Research Results
1. Scientists Improve Yield Predictions Based on Seedling Data
The ability to predict traits from genome-wide sequence information (i.e., genomic prediction) has improved our understanding of the genetic basis of complex traits and transformed breeding practices. Transcriptome (the sum total of all RNA molecules in a cell, a population of cells or in an organism) data may also be useful for genomic prediction. 
Using plant RNA data from 2-week old corn seedlings, scientists at the Michigan State University have shown that adult crop traits can be predicted with accuracy that rivals current approaches using DNA, i.e., genetic data. Shinhan Shiu, professor of plant biology and computational mathematics, science and engineering—and senior author of the published study—says that the traditional breeding methods take months to years, which can be saved if one could predict the desirable traits just from DNA and RNA without growing the crops, and without having to measure the actual traits directly. “It’s like sequencing an infant’s RNA and analyzing what sort of traits the infant may develop later in life,” Shiu adds.
A well-recognized and major challenge in biology is how to connect the information in the DNA, or genotype, with traits, or phenotype. Since RNA is a product of DNA, one step closer to the traits DNA ultimately influences, the RNA blueprints can potentially offer better predictions. Using machine learning approaches, Shiu and his colleagues have taken a step closer to connecting DNA, RNA, and the underlying traits. The findings are complementary to genetic marker-based prediction, and they identify gene expression-trait associations that are not explained by genetic markers.
For more, go to https://www.eurekalert.org/pub_releases/2020-01/msu-siy010820.php
And http://www.plantcell.org/content/32/1/139
2. The Wild Relatives of Major Vegetables, Needed for Climate Resilience, are in Danger
Growing up in the wild makes plants tough. Wild plants evolve to survive in the wild and thrive in difficult biotic and abiotic stressed conditions. Their better-known descendants, the domesticated crop plants that are an essential part of the human diet, are often not nearly as hardy. It is well known, as Colin Khoury, a scientist at the International Center for Tropical Agriculture, or CIAT says, that wild relatives of crops are can be used to improved crop varieties that are better adapted to hotter, colder, drier, wetter, saltier, and other difficult conditions, and often with resistance/tolerance to major pests and diseases. “But they are impacted by habitat destruction, over-harvesting, climate change, pollution, invasive species, and more. Some of them are sure to disappear from their natural habitats without urgent action,” she adds. To correct this situation, extensive work on precise mapping of gaps in the collection needs to be carried out, so that future collecting activities can be focused accordingly.
Using the information on extant collections, researchers have developed detailed maps and have found that, even with protection in the wild, many crop wild relatives require urgent collecting and conserving in genebanks to assure long-term survival. The results of such mapping will help crop breeders to more efficiently find wild relatives with traits needed for crop development.
The research has also highlighted the extent to which the wild relatives of vegetables have not been a priority for conservation when compared to other crops.
Over the years, several agencies and national programmes have explored the wild, and thus collected and conserved a significant number of wild species and accessions. However, gaps still exist, both in the diversity collected and, in the information, available in/on the samples/accessions. Using the gap analysis method, information on the genetic diversity collected (their geographic locations and the environments covered) can be examined, and collecting missions then undertaken to fill the gaps thus identified.
For more, go to https://phys.org/news/2019-12-wild-relatives-major-vegetables-climate.html
And articles on
Wild cucurbits – http://dx.doi.org/10.1002/ppp3.10085
Chile peppers – http://dx.doi.org/10.1111/DDI.13008
Wild lettuce – http://dx.doi.org/10.2135/cropsci2019.05.0350
Wild relatives of carrots – http://dx.doi.org/10.2135/cropsci2019.05.0333
3. The Tips of a Plant Design its Whole Shape
Plants grow throughout their entire life as they have meristematic (undifferentiated cells) cells at the tip of the plant’s shoots, i.e., shoot apical meristem (SAM). Although all plants depend on the meristem for increases in their length or growth, the meristem is different in shape and size in different species, such as maize and thale cress (Arabidopsis thaliana). An international team of researchers, headed by Professor Marja Timmermans of the Center for Plant Molecular Biology at the University of Tübingen, has discovered that the meristem has even greater tasks than scientists had realized. It controls the architecture of the whole plant from the very tip.
