Better photosynthesis in rice from an unexpected source

Something new under the sun… A gene for better photosynthetic rate in rice.

It’s something we knew before, but not in relation to photosynthesis. It’s also something breeders selected for without knowing the actual mechanism. Now it’s a new piece of the puzzle for increasing rice yields and meeting our 2050 yield goals. It’s in this recent report:

A natural variant of NAL1, selected in high-yield rice breeding programs, pleiotropically increases photosynthesis rate

Takai T, Adachi S, Taguchi-Shiobara F, Sanoh-Arai Y, Iwasawa N, Yoshinaga S, Hirose S, Taniguchi Y, Yamanouchi U, Wu J, Matsumoto T, Sugimoto K, Kondo K, Ikka T, Ando T, Kono I, Ito S, Shomura A, Ookawa T, Hirasawa T, Yano M, Kondo M, Yamamoto T.

Sci Rep. 2013; 3: 2149

The different aspects of photosynthesis play a major role in determining the yields of staple crops like rice. There must be a balance among sink size (the amount of sugars stored from photosynthesis), source strength (the capacity to make sugar from photosynthesis), and carbohydrate translocation (the movement of sugars from metabolism to storage). Natural rice cultivars have a wide range of photosynthetic rates per given CO2 levels. This rate is governed by how efficient plants are at taking in CO2 from the atmosphere and how fast CO2 is processed by Rubisco. This physiology is well-characterized but the genes underlying the complex trait of enhanced photosynthesis remain elusive. Takai and co-authors have identified a locus (section of DNA) responsible for photosynthesis rate by controlling CO2 carboxylation. Here’s how they did it.

Observations: Naturally-occurring rice varieties have a range of photosynthetic rates and their genomes should contain useful gene variations for this complex trait.

Hypothesis: The high-yielding, high-photosynthesis rate rice varieties contain specific genes underlying these traits. Identifying these genes will identify new targets for breeding programs aimed at developing rice varieties with even higher yields.

Experiment: Rice lines were chosen for genetic analysis to identify the genes responsible for controlling photosynthesis rate. One line (Takanari) represented the highest-photosynthesis rate of any cultivated rice variety. The other (Koshihikari) represented the leading, high-yielding rice variety with the greatest difference in photosynthetic rate relative to Takanari. Genetic mapping techniques were used to identify the specific gene responsible for the high rate of photosynthesis in the Takanari variety. Physiological measurements were also performed to figure out why this gene confers better photosynthetic rates.

Takai et al Fig 1B Sci Rep. 2013; 3: 2149 Creative Commons License

Takai et al Fig 1B, Sci Rep. 2013; 3: 2149
Creative Commons License

Results: One locus named GREEN FOR PHOTOYSYNTHESIS (GPS) was identified as a contributing factor for increased photosynthetic rate. Takai and co-authors determined that the better photosynthetic rates were due to an increase in Rubisco content, which increased the rate at which CO2 could be converted into sugars. When the researchers identified the DNA sequence of the GPS locus, they found it was a gene that had been previously characterized and named NARROW LEAF1 (NAL1). NAL1 is a plant-specific protein important for plant hormone* transport, which controls plant growth. It had been previously established that nal1 mutants resulted in dwarfed rice plants, but photosynthesis rates had not been examined. So, the researchers in this study went back and had a look at photosynthetic rates in previously characterized nal1 mutants. Sure enough, they had higher photosynthetic rates too. The specific GPS sequence variants identified in this study, however, resulted in higher photosynthetic capacity without the dwarf plant trait. This is because of the difference in severity of the GPS and nal1 mutants; previously characterized nal1 mutants were complete loss-of-function mutations, while the GPS variant in this study was still partially functional. When the researchers looked at the leaves of the GPS variants, they found increased cells and thicker leaves. This is consistent with an abnormality in the function of a gene controlling plant hormone function, and the photosynthetic increase is a secondary effect.

Conclusions: The disruption of the GPS(NAL1) gene in rice results in higher photosynthetic rates because of better CO2 fixation. This trait is intertwined with control of plant stature via a plant hormone pathway. So, leaf shape at the cellular level can have a profound effect on how efficient photosynthesis is. With the identification of this gene, the scientists were able to go back and look at more rice varieties and check for GPS. As it turns out, even though breeders didn’t know the molecular details behind it, this trait had been selected for in high-yielding rice breeding programs.

Think Ahead: Using the GPS(NAL1) gene as a marker for photosynthetic productivity can improve breeding strategies for making higher-yielding rice varieties. This study demonstrates that scientists must look beyond the genes involved in the biochemical reactions of photosynthesis to improve photosynthetic rates. In this case, a gene controlling leaf cell structure was a major determinant for increases in CO2 fixation. While this link is clear, we have no idea what the precise function of the GPS(NAL1) gene is. The story gets more complicated when trying to translate these findings into actual rice grain yield increases. The GPS(NAL1) is not the whole story because the presence of this gene variant alone is insufficient to give appreciable grain yields without the presence of other genes controlling yield or the addition of nitrogen fertilizer. This report provides great new information and tells us we still have more to do on the way for optimizing rice yields.

Check out the full article here**:

This work represents a huge effort in plant genetics just to identify GPS. These researchers used a technique called quantitative trait loci (QTL) mapping to sort through which section of the rice genome was responsible for the trait or phenotype they were interested in. Let’s just say it involved growing a lot of individual rice plants, analyzing their physiology and using statistics to separate what was important from what was insignificant. Because the rice genome is completely sequenced, these researchers were able to determine the specific gene responsible for the trait they observed. They could directly compare the standard sequence to the sequence of their high-photosynthesis rate variety and leverage this information into more specific hypotheses for underlying function. This type of work again illustrates the confluence of specialties (genetics, statistics, physiology) required to answer complex biological problems. Scientists have to be willing to follow the results into whatever field it takes them- especially when the path wanders from photosynthetic carbon fixation to hormones that control plant development and leaf structure.


* Yes, in case you didn’t know, plants make hormones too. While they are chemically quite distinct from the animal hormones you may be familiar with (adrenaline, testosterone, estrogen etc.), they perform analogous functions to control things like plant growth and other physiological responses. Plant hormones are a difficult topic because of their diverse functions and complicated interactions.

** Open access!!!


2 thoughts on “Better photosynthesis in rice from an unexpected source

  1. Pingback: NAL1 Spikes Back | New Under The Sun Blog

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