Molecular Plant Breeding 2024, Vol.15, No.5, 295-307 http://genbreedpublisher.com/index.php/mpb 299 Referencing the characteristics of haplotype blocks within the wheat genome, the detailed characterization of haplotype blocks across the genome provides insights into their distribution and the genes they contain on different chromosomes. This comprehensive mapping helps to understand the genetic architecture influencing various phenotypic traits in rice, thereby enriching the understanding of haplotype analysis applications in rice genetic improvement (Figure 3) (Brinton et al., 2020). Figure 3 Genome-wide characterization of haplotype blocks (Adopted from Brinton et al., 2020) Image caption: a: Length (upper) and gene number (middle) of haplotype blocks sampled at 500 Kbp intervals across all 21 chromosomes (positions scaled to % of maximum chromosome length). Boxplots show distributions of 1% bins. Insets show boxplots for chromosomal compartments (bottom) based on recombination (R1 + R3 > R2a + R2b > C). Pairwise Wilcox test with Benjamini–Hochberg multiple testing correction was used for statistical analysis. b: Leftmost heatmap shows % of the genome (top row) or chromosomes contained within haplotype blocks for all cultivars. Jagger values are highlighted (middle), with a breakdown of how many other cultivars share these Jagger haplotype blocks. Rightmost panel shows the physical positions of Jagger haplotype blocks. c: Summary of highly conserved haplotype blocks across all cultivars (shared with ≥ 5 cultivars; positions scaled to % of maximum chromosome length per cultivar). Values based on haplotype blocks called using 5-Mbp bins. RHT-B1 is indicated by a red arrowhead (Adopted from Brinton et al., 2020) 4.2 Comparative yield outcomes between haplotype-analyzed varieties and conventional breeds The yield outcomes of haplotype-analyzed rice varieties have shown significant improvements compared to conventional breeds. For instance, the superior haplotypes identified in the 3K rice genome panel, such as DEP1-H2 and GS5-H4, have been linked to higher grain yield and better grain quality. These haplotypes were found to have higher frequencies in the population, indicating their advantageous nature. The study reported that varieties with these superior haplotypes exhibited better performance in terms of yield and quality traits, suggesting that HBB can lead to the development of high-yielding rice varieties that outperform traditional breeds. Figure 4 provides a detailed visualization of the haplotype distribution and their phenotypic effects, particularly highlighting the significant impact of haplotypes like H8 on early flowering and H6 on delayed flowering, further supporting the phenotypic outcomes discussed here (Abbai et al., 2019).
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