Biotechnology, Commentaries, Health October 25, 2017

Goodbye to Golden Rice? GM Trait Leads to Drastic Yield Loss and “Metabolic Meltdown”

by Jonathan Latham

by Allison Wilson, PhD.

GMO Golden Rice is promoted as a potent tool to alleviate vitamin A deficiency. However, Indian researchers now report that the genes needed to produce it have unintended effects. When they introduced the engineered DNA, their high-yielding and agronomically superior Indian rice variety became pale and stunted, flowering was delayed and the roots grew abnormally. Yields were so reduced that it was unsuitable for cultivation (Bollinedi et al. 2017).

Rice is a good source of certain nutrients but it lacks Vitamin A. In low-income households in certain countries, a rice-based diet can therefore result in vitamin A and other nutrient deficiencies.

Parent (left) Golden Rice (right)
Parent (left) Golden Rice (right)

According to Syngenta and certain public sector biotechnologists, vitamin A nutrition can be improved by introducing transgenes that specify enzymes in the β-carotene biosynthesis pathway (Ye et al. 2000; Bollinedi et al. 2014). β-carotene is one of several carotenoid precursors to vitamin A.

A short history of Golden Rice

The first GMO Golden Rices had either two or three introduced genes (in addition to a transgene specifying antibiotic resistance as a selectable marker). Plants with two had a daffodil phytoene synthase (psy) transgene and a phytoene desaturase (ctrI) transgene from the bacterium Erwinia uredovora. These were transferred together as a gene cassette. Those with three had in addition a daffodil lycopene β–cyclase (lcy) transgene, co-transferred in a separate cassette (Ye et al. 2000). Each independently generated event consisted of one or more gene cassettes integrated at a particular location in the plant genome.

The public sector group who developed these subsequently created a new set of events using just the psy and ctrI transgenes. They also changed the vector, the selectable marker and used different rice varieties. These changes were intended to make Golden Rice “amenable to deregulation” (Hoa et al. 2003).

As critics pointed out, the rice from both sets of events had very low carotenoid levels, less than 1.6ug/g.

Simultaneously, Syngenta Corporation produced a third set of Golden Rice events (called GR1). For GR1, Syngenta replaced the viral promoter of the ctrI transgene used by the public sector group with a promoter designed to give enzyme activity just in the rice grain. They also removed the selectable marker. Total carotenoid levels in GR1 rice grains were higher: 6ug/g (Al-Babili and Beyer 2005).

The hulled grains of these different iterations of Golden Rice were yellow due to the β-carotene. However, even the best GR1 events still had β-carotene levels too low to alleviate deficiencies (Bollinedi et al. 2014).

Engineering Golden Rice GR2

Syngenta then made the fourth and current version of Golden Rice, called GR2. They introduced three genes as a single cassette. As before, two specified enzymes in the β-carotene biosynthesis pathway — a bacterial ctrI gene and, this time, a maize version of the psy gene (Paine et al. 2005). The third gene specified a (non-antibiotic) selectable marker gene.

In GR2, the ctrI and psy genes were again placed under the control of an endosperm-specific promoter. The GR2 cassette was introduced into the genome of the American rice variety Kaybonnet.

Syngenta researchers selected 23 independent GR2 events with between 9 and 37ug/g total carotenoid in the endosperm (Paine et al. 2005).

Golden Rice for India?

Through its Humanitarian Board on Golden Rice (HumBo), Syngenta made six of these GR2 events available to public sector breeding programs (Chikkappa et al. 2011). The Indian Researchers chose GR2-R1, presumably the most promising event, to breed a Golden Rice variety suitable for India (Bollinedi et al. 2017).

However, when they introduced GR2-R1 into the high-yielding variety Swarna, the plants with the GR2-R1 event were “drastically altered” (Bollinedi et al. 2017). GR2-R1 Swarna rice had pale green leaves, various root defects, and extra side shoots (tillers). The plants also flowered later, were half the height, and half as fertile. Yield was one-third of non-GMO Swarna.

Most of these abnormalities, it transpired, had been present in the original GR2-R1 plants donated by Syngenta.

