CROP BIOTECH UPDATE
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A weekly summary of world developments in agri-biotech for developing countries, produced by the Global Knowledge Center on Crop Biotechnology, International Service for the Acquisition of Agri-biotech Applications SEAsiaCenter (ISAAA)
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October 16, 2019

In This Week’s Issue:

News

Global
• 14% of Global Food Goes to Waste, FAO Reports

Americas
• Study Reveals the Resilience of Rice to Floods
• Hornless Cattle Now Possible Thanks to Genome-editing
• FDA Approves Texas A&M's Ultra-Low Gossypol Cotton for Human and Animal Consumption

Asia and the Pacific
• Genomics-Assisted Breeding Delivers Two Improved Chickpea Varieties in Record Time

Europe
• Family of Crop Viruses Shown at High Resolution for the First Time

Research
• Plant Protein that Triggers Photoprotection Identified
• Genetically Engineered Plants Occur in Large Scale Naturally

New Breeding Technologies
NAL8 Contributes to Leaf and Spikelet Development in Rice
• Large-scale Genomics for Wheat Improvement



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NEWS
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Global
14% OF GLOBAL FOOD GOES TO WASTE, FAO REPORTS

Around 14 percent of global food goes to waste after harvesting and before reaching the retail level, including through on-farm activities, storage, and transportation. This is according to the report on the State of Food and Agriculture released by the Food and Agriculture Organization of the United Nations (FAO).

FAO monitored how much, where, and why food is lost at different stages on the food supply chain. The findings will help identify critical loss points across the supply chains, which have a great impact on food security. Results showed that harvesting is the most frequently identified critical loss point for all types of food. It was also reported that losses and waste are generally higher for fruits and vegetables than cereals and pulses at all stages in the supply chain, except for on-farm losses and those during transportation in Eastern and South-Eastern Asia. For lower-income countries, the cause of great losses in fruits and vegetable supply chain is poor infrastructure, particularly storage facilities. For high-income countries, losses occur when there is technical breakdown, poor management of temperature in storage facilities, humidity or overstocking.

FAO called for consumers and producers' understanding of the problem and taking action on how to effectively reduce food losses globally.

Download the report from FAO.



Americas
STUDY REVEALS THE RESILIENCE OF RICE TO FLOODS

Climate change has increased the severity and frequency of extreme weather conditions such as droughts and floods. This is a big problem for farmers as rice is the only crop with resilience to flooding. A new study conducted by a team of scientists from Emory University; University of California, Davis; University of California, Riverside; Argentina's National University of La Plata, and the Netherland's Ultrecht University has identified the genetic clues to the resilience of rice plants to flooding that may help scientists improve the prospects for other crops.

Rice was domesticated in the tropics, where it has adapted to monsoon rains and waterlogging. The research examined how other crops compare to rice when submerged in water. The plants included species with a range of flooding tolerance, from barrel clover (similar to alfalfa), to domesticated tomato plants, to a wild-growing tomato that is adapted for a desert environment. Results showed that while evolution separated rice ancestors from other species as far back as 180 million years ago, they all share at least 68 gene families that are activated during flooding.

The UC Riverside team conducted flooding experiments and analysis of rice plant genomes, while the UC Davis group did the same with the tomato species, and the barrel clover work was done at Emory. The results suggest that the timing and smoothness of the genetic response may account for the variations in the outcomes for the plants during the experiments.

For more details, read the article in the eScienceCommons.


HORNLESS CATTLE NOW POSSIBLE THANKS TO GENOME-EDITING

Scientists form the University of California, Davis, along with colleagues from the University of Mansoura in Egypt have successfully used genome editing to produce hornless cattle, which can then pass on the genome-edited traits to their calves. Their findings also revealed that the process did not result in any unintended genetic changes in the calves.

"We've demonstrated that healthy hornless calves with only the intended edit can be produced, and we provided data to help inform the process for evaluating genome-edited animals," according to co-author Alison Van Eenennaam, from the UC Davis department of animal science. She added that genome-editing presents a more humane option to dehorning or physically removing the horns, which is an issue among animal welfare advocates since it is a painful process.

After sequencing the genomes of the calves and their parents, a plasmid (short stretch of bacterial DNA) was incorporated next to one of the two hornless genetic variants. With the insertion of the plasmid, the genome-edited bull can technically be considered a genetically-modified organism (GMO) since it now has foreign DNA from another species. The researchers assured that the plasmid does not hurt the animal.

To date, only the AquaAdvantage salmon has been able to pass the rigid regulatory approval process of genetically-modified animals in the US.

For more details, read the full journal article in Nature Biotechnology.


FDA APPROVES TEXAS A&M'S ULTRA-LOW GOSSYPOL COTTON FOR HUMAN AND ANIMAL CONSUMPTION

The U.S. Food and Drug Administration (FDA) has approved an ultra-low gossypol cottonseed, ULGCS, to be utilized as human food and animal feed. ULGCS is derived from a transgenic cotton variety TAM66274 developed by plant biotechnologist Keerti Rathore and his team at Texas A&M AgriLife Research. TAM66274 is a unique cotton plant with ultra-low gossypol levels in the seed, which makes the protein from the seeds safe for food use, but also maintains normal plant-protecting gossypol levels in the rest of the plant, making it ideal for the traditional cotton farmer.

