Retention of AnAFP Sequence Variants in Ammopiptanthus nanus Ex Situ Collections with Contrasting Management Histories

Ammopiptanthus nanus (Fabaceae) is a Class II nationally protected endangered evergreen shrub in China and is endemic to the arid regions of Central Asia. To assess how contrasting ex situ management histories are associated with sequence-variant retention at an ecologically relevant gene, we analyzