Molecular Plant Breeding 2025, Vol.16, No.1, 13-23 http://genbreedpublisher.com/index.php/mpb 19 Anyhow, linkage drag presents a significant challenge in rice breeding, but with the use of advanced genetic tools and techniques such as marker-assisted selection and gene editing, it is possible to mitigate its effects and enhance the efficiency of breeding programs. 6 Case Studies and Examples 6.1 Case study 1: overcoming linkage drag in disease resistance Linkage drag, the phenomenon where undesirable traits are co-inherited with beneficial ones due to their close genetic proximity, poses a significant challenge in breeding disease-resistant rice varieties. One notable example is the effort to incorporate disease resistance genes from wild rice into cultivated varieties. The study (Hasan et al., 2023) highlights the genetic isolation of Australian wild rice populations, which have retained pre-domestication alleles, including those related to disease resistance. These wild populations exhibit a high level of natural variation at domestication loci, such as seed shattering and grain size, which are often linked to disease resistance genes. By leveraging the genetic diversity in these wild populations, breeders can potentially overcome linkage drag by identifying and selecting for alleles that confer disease resistance without the associated undesirable traits. 6.2 Case study 2: improving grain quality while managing linkage drag Improving grain quality in rice, such as grain size and weight, while managing linkage drag is a critical goal in rice breeding programs. The study by Kumar et al. (2020) provides a comprehensive analysis of polymorphisms associated with grain size and weight in Indian rice germplasm. The researchers identified a contiguous ~6 Mb long low diversity region (LDR) on chromosome 5, which carries a major grain weight QTL (quantitative trait locus) harboring the OsTORgene. This region has undergone significant positive selection and multiple selection sweeps, indicating its importance in domestication. By understanding the genetic basis of grain quality traits and their association with domestication-driven evolution, breeders can develop strategies to improve grain quality while minimizing the impact of linkage drag. For instance, the identification of six SNPs significantly associated with grain size/weight provides valuable markers for high-throughput genotyping and selection in breeding programs. 6.3 Case study 3: balancing yield and stress tolerance Balancing yield and stress tolerance in rice is another area where linkage drag presents a challenge. The domestication process has often led to the selection of high-yielding varieties at the expense of stress tolerance traits. The study by Hasan et al. (2023）on Australian wild rice populations reveals that these populations have retained a high level of natural variation at domestication loci, including those related to stress tolerance. This genetic diversity offers a valuable resource for breeding programs aiming to enhance stress tolerance without compromising yield. By utilizing the allelic variations present in wild rice populations, breeders can identify and introgress stress tolerance genes into cultivated varieties, thereby achieving a balance between yield and stress tolerance. This approach not only helps in overcoming linkage drag but also ensures the development of resilient rice varieties capable of thriving under diverse environmental conditions. 7 Evolutionary Insights from Rice Domestication 7.1 Comparative genomics of wild and cultivated rice The comparative genomics of wild and cultivated rice provides significant insights into the genetic factors that have driven the domestication process. A study conducted using an F2 population derived from a cross between O. sativa (cultivated rice) and O. rufipogon (wild rice) identified numerous genetic loci associated with domestication-related traits. Specifically, 19 traits were analyzed, revealing that seven qualitative traits were each controlled by a single Mendelian locus, while 12 quantitative traits were associated with 44 putative QTLs (Xiong et al., 1999). This clustered distribution of genes in specific chromosomal blocks underscores the genetic basis of the “domestication syndrome” and highlights the challenges posed by “linkage drag” in breeding programs (Xiong et al., 1999). 7.2 Insights into adaptation and speciation The process of rice domestication has also provided valuable insights into adaptation and speciation. The genetic factors identified in the comparative genomics studies suggest that both major and minor effect genes play a role
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