How Genomic Sequencing Can Drive Agricultural Advancements

Professor Rajeev Varshney achieved the largest plant genome sequencing study by harnessing MGI’s high throughput sequencing technologies.

AsianScientist (Jul. 27, 2023)–Two decades ago, a global consortium of researchers accomplished the groundbreaking Human Genome Project. By sequencing the entire human genome, the project unlocked a vast reserve of previously untapped potential in the field of genomics. Diseases can now be diagnosed, treated and researched at much quicker speeds, with the help of a map of our genetic code. Despite the popularity and prestige of the project, humans aren’t the only living beings to benefit from genomics. The value of genomics can be translated into agriculture by understanding the genomes of plants.

Today, with the rise of personalized medicine, other human genome projects are taking place to identify the variations between people of different ethnicities. The same goes for plants; variations within a species can mean a world of difference when it comes to improving growing conditions for a better yield.

Growing the industry

In 2021, to offer insight into the variations between chickpea genomes, Professor Rajeev Varshney, Global Research Program Director at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), conducted the world’s largest plant genome sequencing project with a total of 3,366 chickpea genomes. The project has since been the basis of 17 publications that aim to improve agricultural productivity.

“After decoding the genome for a given crop, we could get information about gene repertoire of that species. However, we were not able to get an estimate on genomic variation in the species that we could link with various agronomic traits,” explained Professor Varshney. “Therefore, we planned to sequence a large number of accessions in collaboration with MGI.”

The team was able to sequence several thousand chickpea lines which they later catalogued and used to identify genetic variations. By identifying favorable variations such as drought tolerance, heat tolerance and disease resistance, they could implement crop improvement programs to develop superior lines that would lead to increased yield and greater food security.

“I have worked with MGI for close to 10 years, and I have witnessed the continuous evolution of their sequencing technology for hundreds of thousands of genomes. Their products are 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,” said Professor Varshney. “I believe that MGI is more than a service provider, but a true collaborator in empowering scientists and promoting scientific development.”

Next in genomics

Now based in Australia as the Director of Centre for Crop and Food Innovation at Murdoch University in Western Australia, Professor Varshney will work with MGI to establish an Advanced Genomic Platform that will advance research in crop genomics in Australia. Specifically, the project aims to improve the quality and resilience of five fruits: banana, pineapple, papaya, custard apple and passionfruit. Breeders and growers will be able to access the genetic data through a publicly available database. Similar to the chickpea project, they can use the genetic information to quickly identify key traits and develop more productive varieties.

Professor Varshney and his team at Murdoch University will work with MGI Technologies to develop more productive fruit varieties.

The launch of the platform will be seamlessly facilitated by MGI technologies. MGI’s end-to-end capabilities ensure rapid and accurate sequencing throughout the entire process. Professor Varshney and his team will be using three key systems: the MGISP-960 High-throughput Automated Sample Preparation System, the DNBSEQ-T7 Ultra-high Throughput Genetic Sequencer and the ZTRON All-in-one Genetic Data Platform.

“MGI provides whole workflow for the high throughput sequencing, including automated sample preparation (SP960), DNBSEQ-T7 sequencer and data centre Ztron. The solution can empower high volume sample processing and data generation, the foundation for genomics-assisted breeding,” said Dr Bicheng Yang, Director at MGI Australia.

Looking ahead, Professor Varshney sees spatial transcriptomics and artificial intelligence (AI) becoming key advancements in genomics and genomics-assisted breeding.

“MGI has already created “STOMICS” an approach based on DNBSEQTM technology, and it is currently being used mainly in human genetics. We need to optimize this in complex genome species like wheat while being cognisant of the need to generate large scale sequence data. In addition, we need to use AI and machine learning approaches for a better prediction of phenotypes to enhance the level of crop improvement,” said Professor Varshney.

With a strong commitment to innovation, MGI aims to make genomic research affordable and accessible to everyone—including breeders and farmers. By collaborating with experts like Professor Varshney, MGI has a better understanding of the need to develop quick and effective solutions.

“Learning from our collaboration with Prof Varshney and his journey in advocating genomics for breeding applications, we understand more about the future need and directions to develop faster and more cost-effective solutions to automate sample collection, extraction, and develop faster solutions for genotyping large population lines. These solutions are also more affordable and more intelligent in capturing and analysing multi-omics data. MGI will continue to developing tools and solutions to meet those needs,” said Dr Yang.

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*Unless otherwise informed, StandardMPS and CoolMPS sequencing reagents, and sequencers for use with such reagents are not available in Germany, USA, Spain, UK, Hong Kong, Sweden, Belgium, Italy, Finland, Czech Republic, Switzerland, Portugal and Austria. HotMPS sequencing reagent and sequencers for use with such reagents are only available in selected countries.

Source: MGI Technologies
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