Molecular Plant Breeding 2025, Vol.16, No.5, 268-277 http://genbreedpublisher.com/index.php/mpb 268 Feature Review Open Access Haplotype-Based Breeding of Yield-Related Traits in Oryza sativa: From Genomic Insights to Field Applications Qifu Zhang, Ruchun Chen, Zhongxian Li, Jianquan Li Hier Rice Research Center, Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, Hainan, China Corresponding email: jianquan.li@hitar.org Molecular Plant Breeding, 2025, Vol.16, No.5 doi: 10.5376/mpb.2025.16.0027 Received: 11 Aug., 2025 Accepted: 13 Sep., 2025 Published: 20 Sep., 2025 Copyright © 2025 Zhang 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: Zhang Q.F., Chen R.C., Li Z.X., and Li J.Q., 2025, Haplotype-based breeding of yield-related traits in Oryza sativa: from genomic insights to field applications, Molecular Plant Breeding, 16(5): 268-277 (doi: 10.5376/mpb.2025.16.0027) Abstract This study summarizes the progress made in using haplotype analysis to investigate rice yield, reviews the role of methods such as QTL mapping, GWAS, and pan-genome in discovering genes related to yield, introduces how to identify functional haplotypes, and discusses how to prioritize them during selection. It also elaborates on several applications of haplotypes in breeding. For instance, marker-assisted selection, genomic selection, gene editing, etc. were discussed. The potential of combining multi-omics data, using artificial intelligence as predictive models, and considering the haplotypes of climate change in future molecular breeding was also explored. This study hopes to provide some theoretical and technical references for high-yield, stable-yield and climate change-adaptive rice breeding. Keywords Rice (Oryza sativa); Haplotype-based breeding; Yield-related traits; Molecular breeding; Multi-omics integration 1 Introduction The core of haplotype breeding is to identify and utilize good allele combinations. This can integrate the key genes related to yield together, improving the efficiency of breeding. Studies have found that haplotype combinations of different genotypes, especially functional haplotypes of core regulatory genes such as Ghd7, DTH8, and PRR37, can significantly improve traits such as grain count per panicle and 1000-grain weight of rice, thereby achieving high and stable yields (Sun et al., 2023; Sachdeva et al., 2024). In addition, the introduction of haplotypes from genetic resources such as wild rice also provides more materials for broadening the genetic basis of cultivated rice and discovering new superior haplotypes (Bharamappanavara et al., 2023). Nowadays, technologies such as high-throughput sequencing, genome-wide association study (GWAS), and molecular marker-assisted selection (MAS) are developing rapidly. This enables us to have a more systematic understanding of the genetic basis of rice yield traits. Many studies have identified a large number of haplotypes, quantitative trait loci (QTLs), and candidate genes related to yield and its components through GWAS and QTL mapping, and have also revealed their roles in different genetic backgrounds and environments (Ashfaq et al., 2023). Based on this, haplotype molecular design breeding and QTL pyramiding strategies have successfully achieved simultaneous improvement of multiple traits in the field, and new high-yield lines have also been cultivated (Withanawasam et al., 2022; Yadavalli et al., 2022). This study summarizes the latest progress in haplotype breeding of rice yield traits, introduces the application of haplotype analysis and genomic tools in yield improvement, explores how to identify excellent haplotypes, conduct functional analysis, and their practical application in molecular design breeding. By integrating genomic information and field performance, it promotes a better combination of theory and practice in high-yield rice breeding. This study aims to provide a theoretical basis and technical support for the precise improvement of rice yield traits in the future. 2 Genomic Basis of Yield-Related Traits in Rice 2.1 Key yield traits: grain size, grain number, panicle architecture, and biomass The yield of rice is determined by many complex traits together. It mainly includes grain size (grain length, grain width, grain thickness), the number of grains per panicle, the structure of the panicle (the length of the main
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