Potato has about 100 related wild Solanum species growing naturally in the Americas. The US Potato Genebank aims to keep samples useful for research and breeding to improve the crop, often in the form of botanical seed families. A key component of genebank efficiency is assessing diversity within and among populations, and DNA marker sequence diversity is a powerful proxy for trait diversity. We previously reported on three factors which can cause under-estimation of heterozygosity: ascertainment, allele frequency, and ploidy bias. We here report, using GBS data for four diploid potato species, that average percent of apparent heterozygosity increases as data is more complete—the maximum difference was 2% heterozygotes when only a few individuals are called, to 36% when nearly all individuals were called. However, there was evidence that estimates of average heterozygosity based only on loci for which every individual has data can also be biased upward. Implausibly high levels of heterozygosity suggest non-segregating non-homologous SNPs, which occurred as 5–9% of all loci with complete data. We propose that best estimates of average heterozygosity in unselected seedlings should be based on loci with data for all samples after eliminating those loci that appear to be artificially fixed as heterozygous, which reduces observed heterozygote frequency by 16–26%. On that basis, the wild species examined have similar heterozygosity to the cultivated phureja.

马铃薯有大约 100 种相关的野生茄属植物在美洲自然生长的物种。美国马铃薯基因库旨在保留对研究和育种有用的样本，以改进作物，通常以植物种子家族的形式存在。种质库效率的一个关键组成部分是评估种群内部和种群之间的多样性，而 DNA 标记序列多样性是性状多样性的有力代表。我们之前报道了可能导致杂合性低估的三个因素：确定性、等位基因频率和倍性偏差。我们在此报告，使用四种二倍体马铃薯物种的 GBS 数据，表观杂合性的平均百分比随着数据的更完整而增加——当只有少数个体被称为杂合子时，最大差异为 2%，当几乎所有个体都被称为杂合子时，差异最大为 36% . 然而，有证据表明，仅基于每个人都有数据的位点对平均杂合度的估计也可能存在偏差。难以置信的高水平杂合性表明非分离的非同源 SNP，它占所有具有完整数据的基因座的 5-9%。我们建议对未选择幼苗的平均杂合度的最佳估计应基于所有样本的基因座数据，在消除那些似乎被人为固定为杂合子的基因座后，这将观察到的杂合子频率降低了 16-26%。在此基础上，检查的野生物种与栽培物种具有相似的杂合性。我们建议对未选择幼苗的平均杂合度的最佳估计应基于所有样本的基因座数据，在消除那些似乎被人为固定为杂合子的基因座后，这将观察到的杂合子频率降低了 16-26%。在此基础上，检查的野生物种与栽培物种具有相似的杂合性。我们建议对未选择幼苗的平均杂合度的最佳估计应基于所有样本的基因座数据，在消除那些似乎被人为固定为杂合子的基因座后，这将观察到的杂合子频率降低了 16-26%。在此基础上，检查的野生物种与栽培物种具有相似的杂合性。phureja。