ULGCS has the potential to make a significant impact on food security especially in poor, cotton-growing countries, according to Rathore. "The amount of protein locked up in the annual output of cottonseed worldwide is about 10.8 trillion grams," he said. "That is more than what is present in all the chicken eggs produced globally, and enough to meet the basic protein requirements of over 500 million people."

The FDA approval for ULGCS is only the fifth for a university-developed, genetically engineered crop in the 25-year history of genetically modified products in the U.S., and is the first for a Texas university. According to Rathore, the human food ingredients from TAM66274 cottonseed can be roasted cottonseed kernels, raw cottonseed kernels, cottonseed kernels, partially defatted cottonseed flour, defatted cottonseed flour and cottonseed oil. For animal feed, the low-gossypol cottonseed can be used in the aquaculture and poultry industries.

To get to this point, Rathore and his team sought approval from two government agencies. First, a non-regulated status for TAM66274 was secured from the U.S. Department of Agriculture's Animal and Plant Health Inspection Service. Then, they pursued the FDA approval. "This approval from FDA enables cultivation and use of this promising new cottonseed product within the U.S.," Rathore said.

For more details, read the article in AgriLife Today.



Asia and the Pacific
GENOMICS-ASSISTED BREEDING DELIVERS TWO IMPROVED CHICKPEA VARIETIES IN RECORD TIME

Two new chickpea varieties developed in record time through genomics-assisted breeding with drought tolerance and disease resistance are set to be launched in India. All India Coordinated Research Project (AICRP) for Chickpea identified two desi chickpea (Bengal chana) varieties, ‘Pusa 10216' and ‘MABC-WR-SA-1', which were developed by the Indian Council of Agricultural Research (ICAR)-ICAR-Indian Agricultural Research Institute (IARI) and University of Agricultural Sciences (UAS) in Raichur, Karnataka, respectively, in collaboration with the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT).

Pusa (BMG) 10216 was developed at IARI in collaboration with ICRISAT. Using their extensive knowledge of the chickpea genome, Dr. Rajeev Varshney's team at ICRISAT was able to introgress drought tolerance into the chickpea variety Pusa 372 with genes from ICC 4958, a drought tolerant chickpea landrace. The result, Pusa 10216, is the first chickpea variety to have drought tolerance through molecular breeding, was developed in just four years. It showed 11.9% increase in yield over Pusa 372 during a two-year multi-location testing in drought conditions.

The other crop, MABC-WR-SA-1, was developed by inducing fusarium wilt resistance in Annigeri-1, a variety highly preferred by farmers in Karnataka. The source of resistance to fusarium wilt was WR315, a chickpea landrace. With 7% increased yield potential over Annigeri-1, this new variety is also being called Super Annigeri-1, and was developed by UAS-Raichur in collaboration with ICRISAT.

For more details, read the article in the ICRISAT website.



Europe
FAMILY OF CROP VIRUSES SHOWN AT HIGH RESOLUTION FOR THE FIRST TIME

For the first time, the world's deadliest crop killers are revealed at a molecular level. The Luteoviridae are pathogenic viruses that cause major crop losses worldwide. However, researchers have been unable to generate the quantities of these viruses needed to study them in high resolution. Now a group of researchers at John Innes Centre and the Astbury Biostructure Laboratory at the University of Leeds used recent advances in plant expression technology to derive sufficient quantities of the pathogen to create a more detailed scrutiny with state of the art microscopy techniques.

The method the researchers used involves infiltrating a tobacco plant with the genes necessary to create virus-like particles (VLPs). Using the VLPs, the team observed the viral structures to high resolution by cryo-electron microscopy. This provided, for the first time, a molecular-level insight into how the luteovirid capsid forms and suggests how it is transmitted by aphids.

The Luteoviridae are transmitted by aphids, and infect a wide range of food crops including cereals, legumes, cucurbits, sugar beets, sugarcane, and potato. These viruses attack the plant vasculature which causes severe stunting leading to crop loss. The family includes barley yellow dwarf virus and potato leafroll virus.

For more details, read the article in John Innes Centre website.



Research
PLANT PROTEIN THAT TRIGGERS PHOTOPROTECTION IDENTIFIED

A team of scientists from the United States announced that they have identified the protein in plants responsible for its cellular defense against excessive light, among other stress factors caused by climate change.

Published literature states that photosynthesis occurs in the plant cell's chloroplast. In these chloroplasts, proteins make up the molecular structure that is responsible for the plant's light absorption to produce necessary chemical reactions to support the plant's development. Exposure to too much sunlight causes an overdrive reaction and damages the said proteins. These damaged proteins have to be evaluated, removed and replaced by the plant. The scientists' objective was to know more about the plants' ability to evaluate the healthy and damaged proteins and trigger a protective response, a process in plants that is yet to be thoroughly investigated by researchers.

