Weekly Update from the Texas Seed Trade Association

Member News


AI breakthrough set to advance sorghum breeding efforts - A new industry partnership will harness cutting-edge AI technology to improve sorghum breeding for the benefit of Australian growers.


Fellow Centre for Animal Science researcher Dr Eric Dinglasan has been announced as the winner of an Advance Queensland Industry Research Early-Career Fellowship. In partnership with the University of Queensland (UQ) and Pacific Seeds, Dr Dinglasan will expand his work in predictive agriculture to apply FastStack technology to sorghum breeding efforts. FastStack is an AI-guided breeding technology, where instead of selecting the best individual, scientists choose the best chromosome segments that are good for a trait, then identify the optimal crossing path to combine them with other chromosome segments across the genome to develop the ultimate stack.


Dr Bertus Jacobs, Pacific Seeds, Head of Research said the project would focus on heat tolerance traits for sorghum as part of wider research to ensure new hybrids meet changing climatic conditions over the next 20 years and beyond.


“By combining on-ground farm experience, world-class research, and new AI technologies, we’re set to deliver the best possible new hybrids that not only adapt but thrive in the changing climate conditions,” Dr Jacobs said.


Dr Dinglasan said that together with industry partners, we want to develop an AI breeding scheme to tackle the main issues facing Queensland crop growers like enhancing grain quality and resilience to severe heat stress.


“Incorporating new breeding interventions with chromosome stacking we can ensure that genetic gains don’t plateau but boost both immediate and long-term gain in the face of climate change,” said Dr Dinglasan.


“I’m really grateful for this opportunity to work with industry partners and directly with breeders to see our work translated into the real world and I’m very excited to be applying all these technologies.”


Within three years the project is expected to see hybrids with improved heat tolerance and quality traits flow into the respective Pacific Seeds breeding pipelines. The AI technology will be translatable to other traits and crops across the Pacific Seeds portfolio.


Learn more:

AI deciphers new gene regulatory code in plants and makes accurate predictions for newly sequenced genomes

Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)


Elucidating the relationship between the sequences of non-coding regulatory elements and their target genes is key to understanding gene regulation and its variation between plant species and ecotypes. Now, an international research team led by IPK Leibniz Institute and with the participation of Forschungszentrum Jülich developed deep learning models that link gene sequence data with mRNA copy number for several plant species and predicted the regulatory effect of gene sequence variation. The results were published in the journal “Nature Communications”.


Genome sequencing technology provides thousands of new plant genomes annually. In

agriculture, researchers merge this genomic information with observational data

(measuring various plant traits) to identify correlations between genetic variants and crop

traits like seed count, resistance to fungal infections, fruit color, or flavor. However, the

grasp of how genetic variation influences gene activity at the molecular level is quite

limited. This gap in knowledge hinders the breeding of "smart crops" with enhanced quality and reduced negative environmental impact achieved by combination of specific gene variants of known function.


Researchers from the IPK Leibniz Institute and Forschungszentrum Jülich (FZ) have made a significant breakthrough to tackle this challenge. Led by Dr. Jedrzej Jakub Szymanski, the international research team trained interpretable deep learning models, a subset of AI algorithms, on a vast dataset of genomic information from various plant species. “These models not only were able to accurately predict gene activity from sequences but also pinpoint which sequence parts contribute to these predictions”, explains the head of IPK’s research group “Network Analysis and Modelling”. The AI technology which the researchers applied is akin to that used in computer vision, which involves recognizing facial features in images and inferring emotions.


In contrast to previous approaches based on statistical enrichment, here the researchers

combined identification of sequence features with determination of the mRNA copy

number in the frame of a mathematical model that has been trained accounting for

biological information on gene model structure and sequence homology, thus gene

evolution.


"We were truly amazed by the effectiveness. Within a few days of training, we rediscovered many known regulatory sequences and found that about 50% of the features identified were entirely new. These models excellently generalized across plant species they were not trained on, making them valuable for analyzing newly sequenced genomes”, says Dr. Jedrzej Jakub Szymanski. “And we specifically demonstrated their application in diverse tomato cultivars with long-read sequencing data. We pinpointed specific regulatory sequence variations that explained observed differences in gene activity and, consequently, variations in shape, color, and robustness. This is a remarkable improvement over classically used statistical associations of single nucleotide polymorphisms.”


