NAL1 Spikes Back

Mature rice panicle against blue sky. Part of ...

Mature rice panicle against blue sky. Part of the image collection of the International Rice Research Institute (IRRI) . (Photo credit: Wikipedia)

Earlier this fall, I highlighted a research paper on a gene responsible for increased yields in rice. Variants of this previously characterized gene played a significant role in increased photosynthesis rates and ultimately higher grain production. In this week’s PNAS, a separate group reports on the importance of a NAL1 variant for increased rice yields.*



Briefly, I will go through the experimental highlights of the new paper…

Using different genetic lines of rice, Fujita and co-authors were able to isolate a trait conferring increased grain yield. They designated the genetic element controlling the trait ‘SPIKE**’ for increased spikelet number. When this element was mapped to a specific location within the rice genome, the researchers found that it corresponded to the NAL1 gene that has been previously characterized. The SPIKE allele has three key amino acid changes in the NAL1 gene. The authors perform a number of physiological assays on rice plants containing the following types of NAL1: the SPIKE allele, SPIKE overexpression construct, SPIKE silencing construct and NAL1 (wild-type version for typical rice cultivars). The SPIKE allele was correlated with increase in total spikelet number. The authors were also able to show that the presence of the SPIKE allele had a positive impact on grain yields in certain rice varieties.

Characterization of yield-related traits of a NIL for SPIKE. (A) Plant morphologies. (B) Panicle structures. (C) Flag leaves. (D) Cross-sections of panicle neck. (Scale bars: A, 20 cm; B, 10 cm; C, 5 cm; D, 500 µm.)

Characterization of yield-related traits of a NIL for SPIKE. (A) Plant morphologies. (B) Panicle structures. (C) Flag leaves. (D) Cross-sections of panicle neck. (Scale bars: A, 20 cm; B, 10 cm; C, 5 cm; D, 500 µm.)

What I’d really like to go through in this post is a comparison of the two papers…

  1. By my reading the papers use very similar methodology geared toward uncovering genetic elements in rice that increase yields. I will admit that some of the finer points of rice genetics may elude me, but basically both groups have used rice breeding in various cultivar backgrounds to tease apart the complex trait of grain yield.
  2. It should be noted that the earlier Scientific Reports paper happened upon the NAL1 gene because they were assessing photosynthetic properties. Remember, their working name for the allele they found was GPS (GREEN FOR PHOTOSYNTHESIS). The PNAS paper focused solely on physiological parameters based on yield. This highlights how photosynthesis and yield are connected in crop plants. Of course, given my bias for photosynthesis, you can probably guess which group I’m giving bonus points to.
  3. The natural variants of NAL1 found in both articles hinge on differences in the two main varieties of rice Oryza sativa indica vs. Oryza sativa japonica. You can guess the origin of each based on their names, but that just refers to the stock genetic material. Both types of rice are grown all over Asia. The Scientific Reports study used cultivars of the two varieties that show the greatest photosynthetic difference. Their work showed that the natural variant of the NAL1 gene they found was key to increased yields in the indica variety, but the gene did not appreciably increase yields in the japonica genetic background. The PNAS study emphasizes the importance of the SPIKE allele to the yields of indica cultivars, which is consistent with the earlier report.
  4. I’m still left wondering what NAL1 actually does and what kinds of alleles these are giving these advantageous agronomic traits. I have to admit I got a little lost in the physiological markers used for judging the different rice plants as well as in the genetic nomenclature for the different NAL1 alleles used in both papers. It is still not clear to me whether GPS and SPIKE represent loss of function or gain of function alleles. I’m leaning toward a decrease in expression or function relative to the NAL1 versions found in other rice lines. Don’t get me wrong. I do appreciation the enormous amount of genetics and plant physiology work represented in both of these papers, but the biochemist in me is screaming, “So, what does the NAL1 protein do anyway? What is it not doing or doing differently with the GPS and SPIKE mutations?”
  5. The PNAS paper does not cite the work of the Scientific Reports paper. For those scientists in the audience, the significance of this is immediately apparent. For everyone else, here’s the big deal. When it comes to scientific publishing, there’s no prize for second place. Usually, for such similar articles, the second one just never sees the light of day. The work isn’t novel any more. Now, there are numerous instances when competing groups publish very nearly at the same time (same journal issue) or close enough that both manuscripts would have been in peer review at the same time (not at the same journal). However, when they are several months apart***, the authors of the second article generally have to answer questions about the first one. As in- how is this new work different? more important? better? an extension of the published work? Upon initial submission of the PNAS manuscript, the Scientific Reports paper wasn’t even accepted, but surely Fujita and co-authors would have noticed the Scientific Reports article during the manuscript revision phase. Of course, maybe not, but I really think someone (author or reviewer) should have noticed the earlier work.
  6. I don’t consider these two papers to be completely redundant. I’m sure there is someone out there that will enlighten me to the nuances of rice genetic techniques. Nevertheless, I think that instances such as this strengthen the scientific enterprise. Increasing agricultural yields is a high stakes field, and it is good to know that the science behind novel breeding markers is sound and validated. Given the fact that some reports suggest that an absurd amount of scientific studies are irreproducible, this kind of redundancy or overlap is welcome.

So, there are lessons here for both rice specifically and science in general.



* Check it out. It’s Open Access!

** Geneticists always get to come up with snarky names for the genes or alleles of genes they work on.

*** I realize that the time between actual publication dates for hard copy journals may not always tell the complete story with respect to scientific timelines. Pro-tip: All manuscripts have footnote information on when the manuscript was initially submitted, finally accepted, and published (online and/or) hard copy. For the case of these two papers, the Science Reports article was accepted a week after the PNAS paper was submitted for review. And yes, I’m sure these are different groups. If there was ANY overlap, they definitely would have cited the earlier work. Rule #2 of academic publishing is ‘cite yourself or no one else will.’ (Rule #1 is, of course, Publish or Perish.)


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