Molecular Plant Breeding 2025, Vol.16, No.1, 13-23 http://genbreedpublisher.com/index.php/mpb 13 Research Insight Open Access Linkage Drag and Domestication Syndrome: The Genetic Lessons from Rice Evolution Hui Zhang1,3, JuanLi 1,2,3, QianZhu1,2,3, Xiaoling Zhang4, Chunli Wang1,3, Dongsun Lee 1,2,3, Lijuan Chen1,2,3 1 Rice Research Institute, Yunnan Agricultural University, Kunming, 650201, Yunnan, China 2 The Key Laboratory for Crop Production and Smart Agriculture of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, Yunnan, China 3 College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, Yunnan, China 4 Kunming University, Kunming, 650201, Yunnan, China Corresponding email: chenlijuan@hotmail.com Molecular Plant Breeding, 2024, Vol.16, No.1 doi: 10.5376/mpb.2025.16.0002 Received: 12 Dec., 2024 Accepted: 15 Jan., 2025 Published: 23 Jan., 2025 Copyright © 2025 Zhang et al., 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: Zhang H., Li J., Zhu Q., Zhang X.L., Wang C.L., Lee D.S., and Chen L.J., 2025, Linkage drag and domestication syndrome: the genetic lessons from rice evolution, Molecular Plant Breeding, 16(1): 13-23 (doi: 10.5376/mpb.2025.16.0002) Abstract The domestication of rice (Oryza sativa) from its wild relatives has been a pivotal event in agricultural history, leading to significant genetic changes known as domestication syndrome. This study synthesizes current knowledge on the genetic mechanisms underlying these changes, with a focus on linkage drag and its implications for rice breeding. The severe bottleneck during domestication resulted in a dramatic reduction in genetic diversity in cultivated rice compared to its wild progenitors, O. rufipogon and O. nivara. Multiple independent domestication events have been identified, contributing to the genetic differentiation between the indica and japonica subspeicies. The identification of quantitative trait loci (QTLs) and candidate genes associated with domestication-related traits has provided insights into the clustered distribution of these genes, which may explain the phenomenon of linkage drag. Furthermore, the study of de-domestication in weedy rice has revealed the complexity of genetic changes during the domestication process. This study highlights the importance of understanding the genetic basis of domestication syndrome and linkage drag to improve rice breeding strategies and harness the genetic potential of wild rice species for crop improvement. Keywords Rice domestication; Linkage drag; Genetic diversity; Quantitative trait loci; De-domestication 1 Introduction Rice (Oryza sativa L.) is one of the most important staple crops globally, providing a primary food source for over half of the world's population. The domestication of rice from its wild progenitors, such as O. rufipogon, has been a complex process involving significant genetic changes that have resulted in the cultivated varieties we see today. This process has led to the development of numerous domestication-related traits, including reduced seed shattering, increased grain size, and changes in plant architecture (Xiong et al., 1999; Izawa et al., 2009; Voss-Fels et al., 2017). The genetic basis of these traits has been extensively studied, revealing that both major and minor effect genes are involved, often clustered in specific chromosomal regions (Xiong et al., 1999; Hasan et al., 2023). The domestication of rice has also been characterized by multiple selection steps and introgression events, which have shaped the genetic diversity of modern rice cultivars (Vaughan et al., 2008; Voss-Fels et al., 2017). Linkage drag refers to the phenomenon where undesirable traits are co-inherited with desirable traits due to their physical proximity on the chromosome. This can pose significant challenges in breeding programs, as it can hinder the introduction of beneficial traits from wild relatives into cultivated varieties (Voss-Fels et al., 2017). Understanding the genetic basis of linkage drag is crucial for developing strategies to overcome these challenges and improve crop performance. Domestication syndrome, a collection of traits that distinguish domesticated plants from their wild ancestors, provides insights into the evolutionary processes that have shaped crop genomes. Studying these traits can reveal the underlying genetic mechanisms and help in the identification of key genes involved in domestication (Xiong et al., 1999; Wang et al., 2008; Hasan et al., 2023). This knowledge is essential for crop improvement and for addressing the challenges posed by changing environmental conditions and increasing food demand.
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