With the continuous growth of the global population and the intensification of environmental changes, agriculture is facing multiple challenges such as increasing yield, improving quality, and enhancing resilience. Traditional breeding methods are gradually showing limitations in dealing with these challenges, and the rise of Pan-Genome research has brought new opportunities for agricultural development. Pan-Genome can fully reveal the genetic diversity of species, and provide broader genetic resources and a deeper theoretical basis for crop improvement and agricultural sustainable development.
This paper discusses the various applications of pan-genome in agriculture, and involves the protection of agricultural biodiversity, ecological research and precision agriculture, provides a new path for the sustainable development of agriculture.
Crop-Breeding Based on Pan-Genome
Pan-genome, as a whole genome collection of species, is opening up a new situation for crop breeding and becoming a key technical path to break through the bottleneck of breeding by revealing genetic diversity in a panoramic way.
Excavate Excellent Gene Resources
Pan-genome research can find a large number of genes missing in the reference genome by sequencing several representative individuals and constructing the pan-genome map of species. These genes may contain excellent alleles related to important agronomic traits such as yield, quality, and stress resistance.
Rice is the staple food of more than half of the world's population, and its yield and quality are directly related to food security. In the study of the rice pan-genome, scientists sequenced hundreds of rice germplasm resources with different agronomic traits from different ecological regions and found many disease-resistant genes that did not exist in the traditional reference genome.
Impact of pan-genome representation on dissection of quantitative variation and applications to crop improvement (Della et al., 2021)
Accelerate the Development of Molecular Markers
Molecular marker-assisted breeding is an important means to improve breeding efficiency. Pan-genome analysis can identify a large number of genetic variations such as single nucleotide polymorphism (SNP) and insertion-deletion (InDel), which provides rich materials for developing high-density molecular markers. These molecular markers can be used for gene location, population genetic structure analysis, and molecular marker-assisted selection, thus accelerating the breeding process of excellent varieties.
In practical application, pan-genome analysis breaks through the limitation of traditional single reference genome by integrating the genome information of multiple varieties and can find rare genetic variation sites. Taking maize as an example, molecular markers based on pan-genome development have been successfully applied to the mapping and breeding practice of drought-tolerant genes in maize. By sequencing 26 maize inbred lines in the world, the researchers constructed a pan-genome map containing 32,000 structural variations, and accurately located several key gene sites related to drought tolerance, such as ZmNAC111. Based on these molecular markers, breeders quickly introduced drought-tolerant genes into high-yield but drought-tolerant maize varieties by backcrossing and breeding, and the yield of the cultivated new varieties increased by 15%-20% under drought conditions, effectively alleviating the pressure of maize production in arid areas.
Promote Genome-Wide Selection Breeding
Genome-wide selection breeding predicts individual breeding value by using genome-wide molecular markers, realizes early selection, and improves breeding efficiency. The traditional reference genome has a gene coverage gap due to the singleness of samples, while the pan-genome integrates the genome information of several representative varieties, which breaks through the limitations of a single genome and injects more abundant genetic variation data into the whole genome selection model.
In the improvement of rice quality, the selection strategy based on pan-genome successfully captured rare alleles controlling amylose content, which significantly optimized the eating quality of rice. In addition, for complex quantitative traits controlled by multiple gene loci, such as stress resistance, the polymorphism data of pan-genome can more accurately analyze the regulation mechanism of gene networks and provide more reliable genetic markers for directional breeding. These research results show that genome-wide selection based on pan-genome has obvious advantages in improving crop yield, quality, and other traits, especially in the breeding of complex quantitative traits.
Predicted benefits to plant breeding from future developments in pan-genomics (Tay Fernandez et al., 2022)
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Crop Genetic Improvement in Plant
Faced with climate change and resource constraints, crop genetic improvement needs a more accurate and efficient path. Pan-genome integrates the whole genome variation of species, breaks through the limitation of a traditional single genome, and provides a new possibility for directional improvement of crop quality, stress resistance, and yield with its systematic analysis of gene diversity, which is reshaping the technical paradigm of crop genetic improvement.
Quality Improvement
Crop quality is one of the important goals of agricultural production, covering many dimensions such as nutritional composition, taste, and color, which directly affect the market value of agricultural products and consumers' health. Pan-genome research can break through the limitations of traditional reference genomes by constructing a complete gene set of species, systematically mining quality-related genes and their variations, and providing the theoretical basis and gene resources for crop quality improvement. In the study of the wheat pan-genome, genes related to gluten strength, starch content, and other quality traits were identified, and the processing quality of wheat can be improved directionally through molecular breeding technology.
