Genomics and Applied Biology 2024, Vol.15, No.1, 54-63 http://bioscipublisher.com/index.php/gab 57 gene families. Functional prediction often involves the use of databases like OryzaGenome, which integrates genotype and phenotype information to facilitate the analysis of gene function and structural evolution. Additionally, techniques such as BAC (Bacterial Artificial Chromosome) library construction and analysis provide valuable resources for functional characterization and comparative studies (Zhang et al., 2014). 2.3 Repeats and transposons Repeats and transposons play a significant role in shaping the structure and function of the rice genome. The Oryza genome contains various types of repetitive elements, including LTR retrotransposons, which are the predominant class of repeats. These elements contribute to genome size variation and are involved in processes such as gene duplication and chromosomal rearrangement. Transposons, in particular, are classified into different families based on their structure and mode of transposition. They are known to drive genomic innovation by creating new gene combinations and regulatory elements. The activity of transposable elements is a key factor in the rapid diversification and adaptation of Oryza species, as they facilitate the emergence of novel genetic traits. Comparative analyses have shown that transposon activity and the removal of transposable elements through recombination are crucial mechanisms in the expansion and contraction of the rice genome (Wang and Han, 2022). 3 Comparative Analysis of Genomic Diversity in Three Oryza Genera 3.1 Genomic sequence alignment Genomic sequence alignment is a critical method for comparing the genetic makeup of different rice species within the Oryza genus. Various techniques, such as whole-genome sequencing and the construction of bacterial artificial chromosome (BAC) libraries, have been employed to achieve high-resolution alignments. The construction and analysis of 12 deep-coverage large-insert BAC libraries representing the 10 genome types of the genus Oryza have provided a comprehensive resource for comparative genomic studies. These libraries facilitate the alignment of genomic sequences across different species, enabling the identification of conserved and divergent regions (Table 1) (Ohyanagi et al., 2015). Ohyanagi et al. (2015) provides a detailed analysis of the mapping and detection of genome variants across various Oryza species and cultivars using deep next-generation sequencing (NGS). It covers several cultivars such as Os-japonica (Nipponbare), Os-indica (Guangluai-4), Os-aus (Kasalaath), and others, showcasing the number of read pairs, mapping rates, average depth, and genome coverage. Os-japonica and Os-indica demonstrate high mapping efficiency with significant genome coverage, highlighting their genomic stability. The SNP detection section reveals substantial genetic variability, especially in Os-indica and Os-aus, with over a million SNPs each. Homogeneous and heterogeneous SNP counts further elucidate genetic diversity, with Os-japonica displaying a high heterogeneous ratio. This extensive genomic data is pivotal for understanding genetic diversity within Oryza species, providing valuable insights for breeding programs aimed at enhancing crop resilience and productivity, thereby contributing to global food security and agricultural sustainability (Ohyanagi et al., 2015). Additionally, the de novo assembly of genomes from five diploid AA-genome species closely related to Oryza sativa has revealed significant structural variations, including segmental duplications and rapid gene family turnover. These alignments help in understanding the evolutionary mechanisms driving genomic diversity and adaptation in different environments. 3.2 Genomic diversity measurement Genomic diversity within the Oryza genus can be measured using various indicators such as single nucleotide polymorphisms (SNPs), insertions and deletions (Indels), and simple sequence repeats (SSRs). These markers provide insights into the genetic variation and evolutionary history of rice species.A detailed study using 176 SSR markers across three groups of rice germplasm accessions highlighted the molecular diversity and polymorphism within Oryza sativa and its wild relatives. The study reported a mean of 16 alleles per SSR marker and polymorphism information content values ranging from 0.43 to 0.91, indicating substantial genetic variation (Raza et al., 2023).
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