Molecular-Genetic origins of GR2-R1 defects

DNA analysis revealed a partial explanation for these defects. The GR2-R1 DNA had inserted into and disrupted a native rice gene called OsAux1. OsAux1 specifies a transporter for the important plant hormone auxin. The researchers suggested this disruption explains some of the root and shoot defects. 

A second contributor to the defects seems to be that, although the psy and ctrI genes had been specifically engineered so that their enzyme products would be present only in grains, the researchers found evidence the enzymes were unexpectedly functioning in GR2-R1 leaves.

Chemical analysis of leaves, stems, and flowering parts showed GR2-R1 plants had altered levels of three other key plant hormones: abscisic acid (ABA), gibberellin (GA3), and cytokinin.

To explain this the researchers proposed that the presence of the genetically engineered PSY and CTRI enzymes in leaves depletes a compound (GGDP) needed to make other plant biochemicals, in particular hormones and chlorophylls. Lack of chlorophyll would explain the pale leaves, while altered hormone levels would explain the other growth defects and the yield loss seen in GR2-R1 plants.

The researchers did not report whether metabolic and hormonal disruptions also occurred in the rice endosperm, where PSY and CTRI were intended to function.

The End for Golden Rice?

Golden rice has for over 20 years stood as the exemplar of a “good GMO” and proponents have blamed its failure to reach the market on “over-regulation” of GMOs and on “anti-GMO” opposition (Lee and Krimsky 2016).

This latest research suggests a different narrative. It shows that problems intrinsic to GMO breeding are what have prevented researchers from developing Golden Rice suitable for commercialization (Schubert 2002; Wilson et al. 2006).

The second great significance of this research, is that it implies engineering sufficient levels of β-carotene is disruptive to the basic metabolism of the plants.

“What the Indian researchers show is that the Golden Rice transgenes given to them by Syngenta caused a metabolic meltdown,” says Jonathan Latham, Executive Director of the Bioscience Resource Project. “The classic criticisms of genetic engineering as a plant breeding tool have always been, first, that introduced DNA will disrupt native gene sequences and, second, that unpredictable disruption of normal metabolism may result from introducing new functions. Golden Rice exemplifies these flaws to perfection.”

This then is the fundamental challenge of GMO metabolic engineering. It seems that making the intended metabolic changes (in this case increasing β-carotene levels) is the easy part (Giuliano 2017). The real challenge is to not make unintended changes by disrupting the many intersecting biochemical pathways—and thereby disrupting the complex plant processes that depend on them (Schubert 2008).

With their BioBricks approach to biology, Syngenta and their public sector allies have shown negligible understanding of these complexities, leaving it once again to non-GMO breeders to successfully enhance nutrient levels in plants (Andersson et al. 2017).

For years the quintessential example used to support GMO plant breeding, Golden Rice may now become “Exhibit A” for those wishing to critique it.

Highly Recommended Further Reading: The place of Golden Rice in the broader politics of rice, including its prospects in the Philippines (or elsewhere) are well explained in an important new paper by Stone, G. D., & Glover, D. (2016).”Disembedding grain: Golden Rice, the Green Revolution, and heirloom seeds in the Philippines” This paper is full of insights and up-to-date information.

Stone, G. D., & Glover, D. (2017). Disembedding grain: Golden Rice, the Green Revolution, and heirloom seeds in the Philippines. Agriculture and Human Values, 34(1), 87-102.


Andersson, M. S., Saltzman, A., Virk, P. S., & Pfeiffer, W. H. (2017). Progress update: crop development of biofortified staple food crops under HarvestPlus. African Journal of Food, Agriculture, Nutrition and Development17(2), 11905-11935.

Al-Babili, S., & Beyer, P. (2005). Golden Rice–five years on the road–five years to go?. Trends in plant science, 10(12), 565-573.

Bollinedi, H., Gopala, K. S., Sundaram, R. M., Sudhakar, D., Prabhu, K. V., & Singh, N. K. (2014). Marker assisted biofortification of rice with pro-vitamin A using transgenic Golden Rice lines: progress and prospects. Indian Journal of Genetics, 74(4), 624-630.

