2.4. Population Structure and LD Decay Analysis

The population structure of the 208 accessions was analyzed using Admixture 1.3.0 [27] based on 2000 SNP markers with default cross-validation (K value ranged from 2 to 5). An adhoc quantity statistic ΔK was used to predict the real number of subpopulations and k = 2 was chosen. Besides, the principal component analysis (PCA) and neighbor-jointing trees were also used to validate population stratification with the software Tassel v5.0 (https://www.maizegenetics.net/tassel).

LD decay analysis was done for the whole population. LD decay was measured by correlation coefficients (r²) for all pairs of SNPs within 500 Kb that were calculated using PopLDdecay v3.27 (https://github.com/BGI-shenzhen/PopLDdecay) with the following parameters: -MaxDist 500-MAF 0.05-Het 0.88-Miss 0.999.