Population structure analysis and SNP-based heritability
estimation
A quality control analysis was conducted on the materials using Plink
(Purcell et al., 2007). Initially, SNPs with a minor allele frequency
(MAF) < 0.05 were removed. Subsequently, materials with SNP
missing rates > 0.1 were excluded. Finally, after filtering
the original SNPs (Tang et al., 2021), a final set of 8,503,071 SNPs was
obtained, with a median MAF of 0.21. In addition, Plink was used to
calculate the genomic relationship matrix (GRM) among the 505
accessions. Principal component analysis (PCA) was then performed based
on this matrix. In the resulting PCA plot, the accessions were
differentiated into subgroups reflecting their ecological types. Our
materials included five ecological types: semi-winter 1 (SW1),
semi-winter 2 (SW2), semi-winter mixed (SWM), spring (SPR) and mixed.
Using the GRM above, the SNP-based heritability was calculated with SOC
as the phenotype. This analysis was conducted for each environment using
GCTA (Yang et al., 2011), with the recommended parameters ‘–bfile
–make-grm –make-grm-alg 0 –out; –grm –pheno –reml
–out’.