Bollinedi, H., Prabhu, K. V., Singh, N. K., Mishra, S., Khurana, J. P., & Singh, A. K. (2017). Molecular and Functional Characterization of GR2-R1 Event Based Backcross Derived Lines of Golden Rice in the Genetic Background of a Mega Rice Variety Swarna. PloS one, 12(1), e0169600.

Chikkappa, G. K., Tyagi, N. K., Venkatesh, K., Ashish, M., Prabhu, K. V., Mohapatra, T., & Singh, A. K. (2011). Analysis of transgene (s)(psy+ crtI) inheritance and its stability over generations in the genetic background of indica rice cultivar Swarna. Journal of plant biochemistry and biotechnology, 20(1), 29-38.

Giuliano, G. (2017). Provitamin A biofortification of crop plants: a gold rush with many miners. Current Opinion in Biotechnology44, 169-180.

Hoa, T. T. C., Al-Babili, S., Schaub, P., Potrykus, I., & Beyer, P. (2003). Golden Indica and Japonica rice lines amenable to deregulation. Plant physiology, 133(1), 161-169.

Lee, H., & Krimsky, S. (2016). The Arrested Development of Golden Rice: The Scientific and Social Challenges of a Transgenic Biofortified Crop. International Journal of Social Science Studies, 4(11), 51-64.

Paine, J. A., Shipton, C. A., Chaggar, S., Howells, R. M., Kennedy, M. J., Vernon, G., … & Drake, R. (2005). Improving the nutritional value of Golden Rice through increased pro-vitamin A content. Nature biotechnology, 23(4), 482-487.

Schubert, D. (2002). A different perspective on GM food. Nature biotechnology, 20(10), 969-969.

Schubert, D. R. (2008). The problem with nutritionally enhanced plants. Journal of medicinal food, 11(4), 601-605.

Wilson, Allison K., Jonathan R. Latham, and Ricarda A. Steinbrecher. “Transformation-induced mutations in transgenic plants: analysis and biosafety implications.Biotechnology and Genetic Engineering Reviews 23.1 (2006): 209-238.

Ye, X., Al-Babili, S., Klöti, A., Zhang, J., Lucca, P., Beyer, P., & Potrykus, I. (2000). Engineering the provitamin A (β-carotene) biosynthetic pathway into (carotenoid-free) rice endosperm. Science, 287(5451), 303-305.

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Comments 23
  • I think this is very good article, that simplifies even while communicating the wrong direction of rice research. From this experience, and results, it is obvious that India particularly should abandon all efforts towards Golden Rice. In principle, GM Rice project is misfit to the problems of vitamin deficiency. Agro-ecology ensures wholesome diet, there is no doubt.

    • No, agro-ecology will never see beta-carotene produced in rice endosperm. Income distribution and subsequent improved diet will see more people have more beta-carotene in their diet but in the mean time I think you’d agree that biofortifying rice is a wonderful solution until income distribution is sorted out.

      • Actually solutions have already been implemented and have “slashed” vitamin A deficiencies in the Phillipines: “Recognizing major public health problems with a range of micronutrient deficiencies, the country has undertaken programs including food supplements, nutrition education, and a law in 2000 requiring food fortification of common ingredients with vitamin A, iron, and iodine (Phillipines Department of Health nd). As a result, the incidence of childhood VAD in the Philippines dropped from a peak of 40.1 % in 2003 to 15.2 % in 2008 (Food and Nutrition Research Institution nd). VAD figures from the 2013 national nutrition survey have not been released, but as other types of malnutrition have continued to fall, the VAD rate must be expected to have fallen too.”
        To learn more about this see: Stone, G. D., & Glover, D. (2017). Disembedding grain: Golden Rice, the Green Revolution, and heirloom seeds in the Philippines. Agriculture and Human Values, 34(1), 87-102.

  • Bunkum. It is yielding well in trails in Bangladesh and the Philippines. Release is in 2018 and trials look amazing.

    • Obviously, if the Bangladesh Star says the peer-reviewed literature is bunkum then it must be so.

