How fruit genomic research can in Australia lead to better tasting and more resilient crops

Australian research is underway into creating an advanced genomics platform, which will help producers overcome industry challenges, improve performance and lead to tastier varieties of popular fruit crops.

Murdoch University scientists are studying the genome of five fruits – banana, pineapple, papaya, custard apple and passionfruit - and Centre Director, Professor Rajeev Varshney says while the integration of genomics research in crop improvement has been conducted in several broadacre crops, now is the perfect time for horticultural crops to start building a knowledge base.

"We are interested to address some key traits that are required by consumers, but also those that are required from an industry perspective like climate change," Professor Varshney said. "As the temperature is rising, drought is happening and crop productivity is going down - so we need to address these issues. We need to develop our crops so that they can deliver more produce. If you do these through traditional manners; like developing better varieties by traditional breeding, this takes time, possibly 10-15 years. We know these things are controlled by genes, so we are doubling up a platform known as 'Advanced Genomics Platform', with the help of Hort Innovation, and the purpose is delivering genetic solutions. This will be done by understanding the genomic architecture of crops by sequencing and decoding genomes."

Professor Varshney says that it is hoped that by providing the information gained through his research to the horticulture industry, and the result will be the creation of more desirable varieties in almost half the time of around 5-6 years. This will have flow-on, or indirect, productivity benefits to growers and producers.

"There will be some direct applications for growers from our platform, and some indirect applications," he said. "For instance, we can develop some gene chips and by using them, they can predict what kind of fruit or traits a particular variety will deliver. Second, these gene chips can also be very helpful from a biosecurity perspective. But there will be a lot of indirect benefits because this platform will be used by the breeders to double up the varieties that the growers need. So, the growers will be guiding the development of improved varieties which will have things like higher drought tolerance, higher heat tolerance, and better fruit size and taste. We also want to develop the next generation of scientists to take crop improvement to the next level by integrating genomics research into breeding. We want Australia to be a leader in genomics-assisted breeding, especially in horticulture crops at the international level – and this is a perfect time."

The benefits will not only be seen at an agronomic or grower level, which will provide better food security and more consistent crop cycles for more stable supply to domestic and export markets but also the potential for better tasting varieties for consumers that cater towards what they are needing.

He added that the current focus of the research is on consumer-driven traits like taste and size, but in future decades the studies could expand to cater for long-term crop resilience.

"When you enhance the fruit crop productivity, then definitely this will be giving a better price to the growers because there will be better sales," Professor Varshney said. "A big need for the consumers is taste, so it could even lead to premium prices - especially from export markets. For example, in the case of papaya, consumers want it great in taste, but small in size. When people buy it, they cut it into pieces and put it in the refrigerator, so one hand industry wants bigger fruit sizes, but consumer feedback is some like smaller like the size of a mango. Then they can fit it into their hand, cut it easily, and finish in the one go. It's these types of traits that we are also looking to address."

With the idea coming from Hort Innovation, the development of the Advanced Genomics Platform has many partners, including the Centre for Crop & Food Innovation of Murdoch University, Queensland Alliance for Agriculture and Food Innovation (QAAFI) of the University of Queensland, Department of Agriculture and Fisheries (DAF) Queensland, Griffith University (GU) and the University of Western Australia (UWA). There are also many technology partners such as MGI Pty Ltd., Thermo Fisher Scientific, and international research partners from the United States, France, China, Bangladesh and Thailand.

"With the five crops, we are in different time stages; some of them already have good genomic resources such as bananas and papayas," Professor Varshney said. "For pineapples, we are midway through the gathering stage, but for custard apples and passionfruit, we have to start from scratch. Our timeline is about five years, to provide the genetic solutions to breeding programs - but we don't expect to have all solutions at the end of the five years, we will continue to deliver interim outputs during the course of the project, and we hope to see the impact after the end of the project. We very much hope to see the deployment of our platform and outputs from the project by breeders to develop better varieties after the initial 5-6 years. Because of all the advances in technology and the partnerships, we feel very confident we can deliver the planned outputs to benefit both industry and consumers."

Professor Varshney says while five specific fruits were chosen for the research on the Advanced Genomics Platform, the sequencing and genotyping technologies that we are optimising here at Murdoch University should be benefitting other crops including wheat, barley, canola and pulse crops as well.