Average minor allele frequency (MAF) in P1 and P2 datasets is
approximately half of that in the corresponding P1+P2 datasets (Table
1). In the Pistacia P1+P2 dataset derived from a single cross,
almost all SNPs have MAF values close to 0.5. MAF frequencies in theJuglans dataset are more variable since this population is
derived from three families. Two of these families are at frequencies
close to 0.5, and the third is at less than 0.05 frequency. In theJuglans P1+P2 dataset, three distinct peaks in the MAF
distribution are observed close to 0.5, 0.25, and 0.05. The abundance of
SNPs with MAF ~0.125 in P1 and P2 (but not P1+P2)
datasets likely indicates segregation of diploid SNPs in one of the two
more frequent Juglans crosses.