The team has openly shared their models and provided a web interface for their use.

"Interestingly, much effort went into degrading our model's performance. To avoid overly

optimistic results due to AI finding shortcuts required from me a deep dive into gene

regulation biology to eliminate any potential bias, reduce data leakage and overfitting”, says Fritz Forbang Peleke, the lead machine learning researcher and first author of the study, which was published in the journal “Nature Communications”.


Dr. Simon Zumkeller, a co-author and evolutionary biologist from FZ Jülich, remarked, “With the presented analyses we can investigate and compare gene regulation in plants and infer its evolution. For practical applications, the method provides a new foundation, too. We are approaching the routine identification of gene regulatory elements in known and newly sequenced plant genomes, in various tissues, and under different environmental conditions."


Peleke et al. (2024): Deep learning the cis-regulatory code for gene expression in selected model plants. Nature Communications. DOI: 10.1038/s41467-024-47744-0

FARM JOURNAL'S AG ECONOMISTS' MONITOR REPORTS FURTHER CONSOLIDATION A CONCERN

By Tyne Morgan, AgWeb.com

Farmers across the U.S. push forward to plant, and there's an immense amount of pressure riding on this year's crop production picture. With a margin squeeze setting in across farms, economists think it could accelerate consolidation in the row-crop industry.


The April Ag Economists' Monthly Monitor, a joint survey of 70 ag economists conducted by the University of Missouri and Farm Journal, shows economists views on the ag economy didn't deteriorate from March to April. Their view on the current ag economy, when compared to 12 months ago, continues to show growing concerns.


"Everybody's just continuing to wait and watch input prices stay high, costs stay high for producers, and for crops in particular, crop prices tending to move lower," says Scott Brown, interim director, Rural and Farm Finance Policy Analysis Center (RaFF), University of Missouri. "Everybody's waiting to see what weather is like this summer and what kind of crop we put in the bin."


Brown helps author the Ag Economists' Monthly Monitor. This month's monitor shows economists expect net farm income to fall to $117.82 billion this year, which is steady with both the March and February survey results. It's also in line with USDA's current 2024 net farm income projection of $116 billion. However, when you consider net farm income reached $155 billion in 2023, both USDA and economists are saying they expect net farm income to drop close to 25% this year.

According to data analyzed by the University of Missouri, the change in Net Cash Farm Income is a strong metric to use when looking at the eroding ag economic picture. The change expressed in real 2024 dollars. It shows the 2023/24 change of $42,220,837,000 is second only to the 2022/23 change of $50,206,673,000 and means the largest and second-largest drops in Net Cash Farm Income have happened the past two years.


"I think the biggest one of the biggest concerns by far is this margin squeeze," says Michael Langemeier, associate director, Center For Commercial Agriculture and Professor, Purdue University. "When you really start looking at '24 budgets, I think the word I would use is 'ugly.' It looks as bad as 2019, maybe even slightly worse."


Langemeier is not only one of 70 ag economists surveyed for the Monthly Monitor, he also helps author Purdue University's Ag Economy Barometer each month, a survey of nearly 400 producers across the U.S.


"Looking through February, the Ag Economy Barometer has been relatively flat for about the last six months," he says. "And that's a little bit intriguing, because the prices did tumble a bit a couple months ago, and so that that hasn't been reflected yet in the sentiment. But when you look at the biggest concerns, they're still focusing on high input costs and low crop prices and high interest rates."


Concerns About Consolidation in Ag


The April Ag Economists' Monthly Monitor also asked a question about the risk of consolidation in the row crop side of ag. Economists were asked if the current environment of declining commodity prices and high input costs could accelerate consolidation in row-crop operations and allied industries. Nearly 80% of economists who responded answered yes.


"Maybe as strong of a responses as it was, it did surprise me," Brown says. "In general, when you think about it, we're headed to what's likely a period of tighter margins. I think the economists were saying this is going to make this competition to get bigger to try to offset some of the tighter margins work in their operations."


