Invited Review

Harnessing Genetic Populations in Plant Breeding: Innovative Strategies for Construction and Application  

Xuanjun Fang1,2
1 Hainan Institute of Tropical Agricultural Resources (HITAR), Sanya, 572025, Hainan, China
2 Hainan Provincial Key Laboratory of Crop Molecular Breeding, Sanya, 572025, Hainan, China
Author    Correspondence author
International Journal of Horticulture, 2024, Vol. 14, No. 3   doi: 10.5376/ijh.2024.14.0012
Received: 03 Dec., 2023    Accepted: 10 Jan., 2024    Published: 01 May, 2024
© 2024 BioPublisher Publishing Platform
This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article:

Fang X.J., 2024, Harnessing genetic populations in plant breeding: innovative strategies for construction and application, International Journal of Horticulture, 14(3): 105-110 (doi: 10.5376/ijh.2024.14.0012)


This paper explores innovative strategies for utilizing genetic populations in plant breeding to enhance crop performance and adaptability. We review the foundational concepts of population and quantitative genetics in the context of modern breeding techniques and discuss the application of evolutionary plant breeding for developing resilient crop varieties suited to changing environmental conditions. The integration of advanced genetic tools, such as whole-genome strategies and marker-assisted selection, is emphasized for its role in improving breeding efficiency. Additionally, we explore the emerging role of plant microbiomes in breeding, highlighting how symbiotic relationships enhance plant fitness and genetic diversity. The paper also addresses the importance of conserving genetic diversity during breeding processes and presents case studies that demonstrate the successful application of these strategies worldwide. The potential of these approaches to significantly impact global agriculture, particularly in enhancing food security and sustainability, is discussed. We advocate for the integration of these innovative genetic tools with conventional breeding practices to meet global food demands.

Plant breeding; Genetic populations; Evolutionary plant breeding; Marker-assisted selection; Multi-parent advanced generation inter-cross (MAGIC) populations; Plant microbiomes

Plant breeding has historically leveraged the natural genetic variability within plant populations to cultivate crops that are higher yielding, more resistant to pests and diseases, and better adapted to various environmental conditions. The genetic diversity found within these populations is a fundamental resource for achieving these improvements, as it provides the raw material for selection and adaptation processes. By understanding and harnessing genetic populations, breeders can direct the evolution of crop species more effectively and efficiently (Jain, 1992).


The significance of genetic populations in plant breeding cannot be overstated. These populations are reservoirs of genetic variations that breeders use to introduce new and beneficial traits into crops. These traits can enhance crop productivity, improve nutritional quality, and increase resistance to environmental stresses such as drought, salinity, and pests (Ellstrand, 1992). Moreover, the strategic manipulation of genetic populations can lead to innovations in plant breeding methods, facilitating the development of varieties that are well-suited to sustainable agriculture practices.


This paper aims to explore innovative strategies for constructing and applying genetic populations to improve crop yields, disease resistance, and environmental adaptability. We intend to delve into recent advancements in genetic techniques, such as whole-genome strategies and the use of multi-parent populations, to better understand their potential in enhancing the efficiency and effectiveness of plant breeding. Additionally, the paper will investigate the integration of microbiomes into breeding strategies, which offers a novel approach to increasing genetic variability and enhancing plant fitness. By addressing these areas, the paper seeks to contribute to the development of new breeding strategies that not only meet the demands of global food security but also align with the principles of sustainability and conservation of genetic diversity.


1 Review of Genetic Foundations in Plant Breeding

1.1 Basic principles of population and quantitative genetics in plant breeding

The application of population and quantitative genetics forms the bedrock of modern plant breeding strategies. Jain (1992) elucidates that the essence of plant breeding lies in the manipulation of genetic variation through deliberate selection and breeding cycles. These cycles involve the selection of phenotypically superior plants, followed by their cross-breeding to combine desirable traits, and subsequently selecting the best progeny over successive generations. This process depends critically on the principles of population genetics, which deals with the frequencies of alleles and genotypes in a breeding population and how these frequencies change over time under the influence of forces like selection, mutation, and genetic drift.