      • Correct. The article posted us trying to infer doubt regarding the Golden Rice project. But on reality it is looking like being a huge success. I think we should all be very excited. If you talk tp the breeders at IRRI you will find that is the case

        • Stone and Glover have spoken to IRRI — and their excellent analysis in the academic article “Disembedding grain” linked to above indicates that there are still many problems and hurdles ahead for Golden Rice, even in the Philippines. They include yield issues also the many biosafety and nutritional questions that remain unanswered.

  • In response to Mr. Duggan, I would like to point out a few important things.
    1. The Golden Rice event used in the Phillipines is not GR2-R1, as was studied by the Indian researchers and discussed in this article.
    2. The Phillipine Golden Rice is GR2-E, which is the GR2 event given to HumBo that has the lowest levels of beta-carotene (see the Paine et al. or Chikkappa et al. references above).
    3. The article Mr. Duggan refers to is a newspaper article, not a scientific paper. It does not provide any scientific verification of its claims. Until independent scientists can verify the yields and the levels of beta-carotene, and until the data is made public, we do not have any scientific reason to believe the positive claims about GR2-E.
    4. Important missing data for both GR2-R1 and GR2-E are data on the levels of hormones, nutrients (like Vitamin E and other grain nutrients), potential toxins and other metabolites in the rice grains. For example, it might be that beta-carotene levels are increased but tocopherol (vitamin E) levels are decreased (you can get some idea of this possibility by looking at the link for GGDP in the article — which shows the complex intersecting pathways involved).

    • Actually Allison,
      1) it is
      2)Paine et al used GR1
      3) not sure how familar you are with agronomy by yield is ‘the great indicator’. Fact is beta-carotene levels are at levels now which will overcome Vitamin A deficiency and grain yields are high enough so that farmers will grow Golden rice in preference to current white rice
      4) no indication that other vitamin levels are changed in Golden rice.
      I advise you before you publish articles like this you visit IRRI’s website on Giolden rice. Many of the faux pars you made in your article could have been avoided. Regards

      • If you read Paine et al. you will see that they produced GR2 in that paper. Both GR2-R1 and GR2-E are described within it.

        If you read Stone and Glover 2016 referenced in comments above (who discuss IRRI and their work) and the references therein (including some from HumBo and others who work with GR and have inside knowledge) and if you read the scientific articles referenced in my article you will understand that the GR project has focused on getting decent yields (and failed so far although they are still trying to achieve decent yields) and on improving beta carotene content. To the best of my knowledge, there is no published data so far on other vitamin, metabolite or mineral levels in the grain — for GR2-E, GR2-R1 or any other GR2 events. I would like to be alerted to any published scientific papers that address this issue.

  • Dr Duggan to you thanks. PhD in crop physiology and genetics with 23 years of R&D experience. Anyway I suggest you check with breeders at IRRI. They haven’t published any data from these trials due to attacks from NGO’s but I can assure you that if you do you will see that the newspaper article frpm Bangladesh is correct. Expression levels of beta-carotene in the rice is high and just as importantly the yields are as high or higher than rice hybrids or varieties in the markets where it has been tested. Again release is planned for 2018. Odd that you have no comment from IRRI regarding the progress of Golden Rice. Thanks.

  • Beta carotene expression levels in the Golden Rice strains used in the breeding program at IRRI are high as are the uptake levels in humans.

    • Dr Duggan! Do you have any special knowledge about this project, or just what is in the peer-reviewed literature? I ask because you seem remarkably confident about somethings for which there is very little published research? Second, the peer-reviewed paper you cite states that GR has up to 35ug of Beta-carotene per g. However, the authors dont say which GR they used but, since they fed 200g per person and that gave 1.5mg of Beta-carotene (to take their higher numbers) then that is about 7.5ug per g in the rice they fed the treatment group. Low enough that 6ug was deemed by Syngenta too low so that they then went ahead and made GR2. Am I missing some reason why you think that is high?

