Plant Gene and Traits 2024, Vol.15, No.4, 184-194 http://genbreedpublisher.com/index.php/pgt 188 4.2 Comparative analysis of marker efficiency for classification purposes Different molecular markers vary in their efficiency for species classification. For example, SSR markers have been shown to be more efficient than RAPD markers in accurately determining relationships between closely related accessions of Oryza sativa (Ravi et al., 2003). Similarly, a study comparing the transferability of microsatellite and sequence-tagged site (STS) markers across 16 Oryza species found that microsatellite markers had a higher level of polymorphism and were more effective in detecting genetic diversity compared to STS markers (Brondani et al., 2003). Another study highlighted the utility of sequence-tagged microsatellite sites (STMS) markers, which were found to be highly reproducible and effective in identifying polymorphisms among different Oryza species (Dalai et al., 2021). These findings suggest that while all marker systems have their strengths, SSR and STMS markers may offer higher efficiency for species classification in Oryza. 4.3 Limitations and challenges in species classification using molecular markers Despite their utility, molecular markers also present certain limitations and challenges in species classification. One major challenge is the partial agreement in relationships between individual accessions when different markers are used, as observed in a study comparing AFLP, isozymes, ISSR, and RAPD markers (Virk et al., 2000). Additionally, the transferability of markers across different species can be variable, with some markers showing reduced levels of genetic diversity detection, as seen with STS markers (Brondani et al., 2003). Another limitation is the potential for misidentification due to morphological similarities among closely related species, which can complicate the validation of molecular markers. Furthermore, the development and validation of new markers, such as SNPs, require extensive testing to ensure their reliability and cost-effectiveness for routine use (Gouda et al., 2021). These challenges highlight the need for careful selection and validation of molecular markers to ensure accurate species classification in Oryza genomics. 5 Case Studies 5.1 A Specific case of using ssr markers to construct a phylogenetic tree of the genus Oryza Simple sequence repeats (SSRs) have been extensively used in constructing phylogenetic trees due to their high polymorphism and codominant inheritance. In the genus Oryza, SSR markers have been particularly effective. For instance, a study on the rice genome (Oryza sativa L.) identified a high frequency of SSRs, with Class I SSRs occurring every 16 kb in continuous genomic sequences and Class II SSRs every 1.9 kb. This high density of SSRs allows for detailed genetic mapping and phylogenetic analysis. The study developed 200 Class I SSR markers, which were integrated into the existing microsatellite map of rice, providing a robust framework for phylogenetic studies (Temnykh et al., 2001). This integration facilitates the construction of a detailed phylogenetic tree, revealing the genetic relationships within the genus Oryza. 5.2 Case studies on phylogeny reconstruction using different markers Phylogenetic reconstruction in plants has utilized various molecular markers beyond SSRs. For example, a study on Cryptomeria japonica developed EST-SSR markers from expressed sequence tags, which are useful for genome analysis due to their abundance and polymorphism (Ueno et al., 2012). These markers were found to be less polymorphic than genomic SSRs but still valuable for phylogenetic studies. Another study on Cucurbita pepo used SSR markers to construct a genetic linkage map, demonstrating high inter-species transferability and polymorphism (Gong et al., 2008). This map included 178 SSRs and provided insights into the genetic relationships within the genus Cucurbita. Additionally, a study on Picea abies highlighted the use of both codominant and dominant SSR markers for population studies and phylogenetic analysis, despite the challenges posed by null alleles and dominant markers (Yazdani et al., 2003). These examples illustrate the versatility of different molecular markers in phylogenetic reconstruction across various plant species. 5.3 Insights gained from phylogenetic studies inOryza Phylogenetic studies in the genus Oryza have provided significant insights into the genetic diversity and evolutionary relationships among species. The use of SSR markers has been particularly informative. For instance, the high degree of allelic variation revealed by SSR markers in rice has been attributed to replication slippage and unequal crossing-over during meiosis, which contribute to the genetic diversity observed within the genus (Kalia
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