Quantitative genetics, on the other hand, focuses on traits influenced by multiple genes, known as quantitative trait loci (QTLs). Jain (1992) discusses the importance of understanding polygenic traits, which are controlled by several to many genes and are often significantly influenced by the environment. The breeding methods vary depending on the breeding system of the plant species—whether outbreeding, inbreeding, or asexual—and the specific objectives of the breeding program. Each method leverages these genetic principles to optimize the creation of new, desirable plant varieties that can contribute to increased agricultural productivity and sustainability (Jain, 1992).


1.2 The role of genetic diversity and gene flow in plant populations

Gene flow, the movement of genes between populations, plays a crucial role in maintaining genetic diversity within plant populations. Ellstrand (1992) emphasizes that gene flow is one of the key mechanisms by which genetic variation can be introduced into a plant population, thus counteracting the effects of natural selection and genetic drift which might otherwise lead to a reduction in genetic diversity. High genetic diversity within a plant population is advantageous as it provides a broader base for natural and artificial selection, increasing the population's resilience to environmental stresses and diseases.


According to Ellstrand (1992), gene flow in plants is mediated by various vectors, including wind, water, animals, and human activities, and can occur over varying distances, depending on the species and the ecosystem. The level of gene flow significantly impacts the genetic structure of plant populations, influencing their evolutionary potential and adaptability to changing environments. In the context of plant breeding, managing gene flow can be critical for developing new varieties that are both productive and adapted to local conditions. Enhanced understanding and manipulation of gene flow and genetic diversity are thus vital for the effective breeding of crops capable of meeting the demands of global food security (Ellstrand, 1992).


2 Evolutionary Plant Breeding

2.1 Concept and application of evolutionary breeding to enhance resilience under changing climates

Evolutionary plant breeding is a dynamic approach that harnesses the natural genetic diversity within crop populations to adapt to local environmental conditions and changing climates. This method involves creating crop populations with high genetic diversity and subjecting them to the forces of natural selection through cycles of sowing and re-sowing. Plants that are most suited to the prevailing conditions thrive and contribute more to the genetic makeup of subsequent generations. Over time, this process leads to the evolution of crop populations that are more resilient to environmental stresses, including climate variability. Döring and colleagues highlight the resilience of evolving plant populations as a major advantage, particularly in the face of global climate change. This approach not only enhances crop adaptability but also reduces the reliance on chemical inputs, contributing to sustainable agriculture practices (Döring et al., 2011).


2.2 Case studies demonstrating the success of evolutionary breeding in cereals

The success of evolutionary plant breeding is particularly evident in cereals, where diverse genetic populations have been developed and tested across various environmental conditions. For example, studies have shown that wheat and barley populations derived through evolutionary breeding exhibit enhanced performance and greater disease resistance compared to conventionally bred varieties. These populations are better able to exploit local soil and climatic conditions, resulting in improved yield stability across different seasons and regions. Such case studies underscore the potential of evolutionary breeding as a robust strategy to increase the genetic fitness of cereals, thereby ensuring food security in an era of climate change.


The concept and application of evolutionary breeding, as discussed by Döring et al. (2011), provide a solid foundation for implementing this approach in global agricultural practices. By continuing to study and apply these principles, plant breeders can better equip crops to handle the unpredictable stresses associated with global climate variations.


3 Advanced Genetic Techniques

3.1 Whole-genome strategies for marker-assisted breeding and their impact on plant breeding efficiency

The adoption of whole-genome strategies for marker-assisted breeding has significantly revolutionized plant breeding by enhancing efficiency and precision. Xu et al. (2012) elaborate on how molecular breeding for complex traits in crops necessitates an understanding and manipulation of myriad factors that influence plant growth and stress responses. These strategies employ full genome sequencing and genome-wide molecular markers to address various genomic and environmental factors comprehensively. This holistic approach is crucial in the effective application of genetic resources and breeding materials, optimizing the selection for desirable traits through a detailed understanding of specific genomic regions, genes/alleles, haplotypes, and their phenotypic contributions (Xu et al., 2012).


3.2 The development and use of multi-parent populations (MAGIC) for genetic analysis and selection

Multi-parent advanced generation inter-cross (MAGIC) populations represent a cutting-edge approach in genetic analysis and selection, offering a robust tool for the dissection of complex traits. Arrones et al. (2020) discuss the construction of MAGIC populations, which involves the intermingling and recombination of genomes from multiple founder parents. This results in a set of recombinant inbred lines that display a lack of genetic structure and high genetic and phenotypic diversity. The strength of MAGIC populations lies in their ability to combine significant levels of genetic recombination, thus providing a powerful resource for the genetic analysis of quantitative traits and the selection of elite breeding material. These populations have proven particularly valuable in crop species where complex traits are a focus, allowing breeders to achieve more targeted and efficient selection outcomes (Arrones et al., 2020).


