Juan Li^1,2,3 , Hui Zhang^1,3 , Qian Zhu^1,2,3 , Yanbo Xia⁴ , Zilin Duan⁵ , Jiancheng Wen^1,2 , Lijuan  Chen^1,2,3

1 Rice Research Institute, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
2 The Key Laboratory for Crop Production and Smart Agriculture of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
3 College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, Yunnan, China
4 Seed Management Station of Yunnan Province, Kunming, 650031, Yunnan, China
5 Yunnan Yuanfang Agricultural Science and Technology Limited Company, Kunming, 650201, Yunnan, China
Author    Correspondence author
Molecular Plant Breeding, 2024, Vol. 15, No. 5   doi: 10.5376/mpb.2024.15.0028
Received: 10 Sep., 2024    Accepted: 11 Oct., 2024    Published: 22 Oct., 2024

This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Li J., Zhang H., Zhu Q., Xia Y.B., Duan Z.L., Wen J.C., and Chen L.J., 2024, Tailor-made rice: using haplotype analysis to design high-yielding varieties, Molecular Plant Breeding, 15(5): 295-307 (doi: 10.5376/mpb.2024.15.0028)

This study explores the potential of haplotype analysis in the development of high-yielding rice varieties tailored for specific agronomic needs. Through detailed examination of genetic markers and haplotypes associated with key traits such as grain yield, quality, and resilience to environmental stresses, we demonstrate the efficacy of utilizing advanced genomic tools in rice breeding. Leveraging genome-wide association studies (GWAS) and haplotype-pheno analysis, we then identify specific haplotypes that contribute to enhanced agronomic traits, offering significant improvements in both yield and stability under varying climatic conditions. The integration of next-generation sequencing and machine learning in haplotype analysis has further refined the selection process, enabling the precise development of rice varieties that are not only productive but also suited to diverse environmental challenges and consumer preferences. We also discuss the broader implications of haplotype-based breeding (HBB) techniques, including their role in promoting sustainable agricultural practices and enhancing food security globally. These findings underline the transformative potential of haplotype analysis in rice genomics, paving the way for future innovations in crop improvement.

Haplotype analysis; Rice breeding; Genomic tools; High-yielding varieties; Sustainable agriculture