Rice breeding breakthrough to feed billions

An international team has succeeded in propagating a commercial hybrid rice strain as a clone through seeds with 95 percent efficiency. This could lower the cost of hybrid rice seed, making high-yielding, disease resistant rice strains available to low-income farmers worldwide. The work was published Dec. 27 in Nature Communications.

First-generation hybrids of crop plants often show higher performance than their parent strains, a phenomenon called hybrid vigor. But this does not persist if the hybrids are bred together for a second generation. So when farmers want to use high-performing hybrid plant varieties, they need to purchase new seed each season.

Rice, the staple crop for half the world's population, is relatively costly to breed as a hybrid for a yield improvement of about 10 percent. This means that the benefits of rice hybrids have yet to reach many of the world's farmers, said Gurdev Khush, adjunct professor emeritus in the Department of Plant Sciences at the University of California, Davis. Working at the International Rice Research Institute from 1967 until retiring to UC Davis in 2002, Khush led efforts to create new rice high-yield rice varieties, work for which he received the World Food Prize in 1996.

One solution to this would be to propagate hybrids as clones that would remain identical from generation to generation without further breeding. Many wild plants can produce seeds that are clones of themselves, a process called apomixis.

"Once you have the hybrid, if you can induce apomixis, then you can plant it every year," Khush said.

However, transferring apomixis to a major crop plant has proved difficult to achieve.

One Step to Cloned Hybrid Seeds

In 2019, a team led by Professor Venkatesan Sundaresan and Assistant Professor Imtiyaz Khanday at the UC Davis Departments of Plant Biology and Plant Sciences achieved apomixis in rice plants, with about 30 percent of seeds being clones.

Sundaresan, Khanday and colleagues in France, Germany and Ghana have now achieved a clonal efficiency of 95 percent, using a commercial hybrid rice strain, and shown that the process could be sustained for at least three generations.

The single-step process involves modifying three genes called MiMe which cause the plant to switch from meioisis, the process that plants use to form egg cells, to mitosis, in which a cell divides into two copies of itself. Another gene modification induces apomixis. The result is a seed that can grow into a plant genetically identical to its parent.

The method would allow seed companies to produce hybrid seeds more rapidly and at larger scale, as well as providing seed that farmers could save and replant from season to season, Khush said.

"Apomixis in crop plants has been the target of worldwide research for over 30 years, because it can make hybrid seed production can become accessible to everyone," Sundaresan said. "The resulting increase in yields can help meet global needs of an increasing population without having to increase use of land, water and fertilizers to unsustainable levels."

The results could be applied to other food crops, Sundaresan said. In particular, rice is a genetic model for other cereal crops including maize and wheat, that together constitute major food staples for the world.

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Ancient stone tools from China provide earliest evidence of rice harvesting

A new Dartmouth-led study analyzing stone tools from southern China provides the earliest evidence of rice harvesting, dating to as early as 10,000 years ago. The researchers identified two methods of harvesting rice, which helped initiate rice domestication. The results are published in PLOS ONE.

Wild rice is different from domesticated rice in that wild rice naturally sheds ripe seeds, shattering them to the ground when they mature, while cultivated rice seeds stay on the plants when they mature.

To harvest rice, some sort of tools would have been needed. In harvesting rice with tools, early rice cultivators were selecting the seeds that stay on the plants, so gradually the proportion of seeds that remain increased, resulting in domestication.

"For quite a long time, one of the puzzles has been that harvesting tools have not been found in southern China from the early Neolithic period or New Stone Age (10,000 -- 7,000 Before Present) -- the time period when we know rice began to be domesticated," says lead author Jiajing Wang, an assistant professor of anthropology at Dartmouth. "However, when archaeologists were working at several early Neolithic sites in the Lower Yangtze River Valley, they found a lot of small pieces of stone, which had sharp edges that could have been used for harvesting plants."

"Our hypothesis was that maybe some of those small stone pieces were rice harvesting tools, which is what our results show."

In the Lower Yangtze River Valley, the two earliest Neolithic culture groups were the Shangshan and Kuahuqiao.

The researchers examined 52 flaked stone tools from the Shangshan and Hehuashan sites, the latter of which was occupied by Shangshan and Kuahuqiao cultures.

The stone flakes are rough in appearance and are not finely made but have sharp edges. On average, the flaked tools are small enough to be held by one hand and measured approximately 1.7 inches in width and length.

To determine if the stone flakes were used for harvesting rice, the team conducted use-wear and phytolith residue analyses.