The development and implementation of these advanced genetic techniques are crucial for the future of plant breeding, enabling researchers and breeders to enhance crop varieties with greater precision and efficiency, ultimately contributing to sustainable agricultural practices and food security.


4 Integrating Microbiomes in Plant Breeding

4.1 The potential of microbiomes in enhancing genetic variability and plant fitness

Recent research highlights the significant role of microbiomes in enhancing the genetic variability and fitness of plant populations. Gopal and Gupta (2016) emphasize that plants, though stationary, have developed intricate relationships with microbial communities to counter various biotic and abiotic stresses. These symbiotic relationships not only bolster plant resilience but also introduce a critical source of genetic variability. Microbiomes, particularly those in the rhizosphere and phyllosphere, play pivotal roles in nutrient uptake, disease resistance, and stress tolerance, contributing to the overall adaptability and health of plants. By harnessing these microbial interactions, plant breeders can exploit an untapped reservoir of genetic diversity to enhance crop performance under diverse environmental conditions (Gopal and Gupta, 2016).


4.2 Strategies for incorporating microbiome selection into traditional plant breeding frameworks

To integrate microbiomes effectively into plant breeding, it is essential to develop strategies that consider both the plant and its associated microbial communities as a single holistic unit. One approach is the use of microbial inoculants as a breeding tool, where specific beneficial microbes are introduced to the plant during critical growth phases to enhance performance traits such as yield, drought tolerance, and nutrient utilization. Another strategy involves the selective breeding of plants that naturally attract beneficial microbes, thus selecting for traits that promote a beneficial microbiome. This could involve genomic selection where markers associated with beneficial microbiome traits are targeted.


Additionally, advanced techniques such as synthetic community (SynCom) analysis can be employed (Marin et al., 2021). This involves constructing specific microbial communities in the lab and testing their impact on plant phenotypes under controlled conditions. Successful communities can then be applied in breeding programs to ensure that crop varieties are optimized not only for their genetic traits but also for their ability to harness beneficial microbial functions.


Incorporating microbiome data into decision-making tools for breeders can further refine this integration. By understanding the microbiome's influence on plant phenotypes, breeders can make more informed selections that consider the microbiome as an extension of the plant's phenotype (Martins et al., 2023).


By adopting these strategies, plant breeding can evolve to not only select for optimal genetic traits but also for an optimal microbiome, leading to robust, resilient crops that are well-adapted to their growing conditions and capable of meeting the challenges posed by a changing global climate.


5 Conservation of Genetic Diversity

5.1 The importance of maintaining genetic diversity within cultivated plant populations

Maintaining genetic diversity within cultivated plant populations is crucial for several reasons. Genetic diversity is the foundation of plant adaptability to varying environmental conditions and resistance to pests and diseases. It allows plant populations to evolve over time, enhancing their resilience and ensuring stability in yield across different environments. Gray (1996) highlights that genetic diversity in plant populations correlates strongly with environmental variability, pointing to natural selection's role in shaping this diversity. By preserving a wide range of genetic variation, breeders can ensure that crops are capable of adapting to future changes in climate or agricultural practices, thus supporting sustainable agriculture (Gray, 1996).


5.2 Methods for conserving genetic resources during breeding processes 

Conserving genetic resources during the breeding process involves several strategies aimed at maximizing genetic variation and minimizing the loss of genetic traits. These methods include:


In situ and ex situ conservation: In situ conservation involves protecting plants in their natural habitats, allowing them to evolve under natural conditions and pressures. Ex situ conservation, such as seed banks and botanical gardens, preserves genetic material outside its natural habitat, providing a backup for lost genetic diversity in the wild.


Use of diverse breeding lines and wild relatives: Incorporating a wide range of genetic material, including wild relatives of cultivated plants, can introduce beneficial traits that enhance crop resilience and productivity. These wild strains often contain alleles that confer resistance to diseases and environmental stresses not present in cultivated varieties.


