Molecular Plant Breeding 2024, Vol.15, No.5, 295-307 http://genbreedpublisher.com/index.php/mpb 295 Feature Review Open Access Tailor-Made Rice: Using Haplotype Analysis to Design High-Yielding Varieties JuanLi 1,2,3, Hui Zhang1,3, QianZhu1,2,3,YanboXia4, Zilin Duan5, Jiancheng Wen1,2, Lijuan Chen1,2,3 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 Corresponding email: chenlijuan@hotmail.com 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 Copyright © 2024 Li et al., 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. Preferred citation for this article: 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) Abstract 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. Keywords Haplotype analysis; Rice breeding; Genomic tools; High-yielding varieties; Sustainable agriculture 1 Introduction Rice serves as a staple food for more than half of the world’s population, making its yield and quality essential for global food security. Traditional breeding methods have been used extensively to enhance rice varieties. While these methods have achieved some successes, they often struggle to meet the increasing demands for higher yields and better quality. These conventional methods typically rely on phenotypic selection, which can be time-consuming and imprecise due to the complex nature of genetic traits affecting yield and quality. Moreover, the genetic gains from traditional breeding are generally incremental and insufficient to match the needs of a rising global population and changing environmental conditions, such as climate change and the necessity for sustainable agricultural practices. This slow pace of progress highlights the limitations of traditional methods in addressing urgent agricultural challenges (Abbai et al., 2019; Varshney et al., 2021a; Wang et al., 2023). Haplotype is the combination of a series of genetic mutations that coexist on a single chromosom, contains a complete set of genetic information that is fundamental to the description of an individual genome and an essential aspect of genomic research. Haplotype analysis is a genetic research method for analyzing specific combinations of a set of continuous genetic markers (e.g., SNP) at a locus. These markers can come from different loci on the same chromosome and form haplotypes that are used to describe genetic variation between individuals (Li et al., 2018). Haplotype analysis offers a promising alternative to traditional breeding methods by enabling more precise and efficient selection of desirable genetic traits. This approach involves the identification and utilization of superior haplotype combinations of key genes that govern important traits such as grain yield and quality. Recent studies have demonstrated the potential of haplotype analysis to uncover significant genetic variations and superior haplotypes within large rice genome panels, paving the way for the development of tailor-made rice varieties with enhanced genetic gains (Abbai et al., 2019; Wei et al., 2024). By integrating
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