From Gene-Based Breeding to Haplotype-Based Breeding for Rice (Oryza sativa) Improvement in the Genomics Era
8 affiliations
- 1Faculty of Biotechnology, Vietnam National University of Agriculture, Hanoi City 100000, Vietnam
- 2Faculty of Agricultural Technology, University of Engineering and Technology, Vietnam National University Hanoi, Hanoi City 100000, Vietnam
- 3VinUni Bigdata Research Institute, VinUniversity, Hanoi City 100000, Vietnam
- 4Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409, USA
- 5Department of Integrative Agriculture, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain P.O. Box 15551, Abu Dhabi, United Arab Emirates
- 6Agricultural Genetics Institute, Vietnam Academy of Agricultural Sciences, Hanoi City 100000, Vietnam
- 7Department of Environmental Science, Central University of Kerala, Kasaragod 671316, India
- 8Institute of Scientific Research and Applications, Hanoi Pedagogical University 2, Phuc Yen City 35000, Vietnam
Abstract
Rice (Oryza sativa L.) improvement increasingly uses genome-scale variation, but breeding decisions remain trait-oriented and depend on genetic architecture, recipient background, target environment, and selection resources. This review assesses when phased haplotype information adds value beyond causal-gene markers, single-nucleotide polymorphism assays, phenotypic selection, and genomic prediction. Reported configurations for yield, grain quality, nutrition, biotic resistance, and abiotic-stress adaptation are evaluated according to population structure, carrier frequency, effect uncertainty, haplotype-by-background interaction, haplotype-by-environment interaction, linkage drag, transferability, assay availability, and current breeding use. A three-tier hierarchy classifies configurations as Candidate, Validated, or Breeder-Ready. Most reported favorable haplotypes remain Candidate targets, fewer have controlled genetic validation, and few sequence-defined multi-variant haplotypes have documented use in active breeding programs. Practical deployment requires stable sequence nomenclature, accessible donors, diagnostic assays, elite-background and multi-environment evaluation, cost analysis, and donor-segment recovery. Graph pangenomes, phased long-read assemblies, causal reconstruction, and prospective comparisons with current selection methods can improve future assessment. Haplotype information has greatest value when phase improves a defined breeding decision and increases target-environment performance, annual genetic gain, selection efficiency, or cultivar delivery.
Related
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BibTeX
@article{nguyen2026from,
title = {{From Gene-Based Breeding to Haplotype-Based Breeding for Rice (Oryza sativa) Improvement in the Genomics Era}},
author = {Trung Quoc Nguyen and Anh Quynh Ho and Ha Duc Chu and Nguyen Nguyen Chuong and Touhidur Rahman Anik and Gioi Huy Dong and Saad Sulieman and Nguyet Thi Minh Nguyen and Sudisha Jogaiah and Hong Viet La and Lam-Son Phan Tran},
journal = {International Journal of Molecular Sciences},
year = {2026},
month = oct,
doi = {10.3390/ijms27208972},
url = {https://www.mdpi.com/1422-0067/27/20/8972},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - From Gene-Based Breeding to Haplotype-Based Breeding for Rice (Oryza sativa) Improvement in the Genomics Era
AU - Trung Quoc Nguyen
AU - Anh Quynh Ho
AU - Ha Duc Chu
AU - Nguyen Nguyen Chuong
AU - Touhidur Rahman Anik
AU - Gioi Huy Dong
AU - Saad Sulieman
AU - Nguyet Thi Minh Nguyen
AU - Sudisha Jogaiah
AU - Hong Viet La
AU - Lam-Son Phan Tran
PY - 2026
DA - 2026/10/10
JO - International Journal of Molecular Sciences
DO - 10.3390/ijms27208972
UR - https://www.mdpi.com/1422-0067/27/20/8972
AB - Rice (Oryza sativa L.) improvement increasingly uses genome-scale variation, but breeding decisions remain trait-oriented and depend on genetic architecture, recipient background, target environment, and selection resources. This review assesses when phased haplotype information adds value beyond causal-gene markers, single-nucleotide polymorphism assays, phenotypic selection, and genomic prediction. Reported configurations for yield, grain quality, nutrition, biotic resistance, and abiotic-stress adaptation are evaluated according to population structure, carrier frequency, effect uncertainty, haplotype-by-background interaction, haplotype-by-environment interaction, linkage drag, transferability, assay availability, and current breeding use. A three-tier hierarchy classifies configurations as Candidate, Validated, or Breeder-Ready. Most reported favorable haplotypes remain Candidate targets, fewer have controlled genetic validation, and few sequence-defined multi-variant haplotypes have documented use in active breeding programs. Practical deployment requires stable sequence nomenclature, accessible donors, diagnostic assays, elite-background and multi-environment evaluation, cost analysis, and donor-segment recovery. Graph pangenomes, phased long-read assemblies, causal reconstruction, and prospective comparisons with current selection methods can improve future assessment. Haplotype information has greatest value when phase improves a defined breeding decision and increases target-environment performance, annual genetic gain, selection efficiency, or cultivar delivery.
SN - 1422-0067
ER -