Lowering costs of breeding of high value fragrant rices

plant science

This research received a ‘High’ rating for impact in the Australian Research Council’s Engagement and Impact Assessment 2018-2019 National Report. Aroma is an important characteristic of rice and fragrant rice is in high demand. In the past, sensory and chemical methods (chewing or smelling grains) were used to identify fragrant rice cultivars in breeding programs. These methods were unreliable, so researchers at Southern Cross University identified the gene responsible for aroma formation in rice and developed a simple test for rice fragrance. Their discovery lowered the cost of a rice breeding program by more than 9%. Fragrant rice retails at almost double the price of non-fragrant rice, so the discovery increased the income of farmers (most of whom are in developing countries) by around 30%. Countries such as India have developed new varieties and increased their export income by selling more fragrant rice world-wide. 


Aroma is one of the most important characteristics of rice. Rice consumers all over the world have displayed a preference for fragrant rice. Sensory methods (chewing or smelling grains) to identify fragrant rice cultivars are labour-intensive and unreliable. The ability to detect fragrance varies between individuals, meaning a panel of analysts is required. Furthermore, the ability to distinguish between fragrant and non-fragrant samples diminishes with each successive analysis due to sensory saturation and abrasions to the tongue. Chemical methods of identifying fragrance are also inaccurate as they can damage nasal passages. Given the demand for fragrant rice and the inadequacy of sensory and chemical fragrance tests, rice breeders required a genetic test to identify fragrant cultivars in breeding programs.

Professor Robert Henry and his team moved progressively towards locating the fragrance gene in rice (fgr) (2002-05). The researchers initially identified markers associated with fragrance but these did not allow prediction of the fragrance status of any one rice sample with 100% accuracy. Subsequently, a gene on chromosome 8 was identified as responsible for aroma formation in rice. The team quickly developed a simple and robust screening test for rice fragrance and made it freely available to rice breeders.

The team’s breakthrough discovery added layers of economic value to the rice industry by revealing the biochemical basis of the rice fragrance mechanism and how the gene works. For example, the team explained fragrant rice’s sensitivity to salt (2008) which assisted breeders in optimising stress resistance. Furthermore, genetic fragrance testing required only small tissue samples and large numbers of plants could be accurately analysed. Australian market leader SunRice reports that over a typical 10 year, $1.5 million breeding program for a new fragrant rice variety, the fgr discovery delivered savings of $140,625 (9%). This saving was brought about because fewer lines need to be grown (only those confirmed as having the fgr) early in the breeding program.

Initially a patent was taken out on the fgr, however, this was allowed to lapse because Professor Henry’s team viewed the discovery as ‘enabling’. The researchers were reluctant to own the genetic Intellectual Property (IP) of a staple that feeds 3.5 billion people daily (about half the world’s population).

Rice provides 20% of the world’s caloric intake and is the predominant dietary energy source for 34 developing countries. Professor Henry’s team wished neither to steal the genetic capital of poor farmers nor impede developing countries’ breeding programs.

Free access to the fgr delivered social benefits to developing countries. In 2008, a steep rise in global rice prices cast 100 million people into poverty. When food security is threatened, not only do people go hungry, but they are also likely to resort to social unrest. The researchers’ decision not to pursue IP rights for the fgr meant that developing nations had more control over breeding programs, food security and potential social unrest.

By not claiming fgr IP rights, researchers showed cultural respect in situations where a particular varieties of rice hold significance. Basmati rice is considered an element of national heritage in India and Thais attribute sacred status to jasmine rice.

As well as lowering rice breeding costs by a third, the single gene discovered by Professor Henry’s team also boosted industry revenue. Fragrant rice commands almost double the retail price of non-fragrant rice and this price premium confers economic benefits back along the value chain (to processors, farmers, seed companies and plant breeders). For example, even though basmati has lower yields and higher growing costs, it provides farmers with a 30% positive net return compared to non-fragrant varieties (Singh et al. 2006).

The International Rice Research Institute (IRRI) has called the fgr discovery “a breakthrough for (the) rice industry” and reported wide use of the fgr. This organisation works with 17 in-country partners on breeding programs and more than half the rice planted in Asia is IRRI-bred. With 95% of rice grown in developing countries (92% in Asia), the fgr discovery has delivered significant economic benefit to countries most in need of export revenue. For example, from 1995-2015, 20 new varieties of basmati were developed in India (Ashraf, 2017) and basmati’s proportion of global rice traded increased from 5.2% to 18.3% (2003-11).

The Australian rice industry (which generates 8000 regional jobs) is another beneficiary of the fgr discovery. In 2014, SunRice’s Rice Research Australia Pty Ltd, NSW DPI and Rural Industries Research Development Corporation used the fgr to develop “Topaz”, a new premium fragrant rice variety suitable for Australia's temperate conditions. In Hong Kong market testing, Topaz outperformed other fragrant rice varieties for taste, appearance and flavour.

The global export industry also benefitted from the fgr discovery. Fraudulent adulteration of rice (mixing fragrant and ordinary rice to inflate profits) has adversely impacted the entire value chain. The team’s genetic test is used to curtail this illegal practice and ensure product compliance and quality control.

The fgr discovery also has economic implications beyond the rice industry as the same gene has been found to confer fragrance in other foods (e.g. soya beans and sorghum).
By lowering costs and increasing revenue along the rice industry value chain, the fgr discovery delivered significant economic benefits, especially to developing countries. The fgr discovery being freely available, has delivered cultural and social benefits to these countries. The cultural significance of rice was respected and the fgr ‘enabled’ developing nations to maintain food security and social stability.

Resources

2002 Identification of the first microsatellite marker for detection of fragrance in rice (Henry, Cordeiro, Christopher and Reinke).

2003  The recently-available rice genome sequence was used to find an SNP marker which differentiated fragrant/non-fragrant rice. It was closer to the gene (on the chromosome) than 2002 study - world-first research (Qingsheng , Waters, Cordeiro, Henry and Reinke).

2005 With knowledge of the chromosomal location and using recently-available rice genome sequence, SCU researchers found the gene that determines fragrance in rice (regressive gene on chromosome 8) (Bradbury, Fitzgerald, Henry, Qingsheng and Waters).

2005 Development of  a single tube Allele Specific PCR fragrance assay to classify rice as homozygous fragrant/homozygous non-fragrant/heterozygous non-fragrant (low-cost/robust technique to assist plant breeders) (Bradbury, Henry, Qingsheng, Reink and Waters).

2008 Fragrance gene was put into bacteria to test its function on range of possible chemical substrates. A reduction of 4-aminobutaldehye was identified as the key reaction disabled by the fragrance mutation. The research provided insights for engineering glycine betaine accumulation in rice to enhance stress tolerance (Bradbury, Gillies, Brushett (of SCU) and Waters).

2008  Further research conducted into rice plants’ stress resistance, confirming sensitivity to salt in fragrant rices. (Fitzgerald, Waters, Henry, Reinke and Qingsheng).

 

SCU news item