Genomics-based, longitudinal comparisons between ex situ and in situ agrobiodiversity conservation strategies can contribute to a better understanding of their underlying effects. However, landrace designations, ambiguous common names, and gaps in sampling information complicate the identification of matching ex situ and in situ seed lots. Here we report a 50-year longitudinal comparison of the genetic diversity of a set of 13 accessions from the state of Morelos, Mexico, conserved ex situ since 1967 and retrieved in situ from the same donor families in 2017. We interviewed farmer families who donated in situ landraces to understand their germplasm selection criteria. Samples were genotyped by sequencing, producing 74,739 SNPs. Comparing the two sample groups, we show that ex situ and in situ genome-wide diversity was similar. In situ samples had 3.1% fewer SNPs and lower pairwise genetic distances (F_st 0.008–0.113) than ex situ samples (F_st 0.031–0.128), but displayed the same heterozygosity. Despite genome-wide similarities across samples, we could identify several loci under selection when comparing in situ and ex situ seed lots, suggesting ongoing evolution in farmer fields. Eight loci in chromosomes 3, 5, 6, and 10 showed evidence of selection in situ that could be related with farmers’ selection criteria surveyed with focus groups and interviews at the sampling site in 2017, including wider kernels and larger ear size. Our results have implications for ex situ collection resampling strategies and the in situ conservation of threatened landraces.

异地和原地农业生物多样性保护策略之间基于基因组学的纵向比较有助于更好地了解其潜在影响。然而，地方品种名称、模棱两可的通用名称和抽样信息中的空白使得匹配的非原生境和原生境种子批次的识别变得复杂。在这里，我们报告了对来自墨西哥莫雷洛斯州的一组 13 种材料的遗传多样性进行了 50 年的纵向比较，这些材料自 1967 年以来就进行了异地保护，并于 2017 年从相同的捐赠家庭中原位回收。我们采访了捐赠的农民家庭原位地方品种以了解其种质资源选择标准。通过测序对样品进行基因分型，产生 74,739 个 SNP。比较两个样本组，我们表明非原位和原位全基因组多样性相似。F _st 0.008–0.113) 比非原位样本 ( F _st 0.031–0.128)，但显示出相同的杂合性。尽管样本在全基因组范围内具有相似性，但在比较原位和非原位种子批次时，我们可以识别出几个被选择的位点，这表明农田正在发生进化。3 号、5 号、6 号和 10 号染色体中的八个基因座显示了原位选择的证据，这可能与 2017 年在采样点通过焦点小组调查和访谈的农民选择标准相关，包括更宽的籽粒和更大的穗尺寸。我们的结果对异地采集重采样策略和受威胁地方品种的原位保护具有重要意义。