Molecular Plant Breeding 2025, Vol.16, No.5, 268-277 http://genbreedpublisher.com/index.php/mpb 269 panicle, the number of primary and secondary branches), and the biomass of the entire plant (Wang, 2024). These traits not only directly affect the yield, but also have a significant relationship with indirect traits such as photosynthetic efficiency, nutrient utilization, and stress resistance. Research has found that grain size, 1000-grain weight, number of grains per panicle, panicle length, and effective tillering number are the core traits that determine yield. There are obvious genetic correlations and phenotypic interactions among these traits (Ata-Ul-Karim et al., 2022; Yin et al., 2024). 2.2 Discoveries from QTL mapping, GWAS, and pan-genome studies Over the past three decades, researchers have identified many yield-related QTLs and candidate genes across the entire rice genome by using QTL mapping in parent populations and GWAS in natural populations. QTL mapping has identified major and minor loci that control traits such as grain weight, grain width, panicle length, and tillering number. Some QTLs exhibit stability in different genetic backgrounds and environments (Padmashree et al., 2023; Daryani et al., 2024). GWAS has made localization more precise and has also discovered many new pleiotropic loci and candidate genes. Some genes have a synergistic regulatory effect among multiple traits, such as GS3, GL3.1, OsCIPK17, GNP12, etc. (Yu et al., 2022; Roy et al., 2024). Meanwhile, pan-genome and large population sequencing studies have found that rice yield traits have strong polygenicity and complex genetic interaction networks. Major genes such as OsMADS22 and OsFTL1 have been functionally verified (Wang et al., 2020; Wei et al., 2024). 2.3 Functional validation of major yield-related genes Through gene cloning, expression analysis and mutant studies, many major yield genes have been functionally verified. For example, genes such as GS3, GW2, and GL3.1 respectively control grain length, grain width, and grain type; genes such as NOG1 and qHI6 affect sourge-reservoir relationship and grain filling; genes such as OsMADS22 and OsFTL1 regulate heading number and heading time (Khahani et al., 2020; Li et al., 2022; Wei et al., 2024). Furthermore, some QTLs and candidate genes have been applied in high-yield rice breeding through molecular marker-assisted selection (MAS) and gene editing techniques, significantly improving the efficiency of yield trait improvement (Kulkarni et al., 2020; Zhong et al., 2021). 3 Concept and Identification of Haplotypes 3.1 Definition of haplotypes and haplotype blocks in rice genomics Haplotype refers to a group of alleles or variant sites that are closely linked and inherited together on the same chromosome. In rice genomics, haplotype block usually refers to a region with a relatively high linkage disequilibrium (LD) in the population. These regions have less recombination and relatively stable allele combinations. The structure of haplotype blocks is related to factors such as ancestral recombination, natural selection, and population history, and is an important unit for studying the genetic basis of complex traits and conducting molecular breeding (Figure 1) (Zhang et al., 2021; Shipilina et al., 2022). Figure 1 Haplotype blocks defined through identity by descent (IBD) (Adopted from Shipilina et al., 2022)
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