Genomic selection and marker-assisted breeding: These modern techniques allow breeders to identify and select for genetic traits that promote diversity within the breeding population. By using markers linked to desirable genetic traits, breeders can efficiently incorporate these traits into new cultivars without compromising the genetic base of the population.


Managed gene flow: Intentionally introducing genes from one population to another can help maintain or increase genetic diversity. This method is particularly useful in small or isolated populations at risk of inbreeding depression.


Participatory breeding programs: Engaging local communities in the breeding process helps preserve and utilize traditional knowledge and local crop varieties, which are often well-adapted to specific environmental conditions and cultural preferences.


By implementing these strategies, plant breeders can conserve genetic resources effectively, ensuring that agricultural systems remain productive and sustainable. This conservation is not only a technical challenge but also a fundamental aspect of modern agriculture's ecological and ethical dimensions.


6 Case Studies and Applications

6.1 Examples of successful applications of innovative genetic population strategies in global agriculture

Innovative genetic population strategies have demonstrated significant success across various agricultural contexts globally. One prominent example involves the use of evolutionary plant breeding in cereals, which has proven effective under diverse and changing environmental conditions. Döring et al. (2011) discussed how crop populations with high genetic diversity, subjected to natural selection, show enhanced adaptation capabilities to local growing conditions over successive generations, benefiting crop resilience and yield stability in the face of climatic variability (Döring et al., 2011).


Another example is the development of Multi-parent Advanced Generation Inter-Cross (MAGIC) populations, which have been applied in various crops to create a highly recombined genetic mosaic that combines multiple founder genomes. This approach has facilitated the genetic dissection of complex traits and accelerated the breeding of elite cultivars with desirable characteristics. Arrones et al. (2020) highlighted the significant impact of MAGIC populations in breeding programs, especially in cereals, where they have enabled the integration of desirable traits from multiple parents into new, high-performing lines (Arrones et al., 2020).


6.2 Impact assessment of these strategies on crop productivity and sustainability

The impact of innovative genetic population strategies on crop productivity and sustainability has been profound. The evolutionary breeding approach, as discussed by Döring et al. (2011), not only enhances genetic diversity within crop populations but also improves their overall fitness and adaptability, leading to sustainable crop production systems that are better equipped to withstand environmental stresses (Döring et al., 2011).


MAGIC populations, on the other hand, have contributed to increased genetic gains by combining the benefits of high genetic diversity and minimal population structure. This strategy has allowed breeders to effectively map quantitative trait loci and select for traits that contribute to yield stability and stress resilience, thus enhancing both productivity and sustainability in agricultural systems. The use of MAGIC populations in crops like wheat and rice has shown promising results in improving yield under various environmental conditions while maintaining high genetic diversity (Arrones et al., 2020).


These case studies exemplify how innovative genetic population strategies are pivotal in not only enhancing crop yields but also in promoting sustainable agricultural practices that are crucial for meeting the growing global food demand in a changing climate.


7 Future Directions and Challenges

7.1 Emerging Technologies and their potential impact on plant breeding

Emerging technologies in plant breeding, particularly those involving genomic tools and bioinformatics, are poised to significantly advance our capacity to harness genetic populations. One of the most promising areas is the use of Multi-parent Advanced Generation Inter-Cross (MAGIC) populations, which integrate the genomes of multiple founder parents to enhance genetic recombination and diversity. This approach not only increases the resolution of genetic mapping but also enhances the selection of traits in breeding programs (Arrones et al., 2020). Furthermore, the integration of machine learning algorithms with genomic data is set to revolutionize plant breeding by predicting phenotypic outcomes from genetic data, thus expediting the breeding cycles and enhancing the precision of selection (Scott et al., 2020).


7.2 Policy and ethical considerations in the deployment of genetic population strategies

The deployment of innovative genetic population strategies in plant breeding raises several policy and ethical considerations. First, there is a need for policies that ensure equitable access to genetic resources, which can help prevent the monopolization of genetic materials by a few corporations. This is crucial for maintaining genetic diversity and ensuring that the benefits of plant breeding innovations are shared widely (Louwaars, 2018). Additionally, the ethical implications of genetic modification technologies, such as CRISPR/Cas systems, must be considered. These technologies can drive significant advancements in plant breeding but also raise concerns about potential off-target effects and long-term impacts on ecosystems. Policies need to be in place to govern the safe use of these technologies, ensuring that they do not harm human health or the environment (Cowling, 2013).


