Genomics and Applied Biology 2024, Vol.15, No.1, 54-63 http://bioscipublisher.com/index.php/gab 59 Furthermore, the OryzaGenome database integrates SNP data and genomic variation information for wild Oryza species, offering a valuable resource for genotype-phenotype association studies. This database includes genotype information for 446O. rufipogonaccessions and provides tools for precise inspection of each variant. 3.3 Genomic structural variation Structural variations, such as fragment duplications, deletions, and inversions, play a significant role in shaping the genomes of rice species. These variations can impact gene function and contribute to the evolutionary dynamics of the Oryza genus. Comparative genomic analyses have revealed the dynamic evolution of Oryza genomes, with transposable elements mediating massive replacement of intergenic space, gene disruption, and gene/gene fragment movement. Long Terminal Repeat (LTR) retrotransposons, in particular, have been identified as major contributors to genome size variation and structural changes (Qin et al., 2021). Additionally, the rapid diversification of five Oryza AA genomes has been associated with significant structural variations, including segmental duplications and gene family turnover, particularly in defense-related genes (Qin et al., 2021). These structural changes are crucial for the adaptation of rice species to different ecological niches and environmental conditions. The comparative analysis of genomic diversity in the Oryza genus involves genomic sequence alignment, measurement of genetic diversity using various markers, and the study of structural variations. These approaches provide a comprehensive understanding of the evolutionary mechanisms driving the diversity and adaptation of rice species. 4 The Evolutionary Mechanism of the Rice Genus 4.1 Phylogenetic evolution of the rice genus The phylogenetic evolution of the rice genus, Oryza, has been extensively studied using various molecular systematics methods, including the construction and analysis of phylogenetic trees. Whole chloroplast genome sequences have been utilized to elucidate the evolutionary and phylogenetic relationships within the AA genome Oryza species, providing a well-resolved and strongly supported phylogeny. Amplified fragment length polymorphism (AFLP) markers have also been employed to study species relationships, revealing a polyphyletic path of evolution within the genus Oryza. Additionally, simple sequence repeats (SSR) and their flanking regions in the mitochondrial and chloroplast genomes have been analyzed to gain new insights into phylogenetic relationships among Oryza species. These studies collectively contribute to a robust understanding of the phylogenetic evolution of the rice genus (Wambugu et al., 2015). 4.2 Genomic evolutionary dynamics The genomic evolutionary dynamics of the Oryza genus involve processes such as genome replication, polyploidization, gene loss, and acquisition. The genus Oryza has experienced ancient whole genome duplications, common to all grasses, and more conserved segmental duplications, such as those between the distal regions of chromosomes 11 and 12. Comparative analyses of large genomic regions and whole-genome sequences have revealed molecular mechanisms involved in genome size variation, gene movement, and the transition of euchromatin to heterochromatin. The prevalence of transposon activity and the removal of transposable elements by unequal recombination or illegitimate recombination are significant factors contributing to the expansion or contraction of Oryza genomes (Liu et al., 2021). Furthermore, the genus Oryza consists of both recently formed and older allopolyploid species, providing insights into the process of diploidization and the temporal evolutionary dynamics of polyploid genomes. 4.3 Environmental adaptation and genomic variation Environmental adaptation and genomic variation in the Oryza genus are driven by both natural and artificial selection. The rapid diversification of five OryzaAA genomes has been associated with rice adaptation to different environments across four continents, highlighting specific genetic changes related to defense against pathogens and reproductive diversification. This adaptation is reflected in the high instability of defense-related genes and the expansion or contraction of gene families, which have led to morphological and reproductive diversification. Additionally, the genus Oryza has been a model system for studying the impact of structural variation,
RkJQdWJsaXNoZXIy MjQ4ODYzMg==