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From genes to networks to what-works

To the editor — A recent Editorial in Nature Plants1 on the 11th Plant Genomes meeting at Cold Spring Harbor Laboratory could have been more reflective on the progress that has emanated from the vast research investment in plant functional genomics over the past 20–30 years. Such reflection would have asked what has been gained by decoding the alphabet of gene sequences and how close plant genomics is to assembling the alphabet into words and even paragraphs of understanding. When are these promises going to be translated into actual crops growing in farmer’s fields to produce higher yields? A previous article by Ingram and Porter in Nature Plants2 argued that plant science has an important part to play in meeting the global food security challenge, but advances will be most effective if coupled with agronomic science and the broader food security agenda. The best and most relevant research for crop science begins and ends in the field.

The Editorial cites work by Zeng et al.3 as an example of how knowledge gained from functional genomics leads to higher yields and quality in rice. In fact, this research shows that the rice parent-line 93-11 has an upper yield of 15.3 tonnes ha–1 in farmers’ fields, but only about 10 tonnes ha–1 in the experiment. The derived lines achieve about 11 tonnes ha–1 — that is, lower than the best parent-line yielded in the field. The probable reason for the parent-line yield is that the Chinese farmers used very high amounts of nitrogen per ha in a higher-yield environment, whereas in the experiments only 140 kg of nitrogen per ha were used. Thus, management and environment made a much larger contribution to yield gain than genetic change. One can only claim to have made an improvement when the results of genomic transformation outshine those of the parent material, taking account of environment and management. It is insufficient to simply compare with- and without-modification plants. Studies in many parts of the world show that crop agronomy has contributed about half of the yield gains of crops in farmers’ fields4.

A deeper understanding of the interaction between crop productivity under different environmental conditions and management regimes is crucial to maintain sustainable agriculture and food security and requires truly multidisciplinary approaches5. To agronomists, functional genomics is digging itself deeper and deeper into a hole by revealing the endless complexity of function and, in doing so, is losing sight of the agricultural goal. An impressive agenda for the 12th Cold Spring Harbor Meeting would be a ‘cold’ and less hubristic look at the direction in which functional genomics needs to head for the issues of agricultural science over the coming decades, in which higher-yield growth will be most needed. This requires a deep and genuine focus on multi-disciplinary plant science5.


  1. 1.

    Nature Plants 4, 55 (2018).

  2. 2.

    Ingram, J. S. I. & Porter, J. R. Nat. Plants 1, 15173 (2015).

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    Zeng, D. et al. Nat. Plants 3, 17031 (2017).

    Article  PubMed  Google Scholar 

  4. 4.

    Fischer, T., Byerlee, D. & Edmeades, G. (Australian Centre for International Agricultural Research, 2014).

  5. 5.

    Wollenweber, B., Porter, J. R. & Lübberstedt, T. Curr. Opin. Plant Biol. 8, 337–341 (2005).

    Article  PubMed  Google Scholar 

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Correspondence to John R. Porter.

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Porter, J.R., Wollenweber, B., Jamieson, P.D. et al. From genes to networks to what-works. Nature Plants 4, 234 (2018).

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