Improving the Rice Genome for a More Sustainable Future
Co-Authored with Hawi Adede, a Genetic Scientist at The Africa Genomic Center & Consultancy.
In the last post, we spoke of how genomic breeding of rice is being done using novel biotechnological approaches. These technologies present scientists with an opportunity to make use of functional genetic variations to improve productivity, counter biodiversity loss, and prevent environmental degradation.
These breeding programs seek to achieve such sustainability goals through the development of new rice varieties collectively known as the Green Super Rice (GSR). But first, a little history.
The two kinds of domesticated rice grown today are of the species O. Sativa (Asian rice) and O. Glaberrima (African rice). Rice is one of those crops which just looooove, water. The scientific consensus is that the domestication events took place along two major river valleys.
It is estimated that the Asian specie was first grown some 9500 years ago along China’s Yangtze River. About 000 years later, the Niger River Delta yielded the African specie.
Source: Nature
In the centuries since, different varieties of rice have emerged through intentional breeding as well as natural mutations. These rices, especially the Asian varieties, spread across different regions with varying climatic and soil conditions. They had to adapt to these environments in order to thrive.
Likewise, the crops had to be adapted to the different agronomic practices and culinary cultures of the people in whose lands it grows. People have over centuries selected for and bred rice varieties that met their culinary and agronomic needs. These include the color of grains, height of crops, flowering time, the aroma, among others.
These variations are codified in their genes. As a result, there exists a rich biodiversity in the rice genome. This is especially in the Asian varieties as they are more widely spread and consumed as compared to the African one.
The genes which make these rices adaptable to their respective environments are a natural capital that can be tapped into for genomic breeding programs. That is exactly what the scientists behind efforts to breed the Green Super Rice (GSR) are working towards.
This article is heavily influenced by one journal article in particular. According to it, scientists working on GSR breeding programs seek to achieve its sustainability objectives by focusing on five major characteristics:
- Resistance to Pests and Diseases
Currently, growing of rice heavily relies on agrochemicals to fight pests and diseases. For a more sustainable future, such usage has to be significantly reduced or eliminated. This will lower or prevent their negative effects on the environment. Breeding rice with natural resistance to pests and diseases is one possible approach that is not only feasible, but also economical.
Fungal blast is the most destructive of all rice diseases, as it can cause up to 100% crop failure. It's damaging capabilities are closely followed by bacterial blight, which can damage up to 75% of crops. The major pest in rice fields is the brown planthopper, which can cause a 60% yield loss.
The GSR breeding efforts are meant to isolate genes that yield both effector-triggered and pattern-triggered immunity against pathogens, as well as natural resistance to pests. In this way, rice plants will be less reliant on agro-chemicals for protection.
So far, scientists have identified 27 genes that code for resistance against fungal blast. Additionally, 11 genes have been characterized for resistance against bacterial blight while at least 30 have been shown to code for resistance against the insect. Furthermore, there several other defensive genes which can augment these ones have been identified.
All of these are available for breeding programs.
2. Efficient Nutrient Use
For rice production to become more sustainable, its demand for nutrients has to be scaled down. To achieve this, the plants need to be such that they make use of available nutrients more efficiently. Aside from reducing the amount of fertilizer used, it will enable growth of rice on less fertile land. Presently, GSR efforts have concentrated on Nitrogen and Phosphorus as they are, presently, the best understood.
More than 200 genes have been identified as being essential for improving nutrient usage in plants as a whole. In addition to this, it has been shown that Nitrate transporter genes transferred from one sub-specie of Asian rice to another improve uptake of nitrates. This provides a guideline for future efforts in genetic modifications.
By some accounts, at least a third of all arable lands on the planet do not have sufficient amounts of phosphorus to support optimal plant growth. Despite this, more than 60% of the absorbed phosphorus is allocated to the grains in cereals such as rice. Therefore, the removal of these very grains during harvest leads to loss in the available phosphorus by up to 80%. That needs to be contained.
Some breeding programs are, therefore, concentrating on identification of genes which can confer rice with the ability to grow in soils with low phosphorus levels. Furthermore, there are efforts to alter the gene responsible for allocation of phosphorus to grains.
Successful trials have shown that this approach lowers phosphorus accumulation in the grains, without significantly affecting its nutritive properties. This minimizes removal of nutrients from the field, hence availing them for the next crop cycle.
