Newswise — Agricultural pest management has traditionally relied on chemical insecticides, but their overuse has led to environmental contamination, health risks, and rapidly evolving pesticide resistance. Meanwhile, natural variation in pest resistance exists within crops and their wild relatives, offering valuable resources for breeding. However, resistance traits are difficult to measure accurately, as they are often scored visually using coarse categories that fail to capture continuous variation. This limits the effectiveness of genome-wide association studies and genomic selection. Advances in deep learning provide new opportunities to extract detailed phenotypic information directly from images, overcoming subjectivity and labor constraints. Based on these challenges, there is a pressing need to conduct in-depth research on AI-enabled phenotyping and genomic breeding for pest resistance.

Researchers from the Chinese Academy of Agricultural Sciences and collaborating institutions report (DOI: 10.1093/hr/uhaf128) on 7 May 2025 in Horticulture Research that deep learning can substantially improve genomic selection for pest-resistant grapevine. The team developed convolutional neural networks to automatically assess insect damage on grape leaves and combined these data with genome resequencing, genome-wide association studies, and transcriptomic analyses. By linking AI-derived phenotypes with genetic markers, the study identifies key resistance genes and demonstrates highly accurate machine-learning-based prediction of pest resistance, offering a new framework for precision breeding.

The study analyzed 231 grapevine accessions subjected to natural infestations of the tobacco cutworm, a major leaf-feeding pest. Deep convolutional neural networks were trained to classify pest damage as mild or severe, achieving over 95% accuracy, while a custom regression model generated continuous damage scores strongly correlated with human assessments. These AI-derived phenotypes enabled more precise genetic analyses than traditional categorical scoring. Genome-wide association studies identified 69 quantitative trait loci and 139 candidate genes linked to pest resistance, many involved in jasmonic acid, salicylic acid, ethylene, and calcium-mediated signaling pathways. By integrating transcriptomic data, the researchers pinpointed key defense genes, including calcium-transporting ATPase ACA12 and the protein kinase CRK3, both strongly induced during herbivore attack. Machine-learning-based genomic selection models further demonstrated high predictive power, reaching 95.7% accuracy for binary traits and strong correlations for continuous traits. Together, these results show that combining deep learning phenotyping with genomics reveals subtle resistance mechanisms and enables reliable prediction of complex, polygenic pest-resistance traits.

“This work highlights how artificial intelligence can fundamentally change plant breeding,” said the study’s senior authors. “By replacing subjective visual scoring with fast, objective deep-learning-based phenotyping, we can capture continuous variation in pest damage that was previously overlooked. When these high-quality phenotypes are integrated with genomics and transcriptomics, they reveal the true polygenic architecture of pest resistance. This approach not only improves prediction accuracy, but also allows breeders to make informed selections much earlier in the breeding cycle.”

The findings have broad implications for sustainable agriculture and crop improvement. AI-driven phenomics enables rapid, large-scale assessment of pest resistance without increasing labor costs, making it suitable for breeding programs worldwide. By identifying resistance genes and accurately predicting pest tolerance, breeders can reduce reliance on chemical pesticides while improving crop resilience. The framework established in grapevine can be readily adapted to other crops and stress traits, supporting the development of automated, data-driven breeding platforms. Ultimately, integrating deep learning, genomics, and machine learning could accelerate the creation of pest-resistant varieties essential for food security under increasing environmental pressure.

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References

DOI

10.1093/hr/uhaf128

Original Source URL

https://doi.org/10.1093/hr/uhaf128

Funding information

This work was supported by the National Key Research and Development Program of China (No. 2023YFD2200702), the project of National Key Laboratory for Tropical Crop Breeding (No. NKLTCB202325), the National Natural Science Foundation of China (No. 32372662), and the Science Fund Program for Distinguished Young Scholars of the National Natural Science Foundation of China (Overseas) to Yongfeng Zhou.

About Horticulture Research

Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.

An organization that represents pea, lentil and bean growers in Saskatchewan says it supports a new federal investment intended to spur diversification among its trading partners.

Canada’s agriculture minister announced Tuesday a $75-million investment over five years to expand export activities into new, non-traditional markets and support sectors most affected by trade barriers.