These future directions highlight the dynamic intersection of technology, policy, and ethics in the field of plant breeding. As technologies evolve, so too must the regulatory frameworks that ensure these tools are used responsibly and equitably to benefit global agriculture and food security.


8 Conclusion

In conclusion, the exploration of genetic populations in plant breeding presents a dynamic avenue for enhancing agricultural productivity and sustainability. Through the implementation of evolutionary plant breeding, breeders can develop crops more resilient to environmental changes. The integration of whole-genome strategies and marker-assisted selection further illustrates how technological advancements can revolutionize breeding practices, improving the selection efficiency and genetic diversity of crops. The novel application of microbiomes in plant breeding highlights an emerging strategy that taps into microbial genetics to boost plant health and adaptability.


To truly harness the potential of these innovative strategies, there is a pressing need for the integration of these advanced genetic tools with traditional breeding practices. This synthesis not only promises to propel crop improvement forward but also serves as a fundamental strategy to combat the pressing global food security challenges posed by a rapidly growing population and changing climate conditions. The collaborative efforts of geneticists, breeders, and policymakers are essential to advance these technologies from research to field applications, ensuring that the genetic potential of plant populations is fully realized for future generations.



Arrones A., Vilanova S., Plazas M., Mangino G., Pascual L., Díez M., Prohens J., and Gramazio P., 2020, The dawn of the age of multi-parent MAGIC populations in plant breeding: novel powerful next-generation resources for genetic analysis and selection of recombinant elite material, Biology, 9(8): 229.


Cowling W., 2013, Sustainable plant breeding. Plant Breeding, 132(1): 1-9.


Döring T., Knapp S., Kovács G., Murphy K., and Wolfe M., 2011, Evolutionary plant breeding in cereals-into a new era, Sustainability, 3(10): 1944-1971.


Ellstrand N., 1992, Gene flow among seed plant populations, New Forests, 6, pp. 241-256.


Gopal M., and Gupta A., 2016, Microbiome selection could spur next-generation plant breeding strategies, Frontiers in microbiology, 7: 209912.


Gray A., 1996, Genetic diversity and its conservation in natural populations of plants, Biodiversity Letters, 3(3): 71-80.


Jain S.K., 1992, Population management in new plant breeding approaches, In: Jain, S.K., Botsford, L.W. (eds) Applied Population Biology, Monographiae Biologicae, 67: 121-147. Springer, Dordrecht.


Louwaars N., 2018, Plant breeding and diversity: A troubled relationship?. Euphytica, 214(7): 114.


Marín O., González B., and Poupin M., 2021, From microbial dynamics to functionality in the rhizosphere: a systematic review of the opportunities with synthetic microbial communities, Frontiers in Plant Science, 12: 650609.


Martins S., Pasche J., Silva H., Selten G., Savastano N., Abreu L., Bais H., Garrett K., Kraisitudomsook N., Pieterse C., and Cernava T., 2023, The use of synthetic microbial communities to improve plant health. Phytopathology®, 113(8): 1369-1379.


Scott M., Ladejobi O., Amer S., Bentley A., Biernaskie J., Boden S., Clark M., Dell’Acqua M., Dixon L., Filippi C., Fradgley N., Gardner K., Mackay I., O’Sullivan D., Percival‐Alwyn L., Roorkiwal M., Singh R., Thudi M., Varshney R., Venturini L., Whan A., Cockram J., and Mott R., 2020, Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding, Heredity, 125: 396-416.


Xu Y., Lu Y., Xie C., Gao S., Wan J., and Prasanna B., 2012, Whole-genome strategies for marker-assisted plant breeding, Molecular Breeding, 29: 833-854.

International Journal of Horticulture
• Volume 14
View Options
. PDF(0KB)
Associated material
. Readers' comments
Other articles by authors
. Xuanjun Fang
Related articles
. Plant breeding
. Genetic populations
. Evolutionary plant breeding
. Marker-assisted selection
. Multi-parent advanced generation inter-cross (MAGIC) populations
. Plant microbiomes
. Email to a friend
. Post a comment