Reaction norms at the single-locus and multi-locus combination level
After GWAS and candidate gene examination, the significant SNPs for PR166–195 were used. Five SNPs were selected, with each SNP showing the most significant association with SOC plasticity and closely linked to each candidate gene (Fig. 5b).
The entire population was divided into two groups based on their homozygous genotype at each selected SNP, resulting in the AA and BB groups. In an individual environment, the genotypic value for AA (or BB) was the average phenotypic value across all individuals carrying the AA (or BB) genotype at the locus. Two lines were drawn in the reaction norm graph, one for each group (Fig. S12). Linear regression was applied to show the relationship between the genotypic value and the environment and to show the fitted genotypic values across all environments (Fig. S12).
The five SNPs result in 25 = 32 possible haplotypes, with homozygous genotypes at each SNP. Similar to the calculation of genotypic values for a single locus described above, the genotypic value for each haplotype was the average phenotypic value for all inbred lines harboring each haplotype. There were 10 main haplotypes considered here for each environment (haplotypes represented by fewer than five inbred lines were not considered). Linear regression was applied to show the relationship between genotypic value and the environment and to show the fitted genotypic values across all environments (Guo et al., 2020) (Figs. 6a,b).