Genome Assembly and Annotation of Vietnamese Rice Lines with Diverse Life-Cycle Durations
by
, , , ,
Sara Franco Ortega
1,2,*,†, 
Luu Thi Thuy
3,†,
Nguyen Trong Khanh
3,
Le Thu Hang
3,
Tran Thi Yen
3,
Le Thi Ngoan
3,
Le Thi Thanh
3,
Pham Thien Thanh
3,
Xinhao Ouyang
4,
Wenjing Tao
4,
Sally James
2,
Lesley Gilbert
2,
Amanda M. Davis
2,
Leonardo D. Gomez
1,2,
Andrea L. Harper
1,2,
Simon J. McQueen-Mason
1,2,‡,
Duong Xuan Tu
3,* and
Seth Jon Davis
2,5,* 1
Centre for Novel Agricultural Products, University of York, York YO10 5DD, UK
2
Department of Biology, University of York, York YO10 5DD, UK
3
Field Crops Research Institute (FCRI), Hai Duong V7WM+9QM, Vietnam
4
State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
5
State Key Laboratory of Crop Stress Biology, School of Life Sciences, Henan University, Kaifeng 475004, China
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
‡
Deceased.
DNA 2024, 4(3), 239-251; https://doi.org/10.3390/dna4030016
Submission received: 18 June 2024
/
Revised: 19 July 2024
/
Accepted: 26 July 2024
/
Published: 1 August 2024
Simple Summary
Four Vietnamese breeding lines (2 Japonica and 2 Indica) were directly compared in field settings for phenotypic traits associated with yield. These Vietnamese rice genomes were newly de novo assembled and annotated, and a phylogenetic analysis of the phytochrome C (phyC) confirmed the positioning and diversity between the four varieties. The four lines showed enough phenotypic and genetic differences to be used as parental lines for climate-adaptation breeding programs.
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; Oryza sativa L.; Vietnam
