep driving agrigenomics research and industry development, thereby helping producers overcome challenges and improving the performance and value of important crops to enhance global food security.

*Unless otherwise informed, StandardMPS and CoolMPS sequencing reagents, and sequencers for use with such reagents are not available in Germany, Spain, UK, Sweden, Italy, Czech Republic, Switzerland and Hong Kong (CoolMPS is available in Hong Kong).

*Products are provided for Research Use Only. Not for use in diagnostic procedures (except as specifically noted)