Economists said geographies at the greatest risk of consolidation are areas that rely heavily on wheat and cotton production or where drought continues to be an issue, including the Great Plains and the southeast Cotton Belt. Economists also point out areas of the Corn Belt that have marginal soils and production could also see consolidation. Economists also pointed out the size of an operation will be a factor.


To read the entire report click here.

News Bits


The U.S. corn and soybean planting paces remain ahead of average. That was despite heavy rainfall and severe storms in parts of the Midwest and Plains late last week and early this week, with more rain in the forecast for parts of the region midweek, but that increased soil moisture should be beneficial for early development.


The USDA says 27% of U.S. corn is planted, compared to the five-year average of 22%, with 7% of the crop emerged, compared to 4% on average.


18% of soybeans are planted nationally, compared to 10% normally in late April.


49% of winter wheat is in good to excellent condition, 1% less than last week, but 21% more than this time last year, and 30% of the crop has headed, compared to 21% on average.


34% of spring wheat has been planted, compared to the typical rate of 19%, and 5% has emerged, matching the average.


15% of cotton is planted, compared to the usual pace of 10%.


72% of rice is planted and 48% has emerged, both well ahead of their respective five-year averages.


19% of sorghum is planted, compared to 20% on average.


Average national soil moisture levels improved across the U.S. last week.


The USDA's weekly crop progress and condition reports run through the end of November.


An economic analysis of the 2023 corn crop shows it wasn't budget friendly for farmers.


Brad Zwilling, vice president of data analysis with Illinois Farm Business Farm Management (FBFM), tells Brownfield,

"When we look at costs to produce corn in 2023, when we compare it to '22, they were higher in all areas of the state." He says, "Even though we even had higher yields, we had greater fertility costs, seed costs, machinery depreciation and then also we had higher non-land costs and then also our land cost went up as well."


He says that all added up to the most expensive corn crop planted.


"The highest on record for corn, second highest was in 2012." He says, "We had the drought, so we had lower yields. So, we look at it on a per bushel basis and also costs were increasing in 2012."


Zwilling says some of those costs, such as fertility, are projected to decline this year.


"That's good news, right?" He says, "But we know that operating interests are still continuing to be going up. Land costs are going to continue to go up a little bit. So, when you compile that with these lower projected grain prices, that means we're probably going to be looking at lower returns for 2024 versus what '23 was."

U.S. biotech leadership is rooted in strong IP protection

Bio.news By Tom Popper


For evidence of the link between biotech innovation and intellectual property protections, look no further than the United States.

The world leader in biotech, the U.S. is also listed as the leader in IP protection in the U.S. Chamber’s 2024 International IP Index. That’s probably why some competitors seek to limit global IP protections.


“We often hear calls in the international arena to weaken safeguards for IP, supposedly to help lower-income countries access medicine,” says Hans Sauer, Vice President for Intellectual Property at the Biotechnology Innovation Organization (BIO). “In truth, stronger IP protection encourages drug research and enables patent holders to share medical breakthroughs worldwide.”


Given the importance of IP to the biotech industry, BIO prioritizes work to strengthen and update patent systems in the U.S. and abroad. Legislation can sharpen legal clarity on patents, and sensible IP approaches enable us to use new technologies such as artificial intelligence tools that increase competitiveness.


Every year, World IP Day is held on April 26, and this year it features a focus on how IP can help us achieve the UN Sustainable Development Goals (SDGs). The day underscores why BIO works year-round to ensure IP is protected.


Biotech advances in agriculture play a major role in meeting the 17 goals set out in the U.N. SDGs by reducing our climate impact while increasing food security.


Since the Plant Patent Act of 1930, breeders who develop new plants have the right to patent them. In 1980, the U.S. Supreme Court made it clear genetic alterations could be patented when it upheld a claim that has been called the first patenting of a living thing—a microbe genetically modified to consume oil spills.


“Gene editing breakthroughs are a game changer, allowing production of more nutritious, drought-resistant crops, and other developments to make agriculture more sustainable and resilient,” says David Lachmann, BIO’s Senior Director of Federal Government Relations. “The ability to patent gene editing means investors can support R&D, driving remarkable growth in this area.”


