Molecular Plant Breeding 2025, Vol.16, No.1, 13-23 http://genbreedpublisher.com/index.php/mpb 14 The objective of this study is to synthesize current knowledge on the genetic lessons learned from rice evolution, with a particular focus on linkage drag and domestication syndrome. By examining the genetic factors controlling domestication-related traits and the impact of linkage drag on breeding programs, this study aims to provide a comprehensive understanding of the genetic mechanisms underlying rice domestication. Additionally, this study will explore the implications of these findings for future rice breeding efforts and crop improvement strategies. Through this synthesis, we hope to highlight the importance of integrating genetic insights into practical breeding programs to enhance rice productivity and sustainability in the face of global challenges. 2 The Concept of Linkage Drag 2.1 Definition and mechanisms Linkage drag refers to the phenomenon where undesirable traits are co-inherited with desirable traits due to their close proximity on the same chromosome. This occurs because the genes for these traits are physically linked, making it difficult to separate them through traditional breeding methods. In the context of plant breeding, linkage drag can significantly hinder the improvement of crop varieties by introducing unwanted characteristics alongside beneficial ones (Giovannoni et al., 2018; Fuentes et al., 2021; Egorova et al., 2022). 2.2 Historical context and examples in plant breeding Historically, linkage drag has been a major challenge in the breeding of various crops. For instance, in potato breeding, the introgression of traits such as pathogen resistance from wild germplasm is often accompanied by undesirable features like high steroidal glycoalkaloid content and long stolons, which complicate the breeding process (Egorova et al., 2022). Similarly, in tomato, the breeding of modern varieties has inadvertently included alleles affecting metabolic quality due to linkage drag, demonstrating the pervasive nature of this issue across differentcrops (Giovannoni et al., 2018). In rice, the domestication process has led to the fixation of certain alleles that are beneficial for cultivation but also brought along linked undesirable traits. For example, the seed shattering genes in wild rice populations are functional, while domesticated rice has dysfunctional alleles, indicating a trade-off between ease of harvest and seed dispersal mechanisms (Hasan et al., 2023). Additionally, the modification of plant architecture in rice through the selection of the TIG1 gene has been crucial for domestication, but it also highlights the complexity of managing linked traits during the breeding process (Zhang et al., 2019). 2.3 Implications for crop improvement The implications of linkage drag for crop improvement are profound. It necessitates the development of advanced breeding techniques to break the linkage between desirable and undesirable traits. One promising approach is the de novo domestication strategy, which involves using gene editing technologies to modify candidate genes responsible for undesirable traits before hybridization with cultivated varieties. This method has been proposed for crops like potato and tomato, offering a potential solution to the linkage drag problem (Giovannoni et al., 2018; Egorova et al., 2022). Moreover, understanding the genetic mechanisms underlying domestication and the associated linkage drag can inform breeding strategies. For example, the identification of genes responsible for seed dormancy and their selection across multiple crop families, such as the stay-green G gene in soybean, rice, and tomato, provides insights into parallel domestication processes and potential targets for genetic improvement (Wang et al., 2018). Additionally, the study of recombination patterns in crops like tomato reveals how domestication shapes genetic diversity and linkage disequilibrium, further emphasizing the need for targeted breeding interventions to mitigate linkage drag (Fuentes et al., 2021). Recently, by using a very large rice genetic population (18K), research has found that the superposition of two genes does not necessarily result in the sum of their effects. Therefore, it is proposed that there is a phenomenon of epistasis between genes, such as mutual “suppression” and “masking”. In rice breeding, introducing a gene into the parent may not work, and this gene is influenced by genetic background and belongs to gene epistasis (Wei et al., 2024). Researchers have identified 170 pairs of masked epistasis that determine genetic background effects.
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