Rice (Oryza sativa L) is a staple food for over half of the world's population and serves as a model organism for plant biology research. The genus Oryza includes two domesticated species, O. sativa and O. glaberrima, and 22 wild species, representing a significant reservoir of genetic diversity that is crucial for crop improvement and food security (Zhang et al., 2014). The wild species of Oryza, with their untapped genetic potential, are essential for breeding programs aimed at enhancing disease resistance, stress tolerance, and yield.

The advent of genomics has revolutionized plant research, providing comprehensive insights into genome structure, function, and evolution. The sequencing of the rice genome, particularly the high-quality map-based sequence of O. sativa ssp. japonica 'Nipponbare', has been a landmark achievement, offering a valuable resource for comparative genomic studies and agricultural productivity improvements. Genomic tools such as bacterial artificial chromosome (BAC) libraries, genome-wide association studies (GWAS), and whole-genome sequencing have facilitated the identification of genetic variations and their association with important agronomic traits (Sakai et al., 2014). These advancements enable the exploration of genetic diversity and evolutionary mechanisms within the Oryza genus, providing a foundation for future crop improvement efforts.

This systematic study aims to explore the genomic diversity within the Oryza genus by analyzing various genomic resources and studies. By examining the genetic architecture of both cultivated and wild rice species, we seek to understand the extent of genetic variation and its implications for rice breeding and conservation. The research will cover the construction and analysis of BAC libraries, genome-wide association mapping, and the sequencing of multiple rice genomes to provide a comprehensive overview of the genetic diversity present in the Oryza genus.

In addition to exploring genomic diversity, this study will analyze the evolutionary mechanisms that have shaped the Oryza genus. By comparing the genomes of different Oryza species, we aim to identify specific genetic changes associated with adaptation, speciation, and domestication. The research will highlight the role of natural selection, gene duplication, and structural variations in driving the evolutionary processes within the genus. Understanding these mechanisms will provide insights into the evolutionary history of rice and inform strategies for utilizing wild genetic resources in rice improvement programs.

1 Literature Review

1.1 Classification and distribution of Oryza genus

The genus Oryza comprises approximately 24 species, including two cultivated species, Oryza sativa and Oryza glaberrima, and 22 wild species. These species are distributed across various geographical regions and ecological environments, reflecting a wide range of adaptations (Figure 1) (Stein et al., 2018). The genus is divided into ten distinct genome types, six diploid and four polyploid, with genome sizes varying significantly from 357 Mbp in Oryza glaberrima to 1283 Mbp in the polyploid Oryza ridleyi. The wild species of Oryza are particularly valuable as they harbor a reservoir of agriculturally important genes that can be utilized for crop improvemen.

Stein et al. (2018) provides insights into the evolutionary timeline and biogeography of rice species, which is crucial for understanding genetic diversity and guiding rice breeding programs to enhance crop resilience and productivity. The figure presents a study on the evolutionary history and geographic distribution of Oryza species, the genus to which rice belongs. Panel (a) maps the distribution of various Oryza species and Leersia perrieri across the globe, highlighting distinct geographic regions for each species. For instance, O. glumaepatula is found in South America, while O. nivara and O. rufipogon are primarily located in Asia. Figure 1Panel (b) depicts a phylogenetic tree illustrating the evolutionary divergence among these species over time. Key divergence events are highlighted, such as the fixation of Oryza species at 15 million years ago (mya), the divergence between AA and BB genomes at approximately 6.76 mya, and the divergence within Asian rice species around 0.55 mya (Stein et al., 2018).

1.2 History and current status of rice genome research

Early genome research in rice focused on the sequencing of Oryza sativa, which has served as a model system for plant biology due to its relatively small genome size and economic importance. The completion of the rice genome sequence marked a significant milestone, enabling functional characterization and comparative genomic studies within the genus Oryza. Modern genomics technologies, such as single-molecule real-time (SMRT) sequencing, 10× Genomics, and Hi-C technologies, have further advanced our understanding of rice genomics. These technologies have facilitated high-quality de novo assemblies of wild rice genomes, revealing insights into the genomic basis of rice adaptation and domestication (Chen et al., 2019). Comparative genomic analyses have identified numerous genomic variants and structural variations that contribute to the diversity and evolution of rice species.

