Plant Gene and Traits 2024, Vol.15, No.4, 184-194 http://genbreedpublisher.com/index.php/pgt 187 In Oryza, the integration of both SSR and SNP markers can provide a more comprehensive understanding of genetic variation. For example, SSRs can be used to quickly assess genetic diversity and structure, while SNPs can provide detailed insights into specific genetic loci associated with important traits (Temnykh et al., 2000). The complementary use of these markers allows researchers to leverage the strengths of each type, leading to more robust and informative genetic analyses. 4 Applications of Molecular Markers for Species Classification 4.1 Case studies of molecular markers used for classifying Oryzaspecies Molecular markers have been extensively utilized to classify and differentiate various Oryza species. For instance, a study compared the effectiveness of AFLP, isozymes, ISSR, and RAPD markers in revealing genetic diversity and discriminating between infraspecific groups of Oryza sativa germplasm. The study found that isozymes and AFLPs were most effective in classifying the germplasm into three major groups, although there were differences in the precise classifications generated by ISSR markers (Virk et al., 2000). Another study focused on the use of RAPD and SSR markers to assess genetic diversity among 40 cultivated varieties and five wild relatives of Oryza sativa. The study concluded that SSR markers provided a more definitive separation of clusters of genotypes, indicating a higher level of efficiency for accurate determination of relationships between accessions (Ravi et al., 2003). Additionally, diagnostic SNP markers developed using DArTseq technology have been validated for quality control genotyping in a collection of four rice species, demonstrating their utility in species classification (Figure 2) (Hechanova et al., 2021; Gouda et al., 2021). Figure 2 Physical locations of the polymorphic markers (Adopted from Hechanova et al., 2021) Image caption: Physical locations of the polymorphic markers. The position of each marker was mapped on the rice reference genome (Os-Nipponbare-Reference-IRGSP-1.0) with a horizontal bar. (A) All available 475 polymorphic markers between O. sativa and the other AA-genome species. The selected polymorphic markers showing polymorphism between IR24 and O. barthii (B), O. glaberrima (C), O. glumaepatula (D), O. longistaminata (E), O. meridionalis (F), O. nivara (G), O. rufipogon (H), and O. sativa subsp. japonica (I), respectively. Within a species, the common polymorphic markers among three accessions and between two accessions are highlighted by red and blue bars, respectively, and the accession-specific polymorphic markers are depicted with a black bar. (Adopted from Hechanova et al., 2021)
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