3. Improved Yield
As the global population approaches 10 billion, rice production has to significantly increase. For this to happen, the amount of grain that is produced per plant has to rise. Such improved yield is a factor of several parameters, including:
Increasing the number of panicles per plant; raising the amount of grains on each panicle; increasing the nutrient content in grains; producing heavier grains, and improving the overall plant architecture to support such modifications.
The tricky bit, however, is that most genes which are responsible for regulating yield tend to be pleiotropic. That means that these genes determine other traits, which are often unrelated. This presents a problem because editing for one trait may lead to unintended, often undesirable, effects on other traits.
For instance, one gene that is responsible for regulating the number of grains per panicle also influences the plant size and flowering time. Likewise, another one which influences grain size also has an effect on the number of panicles and the plant architecture. Dozens of other genes exhibit similar behavior.
This characteristic is not unique to rice, as it has also been observed in humans. For the HIV Virus to attack human cells, it needs to attach itself onto a gene known as CCR5. Therefore, deleting the gene could, hypothetically, make one immune to the virus.
He Jiankui, a Chinese researcher tested this hypothesis in 2018. The result was a set of twins with no CCR5 in their DNA, and a 3 year jail term for the scientist due to the unethical nature of this research. The deletion, however, also indicated that the gene plays a role in human intelligence, as it altered their brains.
The twins may have improved cognitive and memory skills as a result of this alteration. Some people are speculating that this could lead to a biotechnological “arms" rac between the USA and China through creation of super intelligent humans via genetic engineering. That aside, this post is focused on rice, so let us proceed with that, first.
The incredible diversity in the functions of rice genes which regulate yield make breeding for it slightly more complicated than the aforementioned traits. Although some genes have been identified and provide a basis for future modifications, that is just the beginning.
There is need to map out the entire regulatory network associated with each gene as well as their interactions. With such information at hand, a balanced approach can be taken in the breeding programs. It will ensure that altering genes to improve one trait does not negatively affect the rest.
4. Resistance to abiotic stresses
Abiotic factors are those physical or chemical elements which originate from non-living things. These include things like extreme temperatures, flooding, pH, strong winds, and salinity. These variables heavily influence plant growth and performance.
The ability of a plant to withstand prevailing abiotic stresses determines its ability to thrive in a given environment. This is especially now as the effects of climate change and environmental degradation are starting to be felt. GSR initiatives are geared towards breeding rices which can withstand extreme conditions.
In addition to this, there is the desire to develop breeds which can grow in non-traditional areas, including temperate lands and drier regions. If developed, rice plants wit such characteristics would help in increasing the crop's resilience and ability to be grown in wider habitats. That will reduce pressure on existing growing zones.
So far, at least 360 genes that code for resistance to abiotic stresses have been identified. These include genes for tolerance against submergence/flooding, low or high temperatures, and high salinity. However, those that are related to drought tolerance have been harder to come by, despite its importance.
Further steps are being taken to identify more genes even as the known ones are incorporated into existing breeding programs.
5. Enhanced grain quality
In the end, the ultimate decision makers with regard to the acceptability of any given rive breed are the consumers and producers (farmers and millers). Therefore, the quality of grains that are produced by GSR programs are meant to be such that they fit the needs of these two groups.
Some of the parameters of rice quality include the shape of the grains (length and width); the color of those grains; milling quality (chalkiness and intactness of milled rice); the cooking and eating quality (amylose content, gel consistency, and gelling temperature), and nutritional content (micro and macro nutrients alongside metabolites).
Quality requirements for rice producers tend to be similar from one region to another- which are easy grain handling and processing. However, the cooking and eating qualities vary greatly depending on the consumer market.
These not only depend on their rice-eating habits as well as the purchasing power and mode of cooking of the target populations. GSR breeding programs are therefore inclined towards selecting genes which would yield quality grains for various regions of the world, depending on what the producers and consumers demand.
Although some strides have been made in this direction through transgenic methods, public acceptance of such GMOs is still low. The only acceptable pathway, currently, is modifications that are reliant on the rice genome only.
Conclusion
Development of the green super rice demands extensive research into the rice genome. As explained in this post, such efforts are ongoing and it can only get better as time goes by. Although the public generally perceives Genetically Modified Organisms such as GSR, that is bound to change.
Once the benefits, especially the environmental and nutritional ones are seen, public acceptance may follow. In the meantime, the science is gathering steam and in the next couple years, more sustainable rice varieties will be in the fields, and on our plates.
Epilogue
That was the last of 7 articles on rice. I don’t know which topic will come next, but I am looking forward to it.
Happy new year!