Panel Specifications
The HaploPanel platform consists of two haplotype-based rice genotyping panels: the 8K HaploPanel (8,046 markers targeting 2,268 genes) and the 4K HaploPanel (4,651 markers targeting 1,788 genes). Both panels integrate 371 functional haplotype markers spanning 187 cloned genes for the identification of favourable alleles. HaploPanel was developed by mining whole-genome resequencing data from the 3K Rice Genome Panel across 4,788 functionally cloned genes to identify over 250,000 SNPs and InDels, which were refined through haplotype-based filtering, SnpEff functional annotation and haplotype block optimisation, resulting in the construction of 8K and 4K HaploPanel, a functionally informed haplotype-based genotyping array. HaploPanel is applicable across all major rice germplasm groups including indica, japonica, aus, and other rice subpopulations. The HaploPanel platform enables a wide range of genomic applications, including genetic diversity analysis, gene discovery, genome-wide association studies (GWAS), QTL mapping, QTL-seq, bulk segregant analysis (BSA), recombination profiling, introgression breeding (foreground and background selection), haplotype-based breeding, genomic selection, and fingerprinting of elite germplasm.
Figure1. SNP distribution along the 12 rice chromosomes in 8K (Left) and 4K (Right) HaploPanel
Figure 2. Distribution of trait categories in the 8K (Left) and 4K (Right) HaploPanel
Use in breeding
This HaploPanel can be used for diversity analysis, gene discovery, GWAS, QTL profiling, Recombination profiling, Background selection, Marker-assisted forward breeding, Haplotype based breeding, Genomic selection and Fingerprinting of elite material.
