Molecular Plant Breeding 2025, Vol.16, No.5, 268-277 http://genbreedpublisher.com/index.php/mpb 271 5 Breeding Strategies Using Superior Haplotypes 5.1 Marker-assisted haplotype selection and pyramiding Marker-assisted selection precisely screens and aggregates haplotypes related to the target trait by developing molecular markers that can distinguish different haplotypes. For important traits such as yield and stress resistance, haplotype analysis can identify “superior haplotypes” that are significantly superior to other haplotypes, and they can be aggregated into breeding materials through labeling assistance. Researchers have developed a series of haplotype-specific markers on traits such as grain weight and grain length in rice, which can effectively distinguish and track the transmission of superior haplotypes, improving genetic gain and breeding efficiency (Liu et al., 2023; Alam et al., 2024). Haplotype aggregation strategies can also help overcome linkage arrest by combining superior haplotypes of multiple genes, supporting the realization of “design breeding” (Sivabharathi et al., 2024; Meena et al., 2025). 5.2 Integration with genomic selection, speed breeding, and genome editing The combination of haplotype information and modern breeding techniques such as genome selection (GS), speed breeding, and genome editing can accelerate the utilization of superior haplotypes. Haplotype-based genomic selection models are more accurate than traditional SNP models in predicting complex traits such as yield and stress resistance, and can better reflect the complex relationship between genotype and phenotype (Figure 2) (Bhat et al., 2021; Yoosefzadeh-Najafabadi et al., 2022; Weber et al., 2023). Rapid incubation technology shortens the generation cycle, enabling superior haplotypes to aggregate and fix more quickly. Genome editing technology can also directly modify target genes, create or introduce superior haplotypes, and accelerate the creation of new varieties (Sivabharathi et al., 2024; Meena et al., 2025). Figure 1 Mining of SNPs and construction of haplotypes for detecting marker-trait associations (GWAS) and computing genomic estimated breeding values (GS) (Adopted from Bhat et al., 2021) Image caption: This diagram describes the comparative potential of the Haplotype-Based GWAS/Haplotype-Based GS in relation to SNP-Based GWAS/SNP-Based GS for the development of improved crop cultivars via genomics-assisted breeding (GAB). It showed that Haplotype-Based GWAS/Haplotype-Based GS in combination with the high-throughput phenotyping (HTP) has great potential to enhance the precision and accuracy in the gene identification and GAB (Adopted from Bhat et al., 2021) 5.3 Combining haplotype information with hybrid rice breeding programs Haplotype information has brought new ideas for parent selection and hybrid combination design in hybrid rice breeding. Liu et al. (2023) and Singh et al. (2024) found that by analyzing the haplotypes of key genes in parental materials such as restorer lines and maintainer lines, parents carrying superior haplotypes can be selected, thereby enhancing the yield potential and stability of hybrid offspring. The utilization of haplotype diversity can also broaden the genetic basis of hybrid rice and enhance its stress resistance and adaptability. Studies have shown that
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