1.3 Current status of genomic diversity research

Genomic diversity research in the Oryza genus has employed various diversity indicators, such as single nucleotide polymorphisms (SNPs), simple sequence repeats (SSRs), and linkage disequilibrium (LD) patterns. These indicators have been used to assess genetic diversity within and between different rice populations. For instance, a study using 176 SSR markers revealed significant molecular diversity and polymorphism among three groups of rice germplasm accessions, including domesticated and wild relatives. The analysis of molecular variance and principal coordinates analysis further highlighted the genetic differentiation among these groups. Additionally, the study of transposable elements has shown that these elements play a crucial role in genome size variation and structural evolution within the Oryza genus. The identification of lineage-specific gene expansions and contractions has provided insights into the adaptive evolution of rice species to diverse ecological niches (Li et al., 2020).

The classification and distribution of the Oryza genus, the advancements in rice genome research, and the ongoing studies on genomic diversity collectively enhance our understanding of the evolutionary mechanisms and genetic diversity within this important genus. These insights are crucial for the continued improvement and conservation of rice as a vital global food resource.

2 The Structure and Function of the Rice Genome

2.1 Basic structure of rice genome

The rice genome, particularly that of Oryza sativa, is composed of 12 chromosomes, which collectively harbor a diverse array of genes essential for various biological functions (Stein et al., 2018). The genome structure is characterized by a high degree of conservation across different species within the Oryza genus, despite the presence of lineage-specific variations and chromosomal rearrangements. Gene distribution within the rice genome is not uniform; certain regions are densely packed with genes, while others are more sparsely populated. This distribution is influenced by evolutionary processes such as gene duplication and transposon activity, which contribute to the functional diversification of the genome. The rice genome also exhibits significant polymorphism and linkage disequilibrium, which are crucial for understanding the genetic basis of traits and for crop improvement.

2.2 Genomic annotation and functional prediction

Genomic annotation in rice involves the identification and characterization of genes and other functional elements within the genome. This process typically employs a combination of computational and experimental approaches. Methods such as comparative genomics, transcriptomics, and proteomics are used to predict gene functions and validate their roles. Comparative genomic analyses between different Oryza species have been particularly useful in identifying conserved and lineage-specific genes, as well as in understanding the evolutionary dynamics of 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).

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 446 O. rufipogon accessions 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 Oryza AA 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, lineage-specific genes, and the evolution of agriculturally important genes on phenotype diversity and adaptation. The identification of new haplotypes and functionally coupled disease resistance genes in domesticated and wild rice relatives further underscores the role of natural and artificial selection in shaping the genomic variation of cultivated rice (Yu et al., 2023).

5 Research Methods

5.1 Sample collection and genome sequencing

Sample collection and genome sequencing are fundamental steps in understanding the genomic diversity and evolutionary mechanisms in the Oryza genus. Various studies have employed different strategies to collect samples and sequence genomes. For instance, in the study by Stein et al. (2018), 13 reference genomes spanning the Oryza species tree were sequenced to explore genetic conservation and turnover across the genus. Similarly, another study utilized 42 genotypes, including wild and cultivated species, to determine genetic diversity using inter simple sequence repeat (ISSR) polymorphism. The collection of samples from diverse geographical locations and different species within the genus ensures a comprehensive analysis of genomic diversity.

5.2 Data analysis and processing

Data analysis and processing involve several computational and statistical methods to interpret the sequenced genomic data. Comparative genomics is a powerful tool used to decipher gene and genome evolution. For example, comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes revealed highly conserved gene colinearity and structure, providing insights into gene function and genome evolution. Additionally, studies have employed phylogenetic analyses to understand the evolutionary relationships among different Oryza species. The use of highly variable regions of chloroplast DNA has been particularly effective in elucidating these relationships with fine resolution. Advanced bioinformatics tools and software are crucial in processing large datasets and identifying significant genetic variations (Abdullah-Zawawi et al., 2021).