Sustainable aviation fuels, produced with biotech, offer the fastest way to reduce the carbon output of commercial air travel. And synbio uses biotech innovations, like Ginkgo Biowork’s process of fermentation with gene-edited yeast, to create more sustainable versions of a wide variety of consumer goods.

Room for improvement in U.S. patent systems

Supreme Court decisions have undermined confidence in whether innovations can survive patent challenges. Legislation is needed to provide legal clarity that enables innovation by ensuring returns on R&D investment.

The bipartisan Patent Eligibility Restoration Act (PERA) would increase patent-eligible innovations by specifying the few patent-ineligible categories—like ideas based on a mental process that can be done in the human mind or a gene already existing in the human body.


“It is critical that the future path of our patent system is one that preserves and maintains the incentives for innovation that have made the United States the global leader in medical, agricultural, industrial, and environmental biotechnology,”  BIO VP Sauer says of the legislation.


AI is another area where BIO is seeking to maintain straightforward, enforceable patents.

“Current patent law clearly gives IP to a human being with a new idea,” according to Lachmann. “AI is an important tool for innovation, but it is only a tool. The person who used and operated the AI is the one who conceived of the resulting innovation and is therefore listed as the inventor on the patent.”


Despite the clarity in existing laws, guidance issued in February by the U.S. Patent and Trademark Office (USPTO) suggests the possibility of treating inventions developed with AI differently from inventions developed by other means.

“Our patent law should support, not hinder, the responsible use of AI to achieve transformative results for the economy and human health,” writes Claire Laporte, Ginkgo Fellow and former Head of Intellectual Property at BIO member Ginkgo Bioworks in April 10 testimony for Congress. “Subjecting patent applications to new analytical and disclosure requirements depending on which tools were used in making the invention can only hurt our global competitiveness.”

Threats from abroad

The ability for U.S. biotech to expand is limited by IP insecurity abroad, such as the above-mentioned TRIPS waiver for COVID-19 vaccine IP.


“If IP receives global protection, technology can move freely around the world, driving further innovations and enabling universal patient access to medicines,” says Travis. “Unfortunately, the uneven level of IP protections in different countries makes it harder to share innovation.”


BIO’s latest submission to the U.S. Trade Representative’s Special 301 Report, a summary of concerning IP practices abroad, calls out several threats:


  •  Compulsory licenses: some governments can grant compulsory licenses (CLs) that take IP rights from a patent owner and give it to a third party.
  • Technology localization measures: Similar to CLs, these force patent holders seeking to export their technology to localize R&D or manufacturing or force transfer of their IP to a local party.
  • Regulatory data protection: Biotechnology innovators must submit comprehensive information to a country’s regulatory authorities for marketing approval. Inadequate protection allows this sensitive information to be disclosed or exploited for commercial use.
  • Patent acquisition obstacles: These can include prohibiting patents on certain types of inventions; patent office backlog; challenges to submitting patent applications; new disclosure obligations for patents; and difficulties with patent adjustments.
  • Patent enforcement challenges: These include a lack of efficient, early resolution mechanisms for patent disputes, the ability for a party to use a patent that is under dispute, and other legal obstacles.

Celebrating IP on Capitol Hill on May 1

Federal recognition of the importance of IP will include a May 1 gathering on Capitol Hill, with discussions from Kathi Vidal, Director of the U.S. Patent and Trademark Office, Rep. Darrell Issa (R-CA), Chair of the House Judiciary Subcommittee on Courts, Intellectual Property, and the Internet, and other officials.


The theme of this event, which will also be live-streamed, is the contribution of IP to the UN SDGs. Find out more and register here.


“BIO looks forward to fruitful discussion about ongoing efforts by our government on IP protection, and areas where new initiatives are needed,” says Pine. “U.S. vigilance in the face of international threats to IP, and continued efforts to strengthen our patent system, require concerted policy as well as public-private collaboration.”


Editor's Note: What we've learned, from a practical perspective, is that enforcement of PVP and plant patents for open-pollinated crops can be fraught with difficulty. This is particularly true when regulatory agencies provide no help despite the retail of virtually all VNS seed being sourced from non-licensed seed sellers. The IP system is not bad but exploiting the loopholes is common and enforcement of existing seed law is highly selective.

