Rice Genomics and Genetics 2024, Vol.15, No.3, 132-141 http://cropscipublisher.com/index.php/rgg 136 Marker-assisted selection (MAS) enhances the efficiency of traditional breeding by using molecular markers to track the presence of specific alleles associated with desirable traits. This technique allows for the precise selection of progeny carrying the target alleles, thereby accelerating the breeding process. In rice, MAS has been successfully employed to develop ILs with improved agronomic traits by utilizing markers distributed across the genome (Zhang et al., 2022). The integration of genotyping-by-sequencing (GBS) and single-nucleotide polymorphism (SNP) typing further refines this process, enabling the identification of novel SNPs and the assessment of donor introgression patterns in early-backcross populations (Ali et al., 2018). These advancements facilitate the development of markers that support genomic applications in molecular breeding programs. 4.2 Challenges in introgression breeding One of the primary challenges in introgression breeding is linkage drag, which occurs when undesirable traits from the wild donor are co-inherited with the target alleles. This phenomenon can hinder the performance of the cultivated variety and complicate the breeding process. For example, while introgressing beneficial alleles for traits such as drought resistance or disease resistance, breeders may inadvertently introduce alleles that negatively affect yield or other agronomic traits (Zhang et al., 2022). Strategies to mitigate linkage drag include fine mapping of QTLs and the use of advanced backcrossing techniques to break undesirable linkages. Reproductive barriers between wild and cultivated rice species pose another significant challenge in introgression breeding. These barriers can manifest as pre-zygotic or post-zygotic incompatibilities, leading to reduced fertility or hybrid sterility. Overcoming these barriers requires careful selection of compatible parental lines and the use of techniques such as embryo rescue or bridge crossing. Additionally, the genetic structure of wild populations can be altered by gene introgression from cultivated rice, which may impact the conservation of wild relatives (Jin et al., 2018). Therefore, effective in situ conservation measures are necessary to maintain the genetic integrity of wild rice populations while harnessing their genetic diversity for crop improvement. The introgression of wild rice alleles into cultivated varieties involves a combination of traditional breeding approaches and modern molecular techniques. While challenges such as linkage drag and reproductive barriers exist, ongoing advancements in genomics and breeding strategies continue to enhance the efficiency and effectiveness of introgression breeding in rice. 5 Impact on Agronomic Traits 5.1 Yield enhancement The integration of wild rice alleles into cultivated varieties has shown significant potential in enhancing yield. Wild relatives of rice, such as Oryza rufipogon and Oryza nivara, possess genetic diversity that has been largely lost in domesticated rice due to selective breeding practices. By resequencing the genomes of these wild progenitors, researchers have identified numerous single nucleotide polymorphisms (SNPs) that are associated with yield-related traits. These SNPs can be used as molecular markers to guide breeding programs aimed at increasing yield in cultivated rice varieties (Xu et al., 2011). Additionally, the development of introgression libraries, which involve crossing wild rice species with elite cultivars, has led to the identification of novel allelic variations that significantly impact grain size and weight, further contributing to yield enhancement (Zhang et al., 2022). 5.2 Stress tolerance Wild rice species are known for their resilience to various biotic and abiotic stresses, which are critical for maintaining crop productivity in the face of climate change and evolving pathogens. The genetic diversity found in wild rice has been harnessed to improve stress tolerance in cultivated varieties. For instance, wild relatives of rice have been shown to possess alleles that confer resistance to drought, aerobic conditions, and blast disease. These traits have been successfully introgressed into cultivated rice, enhancing their ability to withstand adverse environmental conditions (Zhang et al., 2022). Moreover, the use of modern genomic technologies has accelerated the identification and transfer of stress-tolerance genes from wild rice to cultivated varieties, making it possible to develop rice strains that are more resilient to environmental stresses (Xie and Liu, 2021).
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