“This added investment will help our sector access new markets, strengthen interprovincial trade and build more resilience in the face of global challenges,” said Heath MacDonald, minister of agriculture and agri-food, at an unrelated policy breakfast in Ottawa.

The program builds on the existing AgriMarketing Program and adds funding for two new streams: national industry associations and small and medium-sized enterprises.

Organizations can apply for funding to expand export activities, with priority given to sectors most impacted by trade barriers, such as pulses and canola, according to a news release from Agriculture and Agri-Food Canada.

“There are opportunities all over the world, but we can’t spread ourselves too thin. We have to target our markets and go after them,” said MacDonald.

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The federal government’s investment is being well-received by the national industry association representing pulse growers.

“Any investment in helping us diversify and helping us find new avenues, new uses, new ways to put more pulses on more plates around the world is something that we support,” said Jeff English, vice-president of public affairs at Pulse Canada.

In January, Canada struck a trade deal with China to remove the 100 per cent tariffs on Canadian yellow peas, effective March 1 through the end of the year.

China imposed this tariff in March 2025 in response to Canada’s previously imposed 100 per cent tariff on Chinese electric vehicles and a 25 per cent import tax on steel and aluminum.

But India’s 30 per cent tariff on Canadian yellow peas remains in place, something local pulse producer associations say is a reason the industry needs to diversify its trading partners.

“The more diversified we are, the less of an impact that will be, and we’ll have stronger prices for farmers at the end of the day,” said Carl Potts, executive director of Saskatchewan Pulse Growers.

Potts said his association is exploring strategies to tap into other markets worldwide, including the Indo-Pacific and Latin America regions.

Alongside diversifying its trading partners, the organization is also focused on increasing demand for other products in new markets, such as pet food and animal feed. This, according to Potts, was a strategy that helped bolster pea imports into China 20 years ago.

“At the time, they might have been importing maybe 200,000 tonnes a year, but we worked with local industry and consultants in the market to help develop more demand for peas,” said Potts.

“We’ve grown that into a market of over two million tonnes in some areas.”

Alongside finding new markets, the pulse grower associations say they are also continuing to advocate for strengthened relations with current trading partners and look forward to new opportunities to do so — from CUSMA renegotiations to a potential India trip by Prime Minister Mark Carney.

“As the government does its job in terms of building a stronger relationship with India, we’re doing things in lockstep as well,” said English.

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While farming is a huge factor in Saskatchewan’s economy, it’s not easy to get into the industry.

An agricultural conference at the Western Development Museum, hosted by Sask Young Ag on February 5th, hopes to bridge the gap between young and experienced farmers through conversation and advice.

“There’s such a big room of knowledge that you may not understand or see. You come here, you take even one thing home, one word home, and that could change a lot of things for you,” says Wyatt Gorrill, a grain farmer and Sask Young Ag board member.

For young people, the insight is very valuable.

“Teaching us the reins and getting those fresh ideas in as early as possible is very important,” says Claire Nagel, a future farmer who is representing Hunters Paradise Farming and Outfitting at the conference.

Sask Young Ag board members say there is a lack of young people going into the industry for a variety of reasons.

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“Toughest thing would be the amount of money it takes to get into it. If you start with nothing, it’s nearly impossible to get somewhere,” says Gorrill.

Many young farmers are generational, learning and inheriting skills from family before them.

“The critical issues that they run into is maybe knowing where to start. If they haven’t had, if their family hasn’t had to experience a transition before,” said Morgan Lehmann, a young producer and master’s student.

The current global market is also presenting new challenges for young farmers, says Nagel.

“The land prices, the grain prices right now are not great, especially with the tariffs with the U.S. and China… I would say that’s a huge challenge. Another challenge is succession planning.”

Both current and upcoming farmers say they would like to see more support, like Grant, who hopes for changes to the crop insurance structure.

“Their crop insurance and their other insurance and stuff and looking into new ways to help out farmers in that way because in the dry areas of the province there definitely is becoming a problem where they haven’t gotten a crop for quite a few years,” Grant said.

Despite the challenges, young farmers say they are excited about the future.

“I think that within the farming industry you have so many different opportunities,” said Nagel, with Lehmann adding, “We support feeding the world and I think that it’s a really honourable thing to care for the land.”

Watch above for more on challenges young producers are facing.