The team found that the meristem regulates the plant’s settings so that each individual grows into the optimal shape for the conditions it is located in. Timmermans adds, “these latest findings can be used for plant breeding and cultivation.” It has been shown that besides defining genes governing the identity and function of critical domains within the maize SAM, the gene expression atlas developed by the authors thus identifies key targets for selection in the improvement of agronomically important traits. For example, in the architecture of the maize plants, the angle and shape of the leaf play a vital role in the plant’s ability to efficiently catch the light and carry out high-performance photosynthesis.
For more, go to https://phys.org/news/2019-12-the-tips-of-a-plant.html
Access the full article at https://genome.cshlp.org/content/29/12/1962.full.pdf+html
4. Genomic Gymnastics Help Sorghum Plant Survive Drought
The sorghum crop is known to survive in scorching temperatures, growing in parched lands. Sorghum, a C4 cereal crop native to Africa and Australia, remains green and productive even under conditions that would render other plants brown, brittle, and barren. A new study published in the Proceedings of the National Academy of Sciences provides the first detailed look at how the plant exercises exquisite control over its genome. “Sorghum really is drought tolerant, and if we learn how it can be so drought-tolerant, then perhaps we can help some other plants survive in the same way,” said Peggy Lemauxat, University of California, co-author of the paper. A massive dataset, collected from 400 samples of sorghum plants grown during 17 weeks in open fields in California’s Central Valley, revealed that the plant modulates the expression of a total of 10,727 genes, or more than 40% of its genome, in response to drought stress.
The research was carried out on sorghum plants grown under three different watering conditions—pre-flowering drought, post-flowering drought, and controlled applications of water—over three consecutive years at the UC Kearney Agricultural Research and Extension Center in Parlier, California. A massive transcriptome data set was analyzed to pinpoint how gene expression changed as the plants grew and were subjected to drought or relief from drought conditions. First, it was found that a set of genes known to help the plant foster symbiotic relationships with a type of fungus that lives around its roots was switched off in drought conditions. Second, it was noticed that certain genes known to be involved with photosynthesis were also turned off in response to drought and turned up during drought recovery. Molecular differences were found in the 2 cultivars that help explain their differing tolerances to drought, providing evidence of a disruption in the plant’s symbiosis with arbuscular mycorrhizal fungi. These findings are of practical importance for agricultural breeding programmes, while the resulting data are a resource for the plant and microbial communities for studying the dynamics of drought response.
For more, go to https://news.berkeley.edu/2019/12/02/genomic-gymnastics-help-sorghum-plant-survive-drought/
And
https://www.pnas.org/content/116/52/27124.short
5. Sorghum Study Illuminates Relationship Between Humans, Crops, and the Environment in Domestication
Here is a picture of a purple-throated Carib feeding from and pollinating a flower, which has often been shown as an example of the co-evolution of this bird and plant species. A new study, at the Department of Agronomy, University of Iowa, examined the genetics behind the bitter taste of some sorghum plants and one of Africa’s most reviled bird species. It illustrates how human genetics, crops, and the environment influence one another in the process of plant domestication and co-evolution of three species. The study, published recently in Nature, looked at how human genetics and the presence of bird species with a taste for sorghum seeds might have influenced the traits farmers in Africa selected in their crops over thousands of years. The unique geographic distribution in Africa of sorghum plants that contain condensed tannins, or biomolecules that often induce a bitter taste, provided one side of a “Domestication triangle” that helped the researchers piece together the domestication puzzle, said Xianran Li, the corresponding author. Sorghum varieties with high levels of tannins commonly grow in eastern and southern Africa, while western African farmers tend to prefer varieties with low tannin content. Li called this unique interaction among sorghum tannin, human taste receptors, and herbivorous birds a unique triangle that offers distinct insight into crop domestication.
To arrive at their conclusions, the research team grew sorghum varieties with and without tannin and analyzed publicly available datasets on human genetics and wild bird populations in Africa to untangle how these factors interact with one another to influence the domestication of sorghum in Africa. The experiments involving sorghum grown in Iowa found sparrows would feed on the seeds of plants without tannin but left alone the cultivars that contained tannin, reinforcing the concept that herbivore threats to sorghum crops prefer non-tannin varieties. Authors conclude that their research uncovered coevolution among humans, plants, and environments linked by allelochemicals.
For more, go to https://www.sciencedaily.com/releases/2019/12/191211100300.htm
And https://www.nature.com/articles/s41477-019-0563-0
Potential Crops/Technologies
1. Sweet Potato can Warn Neighbours of Insect Attacks
Sweet potato plants don’t have spines or poisons to defend themselves. Breeders could potentially engineer the plants to produce the chemical needed as an all-natural pest defence. Plant ecologists, led by Axel Mithöfer of the Max Planck Institute for Chemical Ecology in Jena, Germany, have been looking into sweet potato defences after they noticed something interesting about two varieties of the plant grown in Taiwan: the yellow-skinned, yellow-fleshed Tainong 57 is generally herbivore-resistant, but its darker orange cousin, Tainong 66, is plagued by insect pests.
The compound (E)-4,8-dimethylnona-1,3,7-triene (DMNT) is not new; researchers have isolated the smelly chemical from other plants, such as corn and cabbage, and it is known to induce defence responses in some species. Sporamin is the main protein in sweet potato tubers; it is indigestible raw, which is why sweet potatoes must be cooked for humans to enjoy them. Theoretically, sweet potato breeders could use genetic engineering to make different varieties of sweet potato produce as much DMNT as Tainong 57, and display the same defence responses. These results indicate a potential to develop genetically engineered sweet potato plants that can defend themselves, as well as warn other sweet potato plants nearby.
For more, go to https://www.sciencemag.org/news/2019/12/sweet-potato-can-warn-neighbors-insect-attacks
2. Scientists Discover Potential Way to Manage Insects Without Chemicals
A new study, published in the Proceedings of the Royal Society B, reveals how insects use polarized light to differentiate which plants to eat or lay eggs on—by looking at how light reflects from their leaves. “To effectively manage insect crop pests, there is need to understand how they see the world and what drives their attraction to certain plants,” says Adam Blake, one of the co-authors of the paper. He thinks that with a better understanding, it may be possible to make crop plants less attractive to pests and reduce the need for pesticides.
Their findings suggest polarization may be more important than the brightness, colour, or shape of plants when insects are selecting plants to eat or lay eggs on. “The work has demonstrated that polarization from leaves is an important cue for insects to recognize plants,” says Gries, SFU biological sciences professor and NSERC-Industrial Research Chair in Multimodal Animal Communication Ecology. This study shows that there may be ways to alter the polarization signature of crop plants and make them less recognizable/obvious by insects to feed or lay eggs on, thereby reducing damage by insects without using harmful chemicals.
For more, go to https://www.tunisiesoir.com/science/scientists-discover-potential-way-to-manage-insects-without-chemicals-18374-2019/
And https://royalsocietypublishing.org/doi/full/10.1098/rspb.2019.2198
3. Protein Antibiotics Offer New Hope for Fighting Common Crop Diseases
An interdisciplinary team at the University of Glasgow have revealed a new method that could protect many important crop species against the common crop bacteria Pseudomonas syringae (Ps). Plant diseases are responsible for the loss of about 15% of world crops, of which a third is caused by bacteria such as Ps. The Ps species complex consists of over 50 known variants, which are responsible for diseases like blight, spot, and bacterial speck. Using genetic modification, the team were able to make plants express a targeted protein antibiotic, or bacteriocin.
These plants then successfully fought off the bacterial infection without any damage to the plants themselves or the surrounding environment. Currently, chemicals, conventional antibiotics, and resistance genes introduced by plant breeding are used to protect plants against these bacteria, but they have limited success and often have adverse environmental impacts. Hence, the expression of bacteriocins in crops might offer an effective strategy for managing the bacterial disease, in the same way that the genetic modification of crops to express insecticidal proteins has proven to be an extremely successful strategy for pest management. Crucially, nearly all genera of bacteria, including many plant pathogenic species, produce bacteriocins, providing an extensive source of these antimicrobial agents.
For more, go to https://phys.org/news/2019-12-protein-antibiotics-common-crop-diseases.html
And access the full article at
https://onlinelibrary.wiley.com/doi/full/10.1111/pbi.13294
4. Seaweed-Based Biostimulants to Enhance Productivity
One of the institutes of the Council of Scientific and Industrial Research (CSIR), India, the Central Salt & Marine Chemicals Research Institute (CSMCRI), Bhavnagar has developed pioneering technologies for both seaweed cultivation (upstream) and deriving value-added products from different seaweeds (downstream). Dr Arup Ghosh of CSMCRI has been working on the development of seaweed-based biostimulants that could help increase crop productivity in India by up to 37%. He and his colleagues have been working for the last 10 to 15 years on seaweeds, and they have developed technologies for seaweed cultivation for 3 to 4 species of seaweed, such as Brasileirao, Gracilaria edulis, Sargassum, and others. Kappaphycusalvarezii seaweed is cultivated from several macroalgae like Gracilaria and Kappaphycus at the plant in Bhavnagar in Gujarat state. The institute has a US patent for the process to obtain liquid seaweed fertilizers from red seaweed. However, India currently produces only 5% to 8% of the quantity of seaweeds needed; the rest is imported.
The seaweed stimulant has been tested on several crops. Presently, seaweeds have been used on more than 20 crops. Trials have been conducted on rice, maize, soybean, sesame, green gram, sugarcane, potato, tomato, and other vegetables. These trials have shown good results, with an 11 to 37% increase in productivity. Farmers who use seaweeds use 25% less fertilizers. Trials are going on at 43 agricultural universities and several sites of the Indian Council of Agricultural Research (ICAR). Further spread of the technology will depend on private players coming into the picture. Indian companies are welcome to partner with CSIR to take the technology to the end-users.
For more, go to
And access the presentation at
http://pmfaiicsce.org/wp-content/uploads/2019/11/icsce_2019_arup_ghosh.pdf
5. New Technique May Yield Gene-Edited Plants in a Few Weeks, Instead of 9 Months
A University of Minnesota research team recently developed new methods that will make it significantly faster to produce gene-edited plants. Although there have been dramatic advances in scientists’ ability to edit plant genomes using gene-editing tools such as CRISPR and TALENs, researchers were stuck using an antiquated and time-consuming approach—tissue culture. Dan Voytas, a professor in Genetics, Cell Biology and Development in the College of Biological Sciences and senior author of the published study, said the study presents a whole new way to solve the tissue culture bottleneck and can reduce the time needed to edit plant genes from as long as nine months to as short as a few weeks. The paper describes two methods to generate gene-edited dicotyledonous plants through de novo meristem induction, using plant growth regulators along with gene-editing reagents. The de novo induction of gene-edited meristems sidesteps the need for tissue culture and promises to overcome a bottleneck in plant gene editing.
For more, go to https://geneticliteracyproject.org/2019/12/18/new-technique-may-yield-gene-edited-plants-in-a-few-weeks-instead-of-9-months/
And https://www.nature.com/articles/s41587-019-0337-2
News
1. What is Biodiversity Net Gain?
The need to conserve biodiversity along with the imperatives of development has given rise to the concept of biodiversity net gain. In simple terms, biodiversity net gain (BNG) aims to ensure that with any new development, on-site biodiversity is first assessed and recorded and once the work is complete, the developer must prove that the recorded level of biodiversity has been enhanced by a minimum of 10%. Biodiversity loss is up there with climate change as an issue to concern us all. Economic models, such as Kate Raworth’s Doughnut Economics, recognize the loss of biodiversity as an economic disaster. If present indifference to biodiversity loss continues, she argues that it will undermine future economic development on a worldwide scale.
All stakeholders need to be engaged in the aims of BNG if it is to deliver real success. Get BNG right and there will be many beneficiaries; if not, it will be a huge failure. The developers and landscape professionals can be safe in the knowledge that they have done their bit for nature and society. Communities will have green space—and all the health and wellbeing benefits this brings. And wildlife will be thrown a lifeline in their increasingly fragile world. The BNG initiative, if undertaken in a positive way, will deliver the shift in mindset needed to see genuine improvements in biodiversity and wildlife to make nature the ‘new normal’ in the years to come, after many years of suppression.
For more, go to https://www.prolandscapermagazine.com/what-is-biodiversity-net-gain/
2. Taking Advantage of the Benefits of Plant Breeding
In 2018, the European Court of Justice gave a ruling that interpreted the definition of the term ‘genetically modified organism’ (GMO). Its blanket legal classification of a GMO did not distinguish whether the type of genetic modification present in the genome-edited organism could have occurred accidentally or through traditional breeding methods. Such a broad definition has put the European plant breeding community at a great disadvantage, making it difficult to pass on scientific innovations in crop improvement to needy farmers.
Consequently, the Union of the German Academies of Sciences and Humanities and the German Research Foundation (DFG) have released a public statement to raise awareness of the benefits to be derived from plant breeding. In their statement entitled “Towards a scientifically justified, differentiated regulation of genome-edited plants in the EU”, the science academies and the DFG stress that the blanket classification of genome-edited plants as genetically modified organisms (GMOs) is unjustified and impracticable. It follows from the ruling that all organisms produced by genome editing are subject to the legal framework applicable to release, placing on the market, labelling, and traceability of GMOs. In contrast to traditional breeding methods, genome editing methods enable directed, cost and time-saving modifications (mutations) of the genome of crops, which are often indistinguishable from naturally occurring mutations. The blanket legal classification as a GMO, therefore, fails to consider the type of genetic modification present in the genome-edited organism and whether this modification could have occurred accidentally or through traditional breeding methods. Assessment of risks should be based on the traits and not the processes through which the varieties were created, the statement said.
For more, go to https://www.eurekalert.org/pub_releases/2019-12/l-tao120419.php
Access the full report at
3. New Fee System for Access to Genetic Resources Discussed at FAO
Representatives of NordGen are in Rome to participate in the international cooperation for plant genetic resources. Delegates and observers from 146 countries have travelled to Rome, the headquarters of the Food and Agriculture Organization (FAO) to discuss different matters. NordGen is an observer in the Governing Body of the International Treaty for Plant Genetic Resources for Food and Agriculture (ITPGRFA). The system aims to raise more money that is to be reinvested in developing countries to ensure the sustainable use of their plant genetic resources. The Treaty has its secretariat at FAO, Rome and is working with three aims: (1) recognizing the enormous contribution of farmers to the diversity of crops that feed the world; (2) establishing a global system to provide farmers, plant breeders, and scientists with access to plant genetic materials; and (3) ensuring that the recipients share the benefits they derive from the use of these genetic materials with the countries where they originated.
In practice, this would translate into the distribution of 400 seed samples each year to researchers, plant breeders, and others needing the genetic resources in their profession by NORDGEN. One proposal under discussion is to charge for this service. If the members of The Treaty agree to change the existing Multilateral System, those needing the genetic resources would need to pay a prescribed sum (towards the cost of supply), which would then enable them to order seed samples from the world’s genebanks.
For more, go to
https://www.seedquest.com/news.php?type=news&id_article=112229&id_region=&id_category=
And https://www.nordgen.org/en/new-fee-system-for-access-to-genetic-resources-discussed-in-fao/
4. Toward Realizing a Biotechnology Dream: Nitrogen-Fixing Cereal Crops
Legumes can provide their own nitrogen needs through a symbiotic relationship with bacteria that are capable of fixing nitrogen from the air and putting it into the soil, which is then drawn up by the plants through their roots. Other crops, including major food crops such as corn, wheat, and rice, typically rely on added fertilizers for nitrogen, including manure, compost, and chemical fertilizers. If the genes enabling nitrogen fixation in legumes could be successfully transferred and expressed in cereal crops, chemical fertilizers would no longer be required to provide the nitrogen they need. The Voigt lab in the Department of Biological Engineering, led by Christopher Voigt, the Daniel I.C. Wang Professor of Advanced Biotechnology, at the Massachusetts Institute of Technology (MIT) is working on this challenge.
The microbes responsible for nitrogen fixation in legumes are bacteria (prokaryotes), and, as explained by Eszter Majer, a postdoctoral researcher in the Voigt lab who has been working on the project for the past two years, “the gene expression is completely different in plants which are eukaryotes.” For example, prokaryotes organize their genes into operons, a genetic organization system that does not exist in eukaryotes, such as the tobacco leaves the Voigt is using in its experiments. To successfully transfer the pathway’s nitrogen-fixing capabilities, researchers not only have to transfer the genes themselves but also replicate the cellular components responsible for controlling the pathway. If these genes were able to be successfully transferred and expressed in cereal crops, chemical fertilizers would no longer be required to add needed nitrogen, as these crops would be able to obtain nitrogen themselves. The strategy they have developed is to target the specific genes in the nitrogen-fixing bacteria that operate symbiotically with legumes, called the ‘nif’ genes.
