Genome Assembly and Annotation of Vietnamese Rice Lines with Diverse Life-Cycle Durations

Abstract

This study begins by examining phenotypic variations in field growth among four parental Vietnamese rice lines, consisting of two Indica (PD211/GL37) and two Japonica (J23/SRA2-1) cultivars, which differ in life-cycle durations. Their phenotypic observations revealed both similarities and differences in growth patterns and field responses, setting the stage for further genomic investigation. We then focused on the sequencing and de novo genome assembly of these lines using high-coverage Illumina sequencing and achieving pseudochromosome assemblies ranging between 379 Mbp and 384 Mbp. The assemblies were further enhanced by annotation processes, designating between 44,427 and 48,704 gene models/genome. A comparative genomic analysis revealed that the Japonica varieties (J23/SRA2-1) exhibited more genetic similarity than the Indica varieties (PD211/GL37). From this, a phylogenetic analysis on the phytochrome C (phyC) gene distinctly positions the Indica and Japonica lines within their respective clades, affirming their genetic diversity and lineage accuracy. These genomic resources will pave the way for identifying quantitative trait loci (QTLs) critical for developing rice cultivars with shorter life cycles, thus enhancing resilience to adverse climatic impacts in Vietnam. This study provides a foundational step towards leveraging genomic data for rice breeding programs aimed at ensuring food security in the face of climate change.

Keywords

• phenotypic traits
• genome assembly
• Illumina
• <i>Oryza sativa</i> L.
• Vietnam