Plant Gene and Traits 2024, Vol.15, No.4, 184-194 http://genbreedpublisher.com/index.php/pgt 184 Research Report Open Access Molecular Markers in Oryza Genomics: Tools for Species Classification and Phylogeny Danyan Ding Institute of Life Sciences, Jiyang Colloge of Zhejiang A&F University, Zhuji, 311800, Zhejiang, China Corresponding email: 723822780@qq.com Plant Gene and Trait, 2024, Vol.15, No.4 doi: 10.5376/pgt.2024.15.0019 Received: 29 Jun., 2024 Accepted: 31 Jul., 2024 Published: 08 Aug., 2024 Copyright © 2024 Ding, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Ding D.Y., 2024, Molecular markers in Oryza genomics: tools for species classification and phylogeny, Plant Gene and Trait, 15(4): 184-194 (doi: 10.5376/pgt.2024.15.0019) Abstract The study explored the utilization of various molecular markers to classify and understand the phylogenetic relationships among Oryza species. The genus Oryza, which includes the globally significant crop rice (Oryza sativa), comprises 22 species with diverse genetic backgrounds. This research evaluates the effectiveness of different molecular markers, including SNPs, AFLPs, ISSRs, and microsatellites, in revealing genetic diversity and phylogenetic relationships. SNP markers, particularly those developed using DArTseq technology, have shown high efficiency in species identification and quality control genotyping. AFLP markers have been instrumental in elucidating the polyphyletic evolution of Oryza, indicating multiple independent lineages. ISSR markers have provided insights into the genetic diversity and evolutionary pathways of various Oryza genomes. Microsatellite markers, especially those derived from miRNA genes, have proven to be highly polymorphic and useful for genotyping applications. The study underscores the importance of integrating multiple molecular markers to achieve a comprehensive understanding of the genetic diversity and evolutionary history of Oryza species, which is crucial for effective germplasm conservation and breeding programs. Keywords Oryza genomics; Molecular markers; Species classification; Phylogeny; Genetic diversity 1 Introduction The genus Oryza, encompassing both wild and cultivated rice species, is of paramount importance in global agriculture. Rice (Oryza sativa) serves as the staple food for over half of the world's population, underscoring its critical role in food security (Ganie and Mondal, 2015; Song et al., 2017). The genus includes 24 species with 11 different genome types, providing a vast genetic reservoir that is invaluable for the genetic improvement of rice cultivars. Wild species of Oryza, in particular, represent an enormous gene pool that can be harnessed for enhancing disease resistance, stress tolerance, and other agronomic traits in cultivated rice (Stein et al., 2018; Brondani et al., 2003). Accurate species classification and understanding the phylogenetic relationships within the Oryza genus are essential for effective utilization of its genetic resources. Phylogenetic studies reveal the evolutionary pathways and genetic diversity among species, which are crucial for breeding programs and conservation efforts (Joshi et al., 2000). For instance, the identification of species-specific markers and the resolution of phylogenetic relationships help in tracing the lineage-specific emergence and turnover of novel genetic elements, including transposons and potential new coding and noncoding genes (Stein et al., 2018). Such insights are vital for developing strategies to introgress beneficial traits from wild species into cultivated varieties (Tabassum et al., 2022). Molecular markers are indispensable tools in genomics for species identification, genetic diversity analysis, and phylogenetic studies. Various types of molecular markers, such as chloroplast DNA barcodes, amplified fragment length polymorphisms (AFLP), simple sequence repeats (SSRs), and inter simple sequence repeats (ISSR), have been employed to elucidate genetic relationships and species divergence within the Oryza genus (Joshi et al., 2000). For example, chloroplast genomic resources have been developed to provide high-resolution species discrimination and phylogenetic analysis, identifying variable regions that serve as reliable DNA barcodes (Song et al., 2017). Similarly, genome-wide development of novel markers, such as miRNA-based SSRs and InDel markers, has facilitated the genetic analysis and breeding of rice by revealing polymorphisms and genetic
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