Molecular Plant Breeding 2024, Vol.15, No.5, 295-307 http://genbreedpublisher.com/index.php/mpb 300 Figure 4 Haplotype analysis of Ghd7andOsNAS3across the 3K RG panel (Adopted from Abbai et al., 2019) Image caption: (a) Ghd7, a key gene associated with heading date has about 14 haplotypes in the 3K RG panel with wide phenotypic variations. (b) Ghd7-H8 was the most diverse one based on SNP and (c) interestingly was the earliest to flower, while Ghd7-H6 took greater than 100 days to flower. (d) OsNAS3 that influences grain Fe and Zn concentration has three haplotypes in the 3K RG panel with significant phenotypic variations in the subset. OsNAS3-H2 had the highest grain (e) Fe and (f) Zn profile. The geographical distribution of various haplotypes of (g) Ghd7and (h) OsNAS3(Adopted from Abbai et al., 2019) Furthermore, the researchers discovered the elite haplotype EPN4-1 of the effective panicle number per plant (EPN4), the elite haplotype GNP1-6 of the grain number per panicle (GNP). Pyramiding of EPN4-1 and GNP1-6 could be a preferred approach to obtain high yield without affecting other yield-related traits, which has application value in high-yield rice breeding (Figure 5) (Wang et al., 2023). Figure 5 Comparison of yield and yield-related traits between accessions carrying an EPN4-1/GNP1-6 combination and accessions carrying the EPN4-1 haplotype (Adopted from Wang et al., 2023) 4.3 Lessons learned from practical applications The practical applications of haplotype analysis in rice breeding have provided several valuable lessons. Firstly, the identification of superior haplotypes requires a comprehensive understanding of the genetic basis of key traits. The study on the 3K rice genome panel highlighted the importance of integrating meta-expression analysis and
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