Qifu  Zhang , Ruchun  Chen , Zhongxian  Li , Jianquan  Li

Hier Rice Research Center, Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, Hainan, China
Author    Correspondence author
Molecular Plant Breeding, 2025, Vol. 16, No. 5   
Received: 11 Aug., 2025    Accepted: 13 Sep., 2025    Published: 20 Sep., 2025

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.

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.

Rice (Oryza sativa); Haplotype-based breeding; Yield-related traits; Molecular breeding; Multi-omics integration