Molecular Plant Breeding 2025, Vol.16, No.1, 13-23 http://genbreedpublisher.com/index.php/mpb 15 For example, Ghd8 affects grain protein content in the background of Ehd1 (wild-type allele), but is masked in the background of ehd1 (mutant allele) due to the epistasis of Ehd1×Ghd8 (Wei et al., 2024). The study provides comprehensive gene interaction information for quantitative traits for rice genetic research and will provide theoretical support for rice molecular design breeding, offering significant insights into linkage drag and domestication syndrome. In brief, addressing linkage drag is essential for the successful improvement of crop varieties. By leveraging modern genetic tools and a deeper understanding of domestication genetics, breeders can more effectively separate desirable traits from undesirable ones, ultimately enhancing crop performance and sustainability. 3 Domestication Syndrome in Rice 3.1 Defining domestication syndrome Domestication syndrome refers to the suite of morphological and physiological traits that differentiate domesticated plants from their wild ancestors. In rice, these traits have been shaped by human selection to enhance agricultural productivity and ease of cultivation. The genetic basis of these traits often involves both major and minor effect genes, which are frequently clustered in specific chromosomal regions. This clustering can lead to “linkage drag”, where undesirable traits are co-inherited with desirable ones due to their proximity on the chromosome (Xiong et al., 1999). 3.2 Traits associated with domestication in rice Seed shattering is a critical trait that has been significantly altered during the domestication of rice. Wild rice species typically exhibit high levels of seed shattering, which aids in natural seed dispersal. However, for cultivated rice, reduced seed shattering is a desirable trait as it prevents loss of grains before harvest. Genetic studies have identified several quantitative trait loci (QTLs) that control seed shattering, and these loci are often conserved across different cereal crops, including maize and sorghum (Poncet et al., 2002). Plant architecture, including traits such as plant height, tiller number, and leaf angle, has been extensively modified during rice domestication. These changes have been driven by the need for higher yield and better adaptability to various growing conditions. The genetic factors controlling these traits are often located in specific chromosomal regions, and their manipulation can lead to significant improvements in plant architecture. For instance, loci on linkage groups 6 and 7 have been identified as central to the developmental control of plant architecture traits in cereals (Poncet et al., 2002). A study found that using the high-quality indica rice variety HJX74 as the background and AA genome wild rice O. rufipogon and O. nivara as donors, the single segment substitution lines (SSSL) was constructed. By comparing chromosome interval and sequence alignment, the allelic variation of domesticated genes was analyzed. Among them, 7 genes have allelic variations with known genes (Table 1), and 4 genes are considered as newly discovered genes (Wang et al., 2023). Grain size and shape are among the most important traits selected during rice domestication. Larger and more uniform grains are preferred for their higher market value and ease of processing. The genetic basis of these traits involves multiple QTLs, with some loci explaining a significant portion of the phenotypic variation. Studies have shown that both major and minor effect genes contribute to the differences in grain size and shape between wild and cultivated rice (Xiong et al., 1999). In summary, the domestication of rice has involved the selection of multiple traits that enhance its suitability for human use. These traits are controlled by a complex interplay of genetic factors, many of which are clustered in specific chromosomal regions, leading to phenomena such as domestication syndrome and linkage drag. Understanding these genetic underpinnings can provide valuable insights for rice breeding programs aimed at improving crop performance and resilience.
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