Plant Gene and Traits 2024, Vol.15, No.4, 184-194 http://genbreedpublisher.com/index.php/pgt 185 diversity among different Oryza species (Stein et al., 2018; Hechanova et al., 2021). These molecular markers not only aid in the classification and phylogenetic studies but also play a crucial role in marker-assisted breeding, enabling the efficient use of wild germplasm for rice improvement (Brondani et al., 2003; Virk et al., 2000). 2 Molecular Markers in Genomics 2.1 Definition and types of molecular markers Molecular markers are specific sequences of DNA that can be used to identify a particular location within the genome. These markers are essential tools in genomics for various applications, including genome mapping, gene tagging, and phylogenetic analysis. The primary types of molecular markers include Restriction Fragment Length Polymorphisms (RFLPs), Random Amplified Polymorphic DNAs (RAPDs), Amplified Fragment Length Polymorphisms (AFLPs), Inter Simple Sequence Repeats (ISSRs), Simple Sequence Repeats (SSRs), and Single Nucleotide Polymorphisms (SNPs) (Grover and Sharma, 2016). Each type of marker has unique characteristics and applications. For instance, SSRs, also known as microsatellites, are highly polymorphic and widely used for evaluating genetic diversity and constructing genetic maps (Ni et al., 2002). SNPs, on the other hand, are the most abundant type of genetic variation and are particularly useful for high-throughput genotyping and genome-wide association studies (Gouda et al., 2021). 2.2 Evolution of molecular marker techniques The development of molecular marker techniques has evolved significantly over the past few decades. Initially, RFLPs were the primary markers used due to their codominant nature and high reproducibility. However, the labor-intensive and time-consuming nature of RFLP analysis led to the development of PCR-based markers such as RAPDs and AFLPs, which allowed for quicker and more efficient genotyping. The advent of microsatellites (SSRs) marked a significant advancement due to their high polymorphism and ease of use in PCR-based assays (Ni et al., 2002). More recently, the focus has shifted towards SNPs and genotyping by sequencing (GBS), which offer high-throughput and ultra-high-throughput capabilities, making them suitable for large-scale genomic studies. The integration of modern transcriptomic and functional markers has further enhanced the resolution and applicability of molecular markers in plant genomics (Grover and Sharma, 2016). 2.3 Advantages of using molecular markers in plant genomics Molecular markers offer several advantages in plant genomics. They provide a stable, cost-effective, and efficient means of assessing genetic diversity, which is crucial for germplasm conservation and breeding programs (Ni et al., 2002). For example, microsatellite markers have been shown to detect a high degree of polymorphism, making them ideal for evaluating genetic variation among rice cultivars and wild species. Additionally, molecular markers facilitate the identification and introgression of valuable traits from wild species into cultivated varieties, thereby enhancing crop improvement efforts (Brondani et al., 2003; Fang et al., 2011). They also enable precise phylogenetic analysis and species classification, as demonstrated by the use of genome-specific repetitive sequences in the genus Oryza to classify unknown species and study genome evolution. Furthermore, the development of diagnostic SNP markers has improved the accuracy of species identification and quality control in breeding programs (Gouda et al., 2021). Overall, molecular markers are indispensable tools in plant genomics, offering numerous benefits for research and practical applications. 3 Commonly Used Molecular Markers inOryza Genomics 3.1 Simple sequence repeats (SSRs) Simple Sequence Repeats (SSRs), also known as microsatellites, are short, tandemly repeated DNA sequences that are widely distributed throughout the genome. They are highly polymorphic due to variations in the number of repeat units, making them valuable for genetic mapping, population genetics, and phylogenetic studies. In Oryza sativa, SSRs have been extensively utilized to enhance the resolution of genetic maps and to study genetic diversity. For instance, a study identified 57.8 Mb of rice DNA sequence to determine the frequency and distribution of SSRs, categorizing them into Class I (hypervariable) and Class II (potentially variable) markers (Figure 1) (Temnykh et al., 2001; Tabassum et al., 2022; Ma et al., 2024). Another research effort developed 200 Class I SSR markers, integrating them into the existing microsatellite map of rice, thus providing links between
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