Japan’s tsunami of March 11 2011 brought a wall of water laden with debris up to 5 kilometres inland from the sea. After the surge receded, the surrounding farming area was left covered in debris and a thick, black sludge. This sludge was extremely saline due to the sodium chloride from seawater.

Rice is the largest agricultural crop in Japan and the five prefectures affected by the 2011 tsunami are among the top producers of rice in Japan. Fortunately, less than 1.5% of Japan’s entire rice producing region was covered by the tsunami. Preliminary rice production statistics from the 2011 growing season show total rice production in Japan has hardly changed from 2010.

This all sounds fine on a national scale, but how did the tsunami affect the subsistence farmers in the tsunami-affected region? Reports indicate the 2011 rice production was severely decreased by salinity stress in the tsunami-affected region. This seriously affected the livelihood of these farmers.

The carpet of sludge and debris left by 2011’s tsunami wreaked havoc on paddyfields. AAP

Rice is a salt sensitive plant

Salinity stress decreases plant growth and therefore also the yield of crop plants. This happens in two ways.

Salt makes it more difficult for the plant to take up enough water. And the sodium or chloride ions can negatively affect important processes – such as photosynthesis, the process plants use to make energy from sunlight – in the leaves.

All plants have some tolerance to salinity. There are very tolerant, predominantly wild species which can grow when supplied with water as saline as sea water (saltbush is one example). Then there are the sensitive, including most common crop species.

Unfortunately for the Japanese farmers affected by the tsunami, not only is rice a salinity sensitive species, it is one of the most salinity sensitive crop species grown.

Breeding salt-tolerant crops

Plants have several defence mechanisms they use to maintain growth and tolerate salinity. The first is to keep the salt out of the sensitive leaves. Crops like rice are poor at it; crops like wheat are relatively good at it.

The second is to tolerate the salt that enters the leaves. Barley is particularly good at this. The third is the ability to survive decreased water uptake despite high levels of salt in the soil, a trait which may also be found in crops tolerant to drought stress.

Researchers know the most about keeping salt out of the leaves and the least about how plants tolerate decreased water uptake. As such, many of the genes known to be important for salinity tolerance in crops encode sodium transporters which stop sodium reaching the leaf.

Plant breeders are actively transferring these salinity tolerance genes into crops that possess other positive traits such as high yield or disease resistance. For example, the wild rice Nona Bokra, which is salt tolerant, has been crossed with the Koshihikari rice variety, which is popular with the Japanese consumer because of its superior appearance and taste. This new line has all the popular traits of Koshihikari, as well as salinity tolerance from Nona Bokra’s more efficient sodium transporter.

Lessons from previous tsunamis

The years following the December 26 2004 tsunami have given agricultural researchers and farmers valuable information about how long it takes to recover from a tsunami. Researchers have learnt the length of time required for land to return to pre-tsunami salinity levels and the best methods for accelerating this process.

Most experts estimate that within two years soil can be returned to its original salinity levels. This requires plenty of rainfall as well as irrigation with non-saline water. The rain or clean water washes the salt down through the soil profile until it is too deep for the rice roots to reach.

This prognosis is good news for the farmers in north-eastern Japan, a region which generally has plentiful rain and good sources of clean water.

Salt-tolerant crops could help farmers

Farmers in the large, relatively dry regions of the Australian agriculture zone are faced with consistently saline soil. For these farmers, crops with improved salinity tolerance are crucial.

But what about Japanese farmers? If, after a tsunami, rainfall and irrigation are sufficient to remediate the saline soil, would farmers still benefit from salt-tolerant rice?

After the March tsunami there was a very short window of time before the 2011 rice sowing season began in April. The salinity levels in the rice paddies would have been very high at sowing time. Seedling establishment is critical for developing yield potential: any increase in growth provided by salinity tolerant rice varieties would have increased yield, and that would have increased the income of farmers on very small economic margins in that difficult year.

Continued development of salinity tolerant rice varieties for release to farmers with low incomes could be vital in helping those farmers. Not only will it be important to help agriculture survive in salinity affected areas, it can also help the short-term recovery from devastating tsunamis.