Crop breeding new techniques and molecular tool (Villalobos-López et al., 2022)
Improvement of Stress Resistance
Facing increasingly severe environmental challenges, it is very important to improve the stress resistance of crops (such as drought resistance, salt resistance, and cold resistance). Pan-genome contains a large number of genes related to stress resistance, and the existence and variation of these genes in different individuals provide rich resources for stress resistance breeding. Through the analysis of the pan-genome, individuals with excellent stress resistance can be screened out, and stress resistance genes can be introduced into excellent varieties by molecular breeding technology. In the study of the soybean pan-genome, many new genes related to drought tolerance were found, which laid the foundation for the cultivation of drought-tolerant soybean varieties.
Yield Increase
Crop yield is the core goal of agricultural production, which is influenced by many genes and environmental factors. Pan-genome research can reveal the gene network and regulation mechanism related to yield, and provide new ideas for yield improvement. Through the mining and functional study of yield-related genes in pan-genome, more reasonable breeding strategies can be designed to achieve a breakthrough in yield improvement. Some new yield-related genes have been found in the study of rice pan-genome, and it is expected to further improve the yield potential of rice by regulating these genes through gene editing and other technologies.
Genome editing to develop high-yielding and climate resilient crops (Nerkar et al., 2022)
Prevention and Control of Pests and Diseases
Pan-genome research has opened up a new accurate and dynamic path for pest control by comprehensively analyzing the genetic diversity of crops and pathogens, and is becoming the core technical support for modern agricultural stress-resistant breeding and green prevention and control.
Disease-Resistant Gene Mining
Under the pressure of natural selection, pathogens have continuously evolved new pathogenic types through gene mutation and gene recombination, while traditional disease-resistant varieties are often difficult to maintain long-term resistance in the face of rapid mutation of pathogens because they rely on a single or a few disease-resistant genes. According to statistics, among the main crops in the world, the cases of resistance loss of disease-resistant varieties caused by pathogenic bacteria variation increased by about 7% annually, which brought huge losses to agricultural production.
Pan-genome research has broken through the limitations of traditional single reference genomes. By integrating the whole genome information of several representative individuals, we can fully explore the disease-resistant genes in species, especially those rare alleles and structural variation genes that are missing in a single reference genome. These disease-resistant genes hidden in the population are like undeveloped treasure houses, which provide brand-new resources for cultivating durable disease-resistant varieties.
Schematics of the recent advances in the improvement of genetic resistance against disease in vegetables crops (Thomas et al., 2024)
Study on Pan-Genome of Pathogens
In addition to the pan-genome research of crops themselves, the pan-genome research of pathogens also provides a new perspective for pest control. Through the analysis of the pathogen pan-genome, we can comprehensively analyze its genetic diversity, evolutionary dynamics, and pathogenic mechanism, so as to formulate more accurate and effective prevention and control strategies.
In practical research, scientists used pan-genome technology to deeply analyze rice blast fungus and constructed a genome set containing multiple geographical strains. It is found that there are a lot of structural variations in the population of Magnaporthe grisea, especially the copy number variation and sequence polymorphism of pathogenic genes, which are significantly related to the virulence evolution of the pathogen. These findings not only reveal the evolution law of Magnaporthe grisea but also provide a theoretical basis for the development of an early warning system based on gene monitoring.
Study on Crop-Pathogen Interaction
Pan-genome technology can be used to study the interaction mechanism between crops and pathogens. In an agricultural ecosystem, the interaction between crops and pathogens is a dynamic and complex process, and pan-genome research can break through the limitations of traditional single reference genomes and reveal their molecular basis from a more comprehensive genetic perspective.
By constructing a pan-genome database of crops and their corresponding pathogens, researchers can systematically compare the whole genome sequences of pathogens from different varieties of crops and different strains, and accurately identify the genes that play a key role in the interaction process and their mutation sites. These key genes include not only NLR family genes encoding disease-resistant proteins in crops, but also genes encoding effector proteins regulating toxicity and infectivity in pathogens, and their variation often directly affects the results of their interaction.
Boxplots indicating prediction accuracies and numbers of genes of different gene sets for antimicrobial resistance (AMR) prediction problems (Yang et al., 2022)
Application in Other Agricultural Field
In the agricultural field, in addition to breeding, genetic improvement, and pest control, the Pan-Genome also shows unique value in many emerging directions. It can lay a solid scientific foundation for the protection of agricultural biodiversity, open a new perspective for agricultural ecological research, and be deeply integrated with the development of precision agriculture to promote agriculture to move in a smarter and more sustainable direction.