For more, go to https://scienceblog.com/513424/making-real-a-biotechnology-dream-nitrogen-fixing-cereal-crops/
5. First ‘Lab in a Field’ Experiment Reveals a Sunnier Side of Climate Change
It is important to be able to understand the role of temperature at different crop-life stages as yield is highly weather-dependent in rapeseed, and climate change will likely have big consequences for the way we can use crops or their varieties. Pioneering experiments have used heated field plots to test the responses of crops to temperature, and they have revealed an unexpected plus side of climate change for farmers. The field trial experiment—the first of its kind—was set up to investigate the link between warmer Octobers in the United Kingdom and higher yields of rapeseed.
Professor Steve Penfield, John Innes Centre, UK and an author of the study, says they found rapeseed plants stop growing when they go through the floral transition at the end of October, and that warmer temperatures at this time of year enable the plant to grow for longer, giving more potential for higher yields. The good news for growers of rapeseed in the area is that Met Office data shows cold Octobers are now much less frequent than they were in the past. The study shows that vernalisation in rapeseed takes place predominantly during October when the mean temperature is between 10-12⁰ C. Temperature is critical for the rapeseed lifecycle because it determines at what point the plant goes through the transition from vegetative state to flowering, with delays in flowering being associated with higher yields. In this study, the team used soil surface warming cables to raise the temperature of field plots by 4-8⁰ C, simulating warmer October temperatures. While it was known earlier that warmer temperatures in October are correlated with higher rapeseed yields, the reason for this trend was unclear.
For more, go to https://phys.org/news/2019-12-lab-field-reveals-sunnier-side.html
Access full article at
Events
1. International Conference on Agricultural and Biological Science (ICABS)
13-14 April 2020, Hotel Le Dome, Brussels, Belgium
For more, see https://10times.com/icabsbrussels
2. 5th Global Food Security, Food Safety and Sustainability
04-05 May 2020, Vancouver, Canada
For more, see https://foodsecurity.conferenceseries.com/
3. 7th Annual Congress on Plant Science and Molecular Biology
18-19 May 2020, Auckland, New Zealand
For more, see https://world.plantscienceconferences.com/
4. 14th International Conference on Agriculture and Plant Science
22-23 June 2020, Sydney, Australia
For more, see https://agriculture.conferenceseries.com/
Other Topics of Interest
1. When science and snacks converge: Bright purple BFY potato chips emerge.
For more, go to https://www.bakeryandsnacks.com/Article/2019/12/05/When-science-and-snacks-converge-Bright-purple-BFY-potato-chips-emerge
2. Cross-bred Cosmic Crisp apples can stay fresh for a whole year
For more, go to https://newatlas.com/science/cross-bred-cosmic-crisp-apples-fresh-year/?utm_source=New+Atlas+Subscribers&utm_campaign=6632a79cd6-EM
3. CRISPR immunizes rice against multiple diseases, preserving crop yields and biodiversity
For more, go to
http://www.isaaa.org/kc/cropbiotechupdate/article/default.asp?ID=17895
4. Conferring leaf rust resistance in cereal crops
For more, go to https://phys.org/news/2019-12-conferring-leaf-rust-resistance-cereal.html or https://www.nature.com/articles/s41477-019-0545-2
5. Australia launches International Year of Plant Health
For more, go to https://www.graincentral.com/news/australia-launches-international-year-of-plant-health/
6. Using mobile technology to understand the impact potential of agricultural interventions
For more, go to https://phys.org/news/2019-12-mobile-technology-impact-potential-agricultural.html
Access the full article at https://science.sciencemag.org/content/366/6471/eaay3038
7. Plant-Based Meat Critics Say It’s Not As Healthy or Sustainable as Proponents Claim. Let’s Look at the Nutrition and Ecological Science