SNP genotypic data were used to study genetic diversity and to understand the genetic relationship among clones. Allele frequencies, polymorphic information content (PIC), heterozygosity, and inbreeding coefficient were calculated in snpReady63 package in R using the diploid genotypic calls.

The average pairwise divergence among genotypes, which represents the nucleotide diversity per bp, π (pi), and the expected number of polymorphic sites per nucleotide, θ (theta), were estimated in TASSEL v5.2.3964 using the default settings for the diploid genotypic calls. The normalized measure of the difference between the observed (π) and expected (θ) nucleotide diversity, known as Tajima’s D, was also computed in TASSEL.

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