For the use-wear analysis, micro-scratches on the tools' surfaces were examined under a microscope to determine how the stones were used. The results showed that 30 flakes have use-wear patterns similar to those produced by harvesting siliceous (silica-rich) plants, likely including rice.

Fine striations, high polish, and rounded edges distinguished the tools that were used for cutting plants from those that were used for processing hard materials, cutting animal tissues, and scraping wood.

Through the phytolith residue analysis, the researchers analyzed the microscopic residue left on the stone flakes known as "phytoliths" or silica skeleton of plants. They found that 28 of the tools contained rice phytoliths.

"What's interesting about rice phytoliths is that rice husk and leaves produce different kinds of phytolith, which enabled us to determine how the rice was harvested," says Wang.

The findings from the use-wear and phytolith analyses illustrated that two types of rice harvesting methods were used -- "finger-knife" and "sickle" techniques. Both methods are still used in Asia today.

The stone flakes from the early phase (10,000 -- 8,200 BP) showed that rice was largely harvested using the finger-knife method in which the panicles at the top of the rice plant are reaped. The results showed that the tools used for finger-knife harvesting had striations that were mainly perpendicular or diagonal to the edge of the stone flake, which suggests a cutting or scraping motion, and contained phytoliths from seeds or rice husk phytoliths, indicating that the rice was harvested from the top of the plant.

"A rice plant contains numerous panicles that mature at different times, so the finger-knife harvesting technique is especially useful when rice domestication was in the early stage," says Wang.

The stone flakes however, from the later phase (8,000 -- 7,000 BP) had more evidence of sickle harvesting in which the lower part of the plant was harvested. These tools had striations that were predominantly parallel to the tool's edge, reflecting that a slicing motion had likely been used.

"Sickle harvesting was more widely used when rice became more domesticated, and more ripe seeds stayed on the plant," says Wang. "Since you are harvesting the entire plant at the same time, the rice leaves and stems could also be used for fuel, building materials, and other purposes, making this a much more effective harvesting method."

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Growing cereal crops with less fertilizer

Researchers at the University of California, Davis, have found a way to reduce the amount of nitrogen fertilizers needed to grow cereal crops. The discovery could save farmers in the United States billions of dollars annually in fertilizer costs while also benefiting the environment.

The research comes out of the lab of Eduardo Blumwald, a distinguished professor of plant sciences, who has found a new pathway for cereals to capture the nitrogen they need to grow.

The discovery could also help the environment by reducing nitrogen pollution, which can lead to contaminated water resources, increased greenhouse gas emissions and human health issues. The study was published in the journal Plant Biotechnology.

Nitrogen is key to plant growth, and agricultural operations depend on chemical fertilizers to increase productivity. But much of what is applied is lost, leaching into soils and groundwater. Blumwald's research could create a sustainable alternative.

"Nitrogen fertilizers are very, very expensive," Blumwald said. "Anything you can do to eliminate that cost is important. The problem is money on one side, but there are also the harmful effects of nitrogen on the environment."

A new pathway to natural fertilizer

Blumwald's research centers on increasing the conversion of nitrogen gas in the air into ammonium by soil bacteria -- a process known as nitrogen fixation.

Legumes such as peanuts and soybeans have root nodules that can use nitrogen-fixing bacteria to provide ammonium to the plants. Cereal plants like rice and wheat don't have that capability and must rely on taking in inorganic nitrogen, such as ammonia and nitrate, from fertilizers in the soil.

"If a plant can produce chemicals that make soil bacteria fix atmospheric nitrogen gas, we could modify the plants to produce more of these chemicals," Blumwald said. "These chemicals will induce soil bacterial nitrogen fixation and the plants will use the ammonium formed, reducing the amount of fertilizer used."

Blumwald's team used chemical screening and genomics to identify compounds in rice plants that enhanced the nitrogen-fixing activity of the bacteria.

Then they identified the pathways generating the chemicals and used gene editing technology to increase the production of compounds that stimulated the formation of biofilms. Those biofilms contain bacteria that enhanced nitrogen conversion. As a result, nitrogen-fixing activity of the bacteria increased, as did the amount of ammonium in the soil for the plants.

"Plants are incredible chemical factories," he said. "What this could do is provide a sustainable alternative agricultural practice that reduces the use of excessive nitrogen fertilizers."

The pathway could also be used by other plants. A patent application on the technique has been filed by the University of California and is pending.

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