      • Hi Jonathon. Well I wouldn’t call it special knowledge, but simply what is 1) in the peer reviewed literature, and 2) what is on IRRI’s webpage. There is plenty of citations of peer-reviewed journal articles pertaining to Golden rice published there, including their data on how 1 cup of rice per day will provide the dietary requirements of a child suffering from Vitamin A deficiency in the developing work. I am just incredulous that the author of this peice never bothered to reference IRRI who is quite successfully developing this rice. And to your point, yes, anecdotal evidence, in the form of a newspaper article, is more credible as it is demonstrating what is happening in the real world. This piece is simply trying to sow the seeds of doubt. Well, the newspaper article proves that those fears are unfounded. Cool huh!

  • Golden rice is, and always has been, a high tech answer to a sociological problem. β-carotene has to be the second most abundant molecule on the planet. If it is missing from the diet then is going to be missing in the diet of the landless poor. Give them the land rather than GM rice. No problem the of Vit A deficiency

    • No, not necessarily Dave. It is not the ‘landless poor’ but rather the urbanised poor. It is a social issue, and one that we should absolutely address in terms of better income distribution etc but that can’t be solved in the short term. Many of the people who suffer from Vitamin A deficiency are urban poor who have very low income. A better diet would improve their lot in life, but all they can afford is rice. On such a diet they become Vitamin A deficient. Supplements degrade and expire and don’t often reach their target. The best short term solution is to bio-fortify the one thing they do eat with beta-carotene (so they can’t develop Vitamin A toxicity). Fantastic short term solution until we can solve income distribution.

      • Well, Dr. Duggan, I respectfully suggest that you are wrong. The “Fantastic short term solution ….” has been at least 20 years in the coming. In that time post revolutionary Cuba had completely reorganised the island’s agriculture, in the face of American embargo. It included intensive,”urban”, horticulture specifically designed to provide water-soluble vitamins in the diet, a move away from the cultivation of sugar and tobacco as cash crops, and a massive drop in the consumption of meat in the Cuban diet – all recognised as tennets of todays, sustainable, agroecology as distinct from the mass commodification of cereals which provide highly profitable, nutritionally poor, pap for the poor in most of the world, and highly profitable animal feed to produce meat for an increasingly obese population in “developed” countries.
        Golden rice is an irrelevance, a sticking plaster at best. It represents a justification for GM technology that appeals to a sense of altruism and reflects a world view in which, western/high-tech, science can be used to “solve” a problem that does not exist. The poor who exist on an exclusively rice diet are perfectly able to balance their diet given the education and opportunity to do so. It is the wrong answer to a social problem. If it ever does “come to market” then I predict it will cause the sort of social chaos represented by the introduction of bt cotton into India.

  • Glenn Davis Stone, who does have an inside track, writes, in his 2016 paper with Dominic Glover, Disembedding Grain (, that
    “Golden Rice……has failed to reach Philippine farmers because it has yet to meet standards of productivity.”

    • No the hold up moreover was that the first gene, GR1, did not express enough beta-carotene. This latest incarnation, GR2, produces enough beta-carotene such that a child only has to eat a cup of cooked Golden rice to receive half their daily requirement to not develop night blindness. The other complication is yield; if grain yield is not sufficient then farmers will not grow it and despite the success of the product in delivering beta-carotene the project will fail for economic reasons. Fortunately this has been overcome and the yields are as high or higher than current varieties and hybrids. I am sure you are looking forward to its launch next year as much as I am.

  • Why not just grow carrots instead? Because carrots cannot be patented?

  • In reading this interesting article and the back and forth discussion that followed, no one mentioned the fact that vitamin A, along with E, D, and K, require dietary fat for proper digestion and absorption into the body. So providing a crop with higher beta-carotene content will not solve the vitamin A deficiency unless dietary fat is also available.

  • My understanding is that it would be a far better solution to help people to grow a varied crop of Vitamin A rich food plants that are also supplemented with animal protein with high levels of Vitamin A, chickens and their eggs and goats and pigs.
    It seems that a global effort in training people in permaculture would be a far better long term solution and putting aid money into this kind of education.
    All other solutions such as food aid and GM crops appear to be pointless short term solutions that really lead to nothing in the end.

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