This article was written by Dr Darren Plett of ACPFG. It was originally published at The Conversation.
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Most genes are expressed in particular places or at particular times. For example your red blood cells express a gene that makes haemoglobin for transporting oxygen, but your hair doesn’t. Where a gene gets expressed depends on its promoter. ACPFG scientists are interested in what promoters cause genes to be expressed in the grains of cereal plants. That will allow the researchers to target nutrients that are important to human health, like iron or zinc, to the grain of the plant which people eat.

Expressing genes in specific parts of plants is an important part of modern plant genetics. Scientists working with genetically modified plants don’t want plants wasting energy expressing the genes throughout the plant. Instead they want to target a gene-product to where it’s needed. If researchers want to fortify a grain with nutrients that are good for human health, then it’s most important for these to be in the part of the plant that we eat. In wheat, barley or rice, that’s the grain.

Researching plant promoters also gives us clues about how plants make grain at a cellular level. TdPR61, the protein on the cover of the Journal of Experimental Botany, transports lipids into different parts of the grain. The clue to finding out that TdPR61 carries lipids came from its structure. TdPR61 is very similar to a protein from Arabidopsis (the lab-rat of plant biology). This similarity allowed scientists to model its structure and find that it has an oily surface suitable for binding lipids. The plant probably uses these lipids to form a waxy layer that keeps out pathogens like bacteria and fungi.

Future research will use the new knowledge of how to express genes in plant grains to improve the quality and nutritional qualities of cereal grains.

The research is the result of a collaboration between the Drought Biotechnology group led by Sergiy Lopato and the Structural Biology group lead by Maria Hrmova. This article was written by Arwen Cross.

The authors on the paper were: Nataliya Kovalchuk, Jessica Smith, Natalia Bazanova, Tatiana Pyvovarenko, Rohan Singh, Neil Shirley, Ainur Ismagul, Alexander Johnson, Andrew S. Milligan, Maria Hrmova,Peter Langridge and Sergiy Lopato

The medical and agricultural biotechnology industries use the patent system as a mechanism to recoup extensive research expenditure. Many public sector organisations do the same. Without gene patents we may indeed have less innovation rather than more; that won’t help patients. As is the case with many new technologies, some of the early gene patents were very broad. These will gradually expire and therefore concerns with that particular group of patents should not form part of this debate.

Gene patents in agriculture are becoming commonplace since it is now possible to improve plants by transferring genes from one plant to another. Genes can be turned on or off and made to work only in particular parts of a plant. The knowledge of genes and their function provides a valuable toolbox for improving the supply and quality of our food. As transgenic crops become more widely accepted, Australian farmers will need to accept new technologies to remain internationally competitive. If gene patents are not issued in Australia, we may see growers “missing out” on access to technologies.

A Senate “Community Affairs References” Committee has been looking closely at a proposal to ban gene patents and has concluded that there is no evidence that such a ban would be effective and, that there may be indeed (unforeseen) consequences for such a ban.

In human health, there are already a number of options to protect patients. Diagnostic tests can be included in the Medicare system through PBS subsidies. In extreme cases, the Commonwealth has the right to compulsorily license patents if there is a perceived societal need. It seems as if there are sufficient safeguards in place to deal with the most extreme use of human gene patents.

The main issue in the gene patenting debate is not really about the patent system or the ethics of gene patents at all; it is about promoting innovation. If genes were not patentable, where would the money come from to pay for the research that generates the knowledge? If there is to be innovation, someone must pay for it; either the taxpayer through publicly funded research or in the private sector, which will no doubt want a return on its money. Either way, someone must pay.

Some argue that genes don’t fit perfectly into the patent system because they are purely discoveries. Even if this is the case, then what system should be used to ensure that innovators are rewarded? Genetic research is an expensive time-consuming business. Before we decide whether or not genes should be patentable, we must ensure that we have suitable incentive mechanisms to stimulate innovation and allow society to benefit from innovations. The patent system currently provides such an incentive system and biological patents should not be removed from it unless a viable alternative is put in place first.

Michael Gilbert is the General Manager of the Australian Centre for Plant Functional Genomics.