Five steps to a gene edited plant

The New Zealand Institute for Plant and Food Research Limited


Gene editing is a new genetic technology where an organism’s DNA can be modified at an exact point in its genetic code. As well as offering the ability to make precise genetic changes, the technique also does not necessarily involve the addition of DNA from another organism.


The most commonly used gene editing technology is the CRISPR-Cas system, a natural bacterial process that has been adapted for use as a genome editing tool in other organisms.


Emmanuelle Charpentier and Jennifer Doudna, the scientists who developed the method, were awarded the Nobel Prize in Chemistry in 2020 for this discovery. Over the past decade, scientists around the world have been learning how to use the technique and fine-tune it in their organism of choice.


Gene editing is currently classified as genetic modification in New Zealand, but many countries are passing new regulations specifically for gene edited crops. Scientists around the world are now finding answers to the five questions that need to be addressed in creating a gene edited plant for commercial use.


1. What trait do we want to change?

Scientists interested in altering a trait in a plant look at many different varieties of that plant to see what natural variation exists. Plant breeders maintain large germplasm collections — libraries of individuals representing the variety of genetic differences found in nature — to ensure access to the full diversity of the species.


If a trait, like blue flowers or star-shaped fruit, exists in a species naturally, you’re likely to be able to create it through gene editing, potentially much faster than if you used a traditional breeding approach. Gene editing allows scientists to make very simple changes to the existing DNA sequence of an organism to create a new version of an existing gene. This may result in a very different version of the trait to that of the original individual, but mirrors a change that could occur through natural mutation. The main advantage is the ability to bring one specific trait into an otherwise elite plant without many rounds of traditional breeding to remove unwanted changes.


Disease resistance in plants is sometimes conferred by a particular version of a single gene. The resistant version may exist in the wild relative but was not needed when breeding the cultivated crop, perhaps because of a lack of disease pressure in the growing region. A cross with the wild relative would introduce the resistant gene into some of the offspring, but would also mix in many thousands of unknown and unwanted versions of genes as well. It might take six or more rounds of breeding to get an elite cultivar back again. In perennial fruit crops, each round of breeding might take five or more years, making this a very slow process. With gene editing, this could be reduced to a single round by changing the gene from the susceptible to the resistant version directly in the elite cultivar.

2. Do we know the gene(s) for that trait?

To be able to use gene editing to alter a trait, you need to know a great deal about how it is controlled at the genetic level. Some traits are controlled by a single gene, others by a network of genes and by influences from the environment.


For example, human height is controlled by a combination of more than 700 genes, with some influence from environmental factors like nutrition.

Gene editing involves programming the CRISPR-Cas system to seek out and make a change to a specific gene that controls the trait of interest.


That means scientists need to have a deep understanding of the trait, the gene they wish to edit, its DNA sequence, how it is controlled and how it interacts with other genes in the plant. Only with all this information can scientists programme the CRISPR-Cas to target a specific DNA sequence within the gene and, with any certainty, alter only that gene and the associated trait.

3. Is there freedom to operate?

Scientific organisations have been patenting genes and DNA sequences since the 1970s, although some countries, like the USA, have changed their rules for gene patenting in recent years. Holding the patent on a gene means that no one else can work with it to create a commercial product without your permission for around 20 years (depending on the rules of the country where it’s been patented).


Therefore scientists may be limited to working with genes that they or their organisation have already patented, that haven’t been patented by anyone yet, that are already in the public domain, or where they can obtain permission from the patent holder.


There are also limitations on using CRISPR-Cas because of its ownership. Scientists can use the CRISPR-Cas technology for research purposes if they have a research licence, but their results can’t be commercialised without an additional, often costly, commercial licence. The terms of these agreements are negotiated with the patent holders, who can decide who to issue licences to, for what purposes, in which regions, and at what cost.

4. Do we know how to edit the plant?

Most of the time, scientists need every cell of the adult plant to contain the edited version of the gene to cause the desired trait change. This involves taking a single cell from an elite donor plant; getting the CRISPR-Cas machinery into that cell so it can edit the DNA sequence; growing the single edited cell up into a full plant; and checking the plant has the required edit and that no other unwanted changes have occurred during the process.


