Fig. 4: Genomic heritability and predictability using identified additive and dominant loci. | Nature Communications

Fig. 4: Genomic heritability and predictability using identified additive and dominant loci.

From: Joint analysis of phenotype-effect-generation identifies loci associated with grain quality traits in rice hybrids

Fig. 4: Genomic heritability and predictability using identified additive and dominant loci.The alternative text for this image may have been generated using AI.

The phenotypes of inbred varieties (V) were analysed to estimate additive heritability using additive kinship derived from the additive genotypes. The phenotypes of hybrid testcrosses (T) were analysed to estimate additive heritability and dominant heritability using additive kinship derived from the additive genotypes and dominant kinship derived from the dominant genotypes, respectively. The total heritability (additive + dominant) was calculated as the sum of the additive heritability and dominant heritability. The predictability of hybrids was evaluated through twofold cross-validation (CV). The reference population contained all parents and random sampled half from all offspring. The random sampling were repeated 100 times. The squared correlation coefficients (R2) between the observed and predicted values were used to examine predictability (R2_CV). Similarly, gBLUP was conducted and evaluated by squared correlation coefficients (R2_gBLUP). The ratio of R2_CV to the total heritability (H2_Total) indicated the percentages of the genome additive and dominant variances explained by the associated additive and dominant loci, which were over 50% for all traits except AC(46%), TD(43%), PC(38%) and ASV(32%). Source data are provided as a Source data file.

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