Protection of Agricultural Biodiversity
Pan-genome research can provide a scientific basis for the protection of agricultural biodiversity. Through the pan-genome analysis of crops and their wild relatives, we can systematically analyze the genetic variation map within species and identify the key genetic elements lost in domestication and breeding. In addition, the genetic diversity assessment model based on pan-genome data can quantify the uniqueness and rarity of different germplasm resources, help researchers establish a clear priority protection strategy, and avoid the disorderly loss of genetic resources. This in-depth analysis of biodiversity from the genome level is promoting the transformation of agricultural germplasm resource protection from experience-driven to data-driven, laying a solid genetic foundation for achieving sustainable agricultural development.
Agricultural Ecological Research
Pan-genome technology can be applied to the study of agroecosystems, and the interaction mechanism between organisms can be deeply explored through the pan-genome analysis of crops, soil microorganisms, insects, and other organisms.
- In the symbiotic system of rhizosphere microorganisms and crops, using pan-genome sequencing technology can analyze the gene reserves of functional microorganisms such as nitrogen-fixing bacteria and phosphorus-solubilizing bacteria, identify key gene clusters involved in nutrient transformation and plant growth promotion, and provide gene resources for developing efficient microbial agents.
- In the study of the interaction between crops and insects, by analyzing the pan-genome of pests and crops, we can reveal the co-evolutionary relationship between crop insect-resistant genes and insect detoxification genes, and provide a theoretical basis for designing new insect-resistant strategies.
In addition, pan-genome analysis can also track the horizontal gene transfer phenomenon in agroecosystems. Whether the foreign genes of transgenic crops will be transferred to wild relatives or non-target organisms through pollen transmission or soil microorganisms, pan-genomics can monitor the path and frequency of gene flow and evaluate potential ecological risks through systematic gene scanning and comparison.
Population structure analysis based on PAVs and SNPs (Wang et al., 2023)
Precision Agriculture
With the development of agricultural intelligence, precision agriculture has become the development direction of agriculture in the future. Pan-genome technology breaks through the limitation of traditional single reference genomes by constructing the whole genome set of species and provides a new perspective for precise crop management. In practical application, scientists can use the pan-genome data of individual crops, combined with the environmental data collected by soil moisture sensors, weather stations, and other equipment to build a dynamic growth model.
Facing the threat of pests and diseases, we should use pan-genome data to quickly locate disease-resistant genes and develop precisely targeted biological pesticides or breeding strategies. For example, in the prevention and control of wheat scab, by analyzing the pan-genome of different wheat varieties, we can screen out germplasm resources carrying new disease-resistant genes for cross-breeding.
Conclusion
Pan-genome research has broad application prospects in agriculture, which provides new ideas and methods for crop breeding, genetic improvement, pest control, and other fields. Although it faces some challenges at present, with the continuous development of technology and in-depth research, the Pan-Genome will play an increasingly important role in solving major problems faced by agriculture and promoting the sustainable development of agriculture. Make full use of pan-genome technology, tap the genetic potential of agricultural organisms, and make contributions to ensuring food security and sustainable development of the agricultural ecological environment.
References
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- Tay Fernandez CG, Nestor BJ., et al. "Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species." Int J Mol Sci. 2022 23(5): 2671 https://doi.org/10.3390/ijms23052671
- Villalobos-López MA, Arroyo-Becerra A., et al. "Biotechnological Advances to Improve Abiotic Stress Tolerance in Crops." Int J Mol Sci. 2022 23(19): 12053 https://doi.org/10.3390/ijms231912053
- Nerkar G, Devarumath S., et al. "Advances in Crop Breeding Through Precision Genome Editing." Front Genet. 2022 13: 880195 https://doi.org/10.3389/fgene.2022.880195
- Thomas WJW, Amas JC., et al. "Recent advances in the improvement of genetic resistance against disease in vegetable crops." Plant Physiol. 2024 196(1): 32-46 https://doi.org/10.1093/plphys/kiae302
- Yang MR, Wu YW. "Enhancing predictions of antimicrobial resistance of pathogens by expanding the potential resistance gene repertoire using a pan-genome-based feature selection approach." BMC Bioinformatics. 2022 23(Suppl 4): 131 https://doi.org/10.1186/s12859-022-04666-2
- Wang J, Yang W., et al. "A pangenome analysis pipeline provides insights into functional gene identification in rice." Genome Biol. 2023 24(1): 19 https://doi.org/10.1186/s13059-023-02861-9
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