Using engineered cells from the algae Chlamydomonas reinhardtii, scientists were able to discover that the chloroplast is able to send a signal to activate the "chloroplast unfolded protein response" (cpUPR). cpUPR is the plant's protective response that is triggered upon overexposure to light, and leads to the production of specialized proteins that helps protect and repair the chloroplast. The finding led to the identification of the gene MARS1, which stands for Mutant Affected in Retrograde Signaling. It plays a significant role in turning on the cpUPR. The scientists noted that the algal cells with defective MARS1 were more vulnerable to chloroplast damage caused by stress factors, including overexposure to light. Cells with defective MARS1 were observed to be unable to turn on the cpUPR and die.

The results highlight the significance of cpUPR in plants, as understanding its process can help future scientists to develop better crop endurance against harsh climates. Moreover, one of the scientists stated that their findings can also lead to future studies that aims to the increase the production of antigen proteins in plants, which are used in the production of vaccines.

See the full paper in eLIFE.


GENETICALLY ENGINEERED PLANTS OCCUR IN LARGE SCALE NATURALLY

Horizontal gene transfer caused by Agrobacterium was found to occur in 39 dicot species. These findings prove that transgenic plants occur in nature on unexpectedly large scale. The results are published in Plant Molecular Biology.

Agrobacterium-mediated gene transfer cause formation of crown galls or hairy roots, due to the expression of transfer DNA (T-DNA) genes. When the transformed cells regenerate naturally, transformants carrying the cellular T-DNA (cT-DNA) are developed. This type of horizontal gene transfer could contribute to plant evolution. However, there is no concrete evidence yet to make generalizations about the role of bacteria in plant evolution. Thus, researchers at St. Petersburg State University in Russia and Institut de Biologie Moléculaire des Plantes in France conducted a study to search for T-DNA-like genes in the genomes of monocots and dicots. They found that cT-DNAs were found in 23 out of 275 dicots, which include those belonging to the genera Eutrema, Arachis, Nissolia, Quillaja, Euphorbia, Parasponia, Trema, Humulus, Psidium, Eugenia, Juglans, Azadirachta, Silene, Dianthus, Vaccinium, Camellia, and Cuscuta. Transcriptome data of 256 dicot species showed that 16 more are naturally transgenic species. For the monocots, T-DNA-like sequences were also found in greater yam and banana.

The identified natural transgenics could help on future research about the function of Agrobacterium-derived genes in plant evolution.

Read the research article in Plant Molecular Biology journal.



New Breeding Technologies
NAL8 CONTRIBUTES TO LEAF AND SPIKELET DEVELOPMENT IN RICE

Researchers identified a protein complex that plays vital roles in many developmental processes, including development  of normal leaf width and spikelet number at the reproductive stage in rice. The functions were confirmed in transgenic plants using CRISPR-Cas9 system, RNAi gene silencing system, and overexpressing system. The results are published in BMC Plant Biology.

Leaf morphology and spikelet number are two important traits linked with grain yield. Understanding the molecular mechanisms that regulate the two traits would be vital in the improvement of cereal crops. Chinese Academic of Sciences researchers identified a prohibitin complex 2α subunit, NAL8, which contributes to multiple developmental process and is required for normal leaf width and spikelet number at the reproductive stage in rice. Using CRISPR-Cas9, RNAi, and overexpressing systems, they found that mutation of NAL8 causes a reduction in cell division. The auxin levels in the nal8 mutants were higher than the control, while cytokinin concentrations were lower. Further analyses showed that NAL8 is involved in several hormone signaling pathways as well as photosynthesis in chloroplasts and respiration in mitochondria.

Based on the results of the study, it was concluded that NAL8 works as a molecular chaperone in controlling plant leaf morphology and spikelet number.

Read more results in BMC Plant Biology.


LARGE-SCALE GENOMICS FOR WHEAT IMPROVEMENT

Improving bread wheat using genomic tools is vital in speeding up development of varieties with enhanced traits. Thus, Carlos Guzman from the International Maize And Wheat Improvement Center (CIMMYT) and other genetics experts used large scale genomics and looked into the validity of genomic selection to improve wheat with less field work and less lab work. Their findings are published in Nature Genetics.

The researchers reported the genomic predictabilities of 35 key traits and demonstrated the potential of genomic selection for wheat end-use quality. They also performed a large genome-wide association study that led them to the identification of several significant marker-trait association for 50 traits evaluated in South Asia, Africa, and the Americas. Moreover, they developed a reference wheat genotype-phenotype map, explored allele frequency dynamics over time and fingerprinted 44,624 wheat lines for trait-associated markers, coming up with over 7.6 million data points.

The results of the study provides a valuable resource to the wheat community for improving productivity and stress resilience.

Read the original article in Nature Genetics.





(c) 2019. ISAAA.