Plant cells are harder to edit than animal cells. Because of the structure of plant cells, the CRISPR-Cas machinery currently has to be introduced into the cell via genetic modification: scientists are looking for a way around this gene-modification step, as it usually leaves DNA from the CRISPR-Cas machinery in the plant cell.


Creating a whole plant from a single cell is also a challenge. A plant cell can be grown into a full plant using tissue culture, but there isn’t a one-size-fits-all process. Different plants, and in some species different varieties, require different tissue culture regimes, and it may take many years of experimentation to find one that works.

5. Does the edited plant perform well?

Even with all the information available to them, scientists can’t guarantee that a plant taken out of the lab will perform well in the field or orchard. Plants are very sensitive to their environment and changing one gene — whether through natural mutation or through gene editing — can have an impact on how a plant behaves in a production setting.


If a gene-edited plant were to be selected as a potential commercial variety, it would then need to enter the pipeline of growing trials used for all new varieties to ensure it had all the characteristics required for commercial success.

The need for regulation & stewardship

Genetic technologies offer benefits for food production, particularly in allowing scientists to deliver at a faster rate the new varieties that address some of the agrifood sector’s most pressing issues, such as climate change adaptation and resistance to new pests and diseases. However, there is still a requirement for ensuring the technologies are used appropriately, and that the varieties offer the same, or better, outcomes for consumers and producers.


Across the world, regulations are changing and it’s important that altered regulations support both scientific advancement and consumer safety. Regulation based on the outcome of breeding programmes, regardless of the technologies used, is likely to offer both. However, there are also social, cultural and economic factors to be considered in introducing any new technology. It is important that all aspects of the debate are considered, to ensure that the deployment of gene technologies in a commercial setting delivers positive impacts for society.

Factoids


On February 14, 2024, EPA issued its Existing Stocks Order for Dicamba Products Previously Registered for Over-the-Top Use on Dicamba-Tolerant Cotton and Soybean.


EPA issued the existing stocks order following the February 6, 2024, order and judgement by the District of Arizona vacating the registrations for three products, XtendiMax with VaporGrip Technology ("XtendiMax") from Bayer, Engenia Herbicide ("Engenia") from BASF, and A21472 Plus VaporGrip Technology (Tavium Plus VaporGrip Technology) ("Tavium") from Syngenta.


As of February 6, 2024, these products are no longer registered, and it is unlawful under the Federal Insecticide, Fungicide, and Rodenticide Act (FIFRA) to sell or distribute them except to the extent otherwise authorized by EPA.


February 6, 2024 - No sale or distribution by registrants after February 6, 2024.


May 13, 2024 - Last day for sale or distribution by co-ops, commercial distributors, or others who are already in possession. These entities may sell or distribute these products until May 13, 2024 in the state of Iowa.


June 12, 2024 - End date for use of existing stocks is June 12, 2024. Application of existing stocks is permitted until June 12, 2024 or V4 growth stage (soybean) whichever comes first.


The above information is a summary reference to highlight important dates for the state of Iowa. End dates assume entity assumed possession of the dicamba products prior to February 6, 2024.


To read the full EPA existing stocks order for all details that may apply to your specific situation click here.


Ukraine's agriculture minister has resigned following a Ukrainian law enforcement agency's investigation that links him to a scheme to "misappropriate 2,500 hectares of state-owned land" and "attempt to seize another 3,300 hectares."


Mykola Solskyi said in a post on Telegram (translated by Agri-Pulse using Google Translate) that he wrote a resignation letter to Ukraine's parliament. If the parliament decides to accept his resignation, he said "I will be grateful for such a decision." If not, he said he "will continue to work."


The law enforcement agency, the National Corruption Bureau of Ukraine, said in a press release that the scheme involved destroying documents "that granted the state enterprises the right to permanent land use." The land plots were not auctioned, but instead "transferred into private ownership to pre-designated individuals under the guise of realizing their right to free land."


While the National Anti-Corruption Bureau did not specifically name Solskyi in their release, he confirmed in another Telegram post that it referred to him.


Editor's Note: We are as sympathetic as anyone to Ukraine's plight but have often wondered how much of the billions of dollars sent by the current administration might be diverted to private bank accounts. Ukraine was part of the Soviet Union long enough to learn some bad habits apparently.


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