Molecular Plant Breeding 2025, Vol.16, No.1, 13-23 http://genbreedpublisher.com/index.php/mpb 17 Figure 1 Seed shattering phenotype and the substitution mapping of SH4-NIV. a shows the shattered seeds and panicle of SN58, and panicles with non-shattered seeds in HJX74. b shows the substitution mapping of SH4-NIVfor seed shattering. c shows the CDS variations of SH4. bar=10 cm (Adapted from Wang et al., 2023) 4.3 Evolutionary changes and selective pressures The domestication of crops is driven by evolutionary changes and selective pressures that favor traits beneficial for cultivation and yield. For example, the fixation of the nonshattering sh4 allele in rice cultivars was driven by strong artificial selection, which facilitated easier harvest and reduced seed loss (Zhang et al., 2009). Similarly, the qSW5 deletion in rice was likely selected to increase grain size and yield, demonstrating the role of selective pressures in shaping domestication traits (Shomura et al., 2008). The presence of functional alleles of seed shattering genes in wild rice populations, such as O. meridionalis, indicates that these populations have remained genetically isolated from domesticated rice, retaining pre-domestication alleles (Hasan et al., 2023). This genetic isolation provides valuable insights into the impact of domestication on the rice genome and highlights the importance of selective pressures in the domestication process. 5 Linkage Drag in Rice Breeding 5.1 Occurrence of linkage drag Linkage drag refers to the co-inheritance of undesirable traits along with desirable ones due to their close proximity on the chromosome. In rice breeding, this phenomenon is often observed when attempting to introduce beneficial traits from wild relatives into cultivated varieties. For instance, the study (Xiong et al., 1999) identified that genetic factors controlling domestication-related traits are concentrated in a few chromosomal blocks. This clustered distribution of genes can lead to linkage drag, as undesirable traits from wild species may be inherited along with beneficial traits. Similarly, the research on the molecular population genetics of rice domestication highlights the existence of highly polymorphic linkage blocks that are much older than the speciation between wild species, which can contribute to linkage drag during breeding programs (Tang et al., 2007). Inter subspecies (indica and japonica) hybrids are usually sterile, limiting gene exchange. The study identified that a killer-protector system at the S5 locus encoded by three tightly linked genes [Open Reading Frame 3 (ORF3) to ORF5] regulates fertility in indica-japonica hybrids (Yang et al., 2012). During female sporogenesis, the action
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