5.3 Gene function validation experiment

Gene function validation experiments are essential to confirm the roles of specific genes identified through genomic analyses. These experiments often involve functional genomics approaches such as gene knockouts, overexpression studies, and phenotypic analyses. For instance, the study on gene family expansion in the Oryza genus investigated the evolutionary dynamics of gene families like F-box and NB-ARC, showing that expansions resulted from both amplification and contraction by gene losses. Functional validation of these genes can be achieved through experimental approaches that assess their impact on plant traits and responses to environmental stresses (Sha et al., 2023). Such experiments provide a deeper understanding of the functional significance of genetic variations observed in the Oryza genus.

6 Discussion

The research findings on genomic diversity and evolutionary mechanisms in the Oryza genus have profound implications for understanding rice evolution and adaptability. The studies collectively highlight the significant contribution of genomic diversity to rice evolution. For instance, the analysis of molecular diversity and polymorphism in various Oryza species has revealed substantial genetic variation, which is crucial for the evolutionary processes at both population and genomic levels. The identification of genome-wide signatures of rice domestication and heterosis has provided insights into the genetic basis of rice adaptation and the origin of cultivated rice. Furthermore, the rapid species diversification and turnover of transposons and other genomic elements have been shown to play a pivotal role in the evolutionary dynamics of the Oryza genus.

The relationship between genomic variation and rice adaptability is also well-documented. Comparative genomic analyses have identified specific genetic changes responsible for adaptations to diverse ecological niches, such as defense against pathogens and reproductive diversification. The presence of functionally coupled disease resistance genes and the identification of new haplotypes offer potential for future crop protection and improvement. Additionally, the role of transposable elements in driving genome size variation and their correlation with genome sizes across different Oryza species further underscore the importance of genomic diversity in rice adaptability (Dai et al., 2022).

Despite the significant advancements, there are limitations and shortcomings in the current research. One major limitation is the sample size. Many studies have focused on a limited number of accessions or species, which may not fully capture the genomic diversity present within the entire Oryza genus. For example, the study on genome size variation included only 166 accessions from 16 non-AA genome Oryza species, which may not be representative of the entire genus.

Another limitation lies in the analysis methods. While advanced sequencing technologies have been employed, there are still challenges in accurately assembling and annotating complex genomes, particularly those with high levels of repetitive elements and structural variations. The reliance on single reference genomes for comparative analyses may also overlook the extensive genomic and allelic diversity within the genus. Additionally, the detection of linkage disequilibrium and marker-trait associations may be influenced by the choice of markers and the resolution of genome-wide scans (Li et al., 2020).

Future research should focus on addressing these limitations by leveraging the development of genomics technology and exploring new prospects for rice genome research. The integration of high-quality de novo assemblies and long-read sequencing technologies can provide more comprehensive and accurate genomic data, facilitating the discovery of novel genetic elements and structural variations. Expanding the sample size to include a broader range of Oryza species and accessions will enhance the understanding of genomic diversity and its role in rice evolution and adaptability.

Moreover, the establishment of comprehensive genomic databases, such as OryzaGenome, can serve as valuable resources for genotype-phenotype association studies and functional analyses. Future research should also focus on the functional characterization of identified genes and genomic elements, particularly those involved in stress responses, reproductive processes, and disease resistance. The application of integrated genomic approaches and comparative phylogenomics will further elucidate the molecular mechanisms underlying rice evolution and provide new opportunities for crop improvement and conservation of wild rice germplasm.

7 Concluding Remarks

The genus Oryza, encompassing both domesticated and wild rice species, has been extensively studied to understand its genomic diversity and evolutionary mechanisms. Key research achievements include the identification of significant genetic conservation, turnover, and innovation across the genus. For instance, the study of 13 reference genomes has highlighted rapid species diversification and the emergence of novel elements such as transposons and new coding and noncoding genes. Additionally, the analysis of molecular diversity and linkage disequilibrium patterns in various Oryza germplasm accessions has provided insights into the genetic structure and evolutionary processes within the genus.

The development of comprehensive genomic resources, such as the Rice TE database (RiTE-db), has facilitated the annotation and comparative analysis of transposable elements across multiple Oryza species. Furthermore, the sequencing and analysis of wild and cultivated rice genomes have shed light on the domestication processes and heterosis in rice, revealing genome-wide signatures and the origin of cultivated rice. The Oryza Map Alignment Project (OMAP) has also contributed significantly by establishing a genus-wide comparative framework, highlighting the impact of structural variations on genome diversity.

The application of genomic research in rice breeding has profound implications for the future of agriculture. The comprehensive genomic resources developed for the Oryza genus provide a valuable foundation for leveraging genetic diversity from wild relatives to improve cultivated rice varieties. For example, the construction of bacterial artificial chromosome (BAC) libraries representing the 10 genome types of Oryza has enabled the exploration of agriculturally important genes from wild species. These resources are crucial for maintaining a safe and secure food supply in the face of global challenges such as climate change and population growth.

Moreover, the integration of genomic and phenotypic data in databases like OryzaGenome facilitates genotype-phenotype association studies, which are essential for understanding the functional and structural evolution of rice genomes. The identification of positively selected genes involved in key traits such as flower development, ripening, and stress response further underscores the potential of genomic research to enhance rice breeding programs.

The advancements in genomic research within the Oryza genus have not only deepened our understanding of rice genome diversity and evolutionary mechanisms but also provided invaluable tools and insights for future rice research and breeding efforts. Continued exploration and conservation of wild Oryza species will be essential to harness their genetic potential for the development of resilient and high-yielding rice varieties, ultimately contributing to global food security.

Acknowledgments

We would like to express our gratitude to the two anonymous peer reviewers for their critical assessment and constructive suggestions on our manuscript.

Conflict of Interest Disclosure

The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest.

References

Abdullah-Zawawi M.R., Ahmad-Nizammuddin N.F., Govender N., Harun S., Mohd-Assaad N., and Mohamed-Hussein Z.A., 2021, Comparative genome-wide analysis of WRKY, MADS-box and MYB transcription factor families in Arabidopsis and rice, Sci. Rep., 11(1): 19678.

https://doi.org/10.1038/s41598-021-99206-y

Chen E., Huang X., Tian Z., Wing R., and Han B., 2019, The genomics of Oryza species provides insights into rice domestication and heterosis, Annu. Rev. Plant. Biol., 70: 639-665.

https://doi.org/10.1146/annurev-arplant-050718-100320

Dai S., Zhu X., Hutang G., Li J., Tian J., Jiang X., Zhang D., and Gao L., 2022, Genome size variation and evolution driven by transposable elements in the genus Oryza. Front. Plant Sci., 13.

https://doi.org/10.3389/fpls.2022.921937

Li W., Li K., Huang Y., Shi C., Hu W., Zhang Y., Zhang Q., Xia E., Hutang G., Zhu X., Liu Y., Liu Y., Tong Y., Zhu T., Huang H., Zhang D., Zhao Y., Jiang W., Yuan J., Niu Y., Gao C., and Gao L., 2020, SMRT sequencing of the Oryza rufipogon genome reveals the genomic basis of rice adaptation, Commun. Biol., 3: 167.

https://doi.org/10.1038/s42003-020-0890-8

Liu Q., Liang Z., Feng D., Jiang S., Wang Y., Du Z., Li R., Hu G., Zhang P., Ma Y., Lohmann J.U., and Gu X., 2021, Transcriptional landscape of rice roots at the single-cell resolution, Mol. Plant., 14(3): 384-394.

https://doi.org/10.1016/j.molp.2020.12.014

Ohyanagi H., Ebata T., Huang X., Gong H., Fujita M., Mochizuki T., Toyoda A., Fujiyama A., Kaminuma E., Nakamura Y., Feng Q., Wang Z., Han B., and Kurata N., 2015, OryzaGenome: genome diversity database of wild Oryza species, Plant and Cell Physiology, 57(1): e1.

https://doi.org/10.1093/pcp/pcv171

Qin P., Lu H., Du H., Wang H., Chen W., Chen Z., He Q., Ou S., Zhang H., Li X., Li X., Li Y., Liao Y., Gao Q., Tu B., Yuan H., Ma B., Wang Y., Qian Y., Fan S., Li W., Wang J., He M., Yin J., Li T., Jiang N., Chen X., Liang C., and Li S., 2021, Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations, Cell, 184(13): 3542-3558.

https://doi.org/10.1016/j.cell.2021.04.046

Raza Q., Rashid M.A.R., Waqas M., Ali Z., Rana I.A., Khan S.H., Khan I.A., and Atif R.M., 2023, Genomic diversity of aquaporins across genus Oryza provides a rich genetic resource for development of climate resilient rice cultivars, BMC Plant Biol., 23(1): 172.

https://doi.org/10.1186/s12870-023-04151-9

Sakai H., Tanaka T., Antonio B., Itoh T., and Sasaki T., 2014, Chapter Five - The First Monocot Genome Sequence: Oryza sativa (Rice), Advances in Botanical Research, 69: 119-135.

https://doi.org/10.1016/B978-0-12-417163-3.00005-6

Sha G., Sun P., Kong X., Han X., Sun Q., Fouillen L., Zhao J., Li Y., Yang L., Wang Y., Gong Q., Zhou Y., Zhou W., Jain R., Gao J., Huang R., Chen X., Zheng L., Zhang W., Qin Z., Zhou Q., Zeng Q., Xie K., Xu J., Chiu T.Y., Guo L., Mortimer J.C., Boutté Y., Li Q., Kang Z., Ronald P.C., and Li G., 2023, Genome editing of a rice CDP-DAG synthase confers multipathogen resistance, Nature, 618(7967): 1017-1023.

https://doi.org/10.1038/s41586-023-06205-2

Stein J., Yu Y., Copetti D., Zwickl D., Zhang L., Zhang C., Chougule K., Gao D., Iwata A., Goicoechea J., Wei S., Wang J., Liao Y., Wang M., Jacquemin J., Becker C., Kudrna D., Zhang J., Londono C., Song X., Lee S., Sanchez P., Zuccolo A., Ammiraju J., Talag J., Danowitz A., Rivera L., Gschwend A., Noutsos C., Wu C., Kao S., Zeng J., Wei F., Zhao Q., Feng Q., Baidouri M., Carpentier M., Lasserre E., Cooke R., Farias D., Maia L., Santos R., Nyberg K., McNally K., Mauleon R., Alexandrov N., Schmutz J., Flowers D., Fan C., Weigel D., Jena K., Wicker T., Chen M., Han B., Henry R., Hsing Y., Kurata N., Oliveira A., Panaud O., Jackson S., Machado C., Sanderson M., Long M., Ware D., and Wing R., 2018, Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza, Nature Genetics, 50: 285-296.

https://doi.org/10.1038/s41588-018-0040-0

Wambugu P., Brozynska M., Furtado A., Waters D., and Henry R., 2015, Relationships of wild and domesticated rices (Oryza AA genome species) based upon whole chloroplast genome sequences, Sci. Rep. 5: 13957.

https://doi.org/10.1038/srep13957

Wang C., and Han B., 2022, Twenty years of rice genomics research: From sequencing and functional genomics to quantitative genomics, Mol. Plant., 15(4): 593-619.

https://doi.org/10.1016/j.molp.2022.03.009

Yu Z., Chen Y., Zhou Y., Zhang Y., Li M., Ouyang Y., Chebotarov D., Mauleon R., Zhao H., Xie W., McNally K.L., Wing R.A., Guo W., and Zhang J., 2023, Rice Gene Index: A comprehensive pan-genome database for comparative and functional genomics of Asian rice, Mol. Plant., 16(5): 798-801.

https://doi.org/10.1016/j.molp.2023.03.012

Zhang Q., Zhu T., Xia E., Shi C., Liu Y., Zhang Y., Liu Y., Jiang W., Zhao Y., Mao S., Zhang L., Huang H., Jiao J., Xu P., Yao Q., Zeng F., Yang L., Gao J., Tao D., Wang Y., Bennetzen J., and Gao L., 2014, Rapid diversification of five Oryza AA genomes associated with rice adaptation, PNAS, 111(46): E4954 - E4962.

https://doi.org/10.1073/pnas.1418307111