Jmp pro statistics version 12

Broad-sense heritability for each phenotype was calculated using the following equations (Schmidt et al., 2019 (link)):
In Equation 3, ${\sigma }_g^2$ and ${\sigma }_p^2$ correspond to the variances in genotypic impact and phenotypic measurements among the replicates, respectively. In Equation 4, ${\sigma }_g^2$ , ${\sigma }_{gy}^2$ , and ${\sigma }_{\epsilon }^2$ represent the variances of the random effect of genotype i: G_i, the genotype i by year k interaction: (GY)_ik, and the residual error: ε_ijk, respectively. The terms y and β used in Equation 4 indicate the numbers of years and blocks, respectively. This study’s statistical analyses and visualization of the resulting data (e.g., histograms) relied on JMP Pro® Statistics, Version 12 (SAS Institute Inc., Cary, NC, USA).

The 15 BLUP datasets (Supplementary Figure 3), calculated by the two equations (Equations 1 and 2), were then scrutinized by correlation tests to assess consistency across the 2 years within each trait as well as to inspect whether any interrelationship between different traits existed or not. Multivariate function equipped on JMP Pro® Statistics, Version 12 (SAS Institute Inc., Cary, NC, USA) was utilized for all the correlation coefficient test trials. A correlation coefficient was considered statistically significant if its associated correlation probability was below the conventional 5% (p-value< 0.05).

After checking the allele effect of the QTL, single-marker analysis was pursued to check whether the allele effects were actually reflected in the original phenotype data or not, as well as to find the most fitted genetic models such as additive, simplex-dominant, etc. When a target QTL and the linked SNP marker were selected, we separated BLUP data by genotype, giving us two to five different groups. We then compared averages of the BLUPs of each genotype group to check whether a significant mean difference existed between two genotype groups or not. The presence of the significant mean difference can indirectly reveal allele effects on phenotype. For instance, if the “B” allele of an SNP marker is associated with an increase in specific gravity and has an additive impact, the greater number of B alleles in a genotype would be expected to confer a higher specific gravity. Tukey-Kramer mean comparison test (JMP Pro® Statistics, Version 12; SAS Institute Inc., Cary, NC, USA) was used for the single-marker analysis (p-value < 0.05).