Pangenome Analysis of Vietnamese Rice Landraces: Towards the Identification of Unique Genomic Regions for Rice Improvement

Abstract

Rice (Oryza sativa L.) is an important food crop, exhibits remarkable genetic diversity across its indica and japonica subgroups, reflecting extensive adaptive evolution and selective breeding. While high-quality single-reference genomes have advanced rice genomics research, they inherently fail to capture the full spectrum of genetic variation within the species. Pangenome construction addresses this limitation by encompassing core, variable, and unique genomic regions. Vietnam, with its diverse geography and climate, harbors a rich repository of native and traditional rice landraces, representing an invaluable genetic resource. In this study, the first pangenome for Vietnamese rice landraces was constructed to comprehensively characterize their genetic landscape and uncover unique genomic regions. The pangenome was constructed using 20 geographically diverse Vietnamese rice landrace accessions, employing an iterative mapping and assembly approach with the IRGSP-1.0 as the base reference genome. The resulting pangenome consisted of 386.89 Mb, with 13.64 Mb contributed by novel sequences derived from Vietnamese rice landraces, of which 1.59 Mb (11.67%) constituted repetitive elements. Annotation of the entire pangenome revealed 37,292 genes, categorized into 33,710 core genes, 3,560 dispensable genes, and 22 unique genes. Notably, 673 genes were newly annotated from non-reference contigs, representing genomic regions absent in the IRGSP-1.0 reference but present in Vietnamese rice. Functional enrichment analysis indicated that core genes are vital for fundamental biological processes like plant growth, development, and stress response, while dispensable genes play critical roles in environmental adaptation, stress signaling, and regulatory flexibility, essential for local adaptation. We identified 33,758 genes conserved across all 20 Vietnamese rice landraces, with 3,570 of these associated with agronomically important traits. These conserved genes are fundamentally involved in macromolecular biosynthesis, metabolism, environmental sensing, and cellular homeostasis, highlighting their essential roles in maintaining cellular processes and influencing yield-related traits such as panicle length, grain size, and tiller number. The consistent presence of these genes underscores the potential of traditional Vietnamese germplasms for breeding programs focused on yield improvement and stress adaptation for food security. Furthermore, subspecies-specific analyses revealed distinct functional enrichments. Thirteen indica-specific conserved genes were identified, though none were directly linked to agronomically important traits. Conversely, among 68 japonica-specific conserved genes, three were associated with multiple agronomic traits and functionally enriched in pathways related to phytoalexin metabolism and biosynthesis, indicating their role in antimicrobial defense. Additionally, 243 japonica accessory genes, absent in all indica landraces, included 20 genes critical for yield and morphology, such as OsJAZ13 for panicle length and OsCDKF;2 for 1000-seed weight. Among 94 indica accessory genes, OsGLP1 was linked to cold tolerance and OsLOL1 to blast disease resistance, suggesting their contribution to stress adaptation. Comparative analysis of gene presence/absence variation (PAV) demonstrated significant functional divergence; while core genes exhibited broad functional distribution, japonica-specific gene sets showed pronounced enrichment in stress response traits, supporting the role of PAV in environmental adaptation. This study provides a valuable genomic resource for Vietnamese rice breeding programs, demonstrating how PAV contributes significantly to both genetic diversity and functional divergence, thereby offering invaluable insights for future breeding efforts aimed at enhancing climate resilience and ensuring food security.

Rice (Oryza sativa L.) is an important food crop, exhibits remarkable genetic diversity across its indica and japonica subgroups, reflecting extensive adaptive evolution and selective breeding. While high-quality single-reference genomes have advanced rice genomics research, they inherently fail to capture the full spectrum of genetic variation within the species. Pangenome construction addresses this limitation by encompassing core, variable, and unique genomic regions. Vietnam, with its diverse geography and climate, harbors a rich repository of native and traditional rice landraces, representing an invaluable genetic resource. In this study, the first pangenome for Vietnamese rice landraces was constructed to comprehensively characterize their genetic landscape and uncover unique genomic regions. The pangenome was constructed using 20 geographically diverse Vietnamese rice landrace accessions, employing an iterative mapping and assembly approach with the IRGSP-1.0 as the base reference genome. The resulting pangenome consisted of 386.89 Mb, with 13.64 Mb contributed by novel sequences derived from Vietnamese rice landraces, of which 1.59 Mb (11.67%) constituted repetitive elements. Annotation of the entire pangenome revealed 37,292 genes, categorized into 33,710 core genes, 3,560 dispensable genes, and 22 unique genes. Notably, 673 genes were newly annotated from non-reference contigs, representing genomic regions absent in the IRGSP-1.0 reference but present in Vietnamese rice. Functional enrichment analysis indicated that core genes are vital for fundamental biological processes like plant growth, development, and stress response, while dispensable genes play critical roles in environmental adaptation, stress signaling, and regulatory flexibility, essential for local adaptation. We identified 33,758 genes conserved across all 20 Vietnamese rice landraces, with 3,570 of these associated with agronomically important traits. These conserved genes are fundamentally involved in macromolecular biosynthesis, metabolism, environmental sensing, and cellular homeostasis, highlighting their essential roles in maintaining cellular processes and influencing yield-related traits such as panicle length, grain size, and tiller number. The consistent presence of these genes underscores the potential of traditional Vietnamese germplasms for breeding programs focused on yield improvement and stress adaptation for food security. Furthermore, subspecies-specific analyses revealed distinct functional enrichments. Thirteen indica-specific conserved genes were identified, though none were directly linked to agronomically important traits. Conversely, among 68 japonica-specific conserved genes, three were associated with multiple agronomic traits and functionally enriched in pathways related to phytoalexin metabolism and biosynthesis, indicating their role in antimicrobial defense. Additionally, 243 japonica accessory genes, absent in all indica landraces, included 20 genes critical for yield and morphology, such as OsJAZ13 for panicle length and OsCDKF;2 for 1000-seed weight. Among 94 indica accessory genes, OsGLP1 was linked to cold tolerance and OsLOL1 to blast disease resistance, suggesting their contribution to stress adaptation. Comparative analysis of gene presence/absence variation (PAV) demonstrated significant functional divergence; while core genes exhibited broad functional distribution, japonica-specific gene sets showed pronounced enrichment in stress response traits, supporting the role of PAV in environmental adaptation. This study provides a valuable genomic resource for Vietnamese rice breeding programs, demonstrating how PAV contributes significantly to both genetic diversity and functional divergence, thereby offering invaluable insights for future breeding efforts aimed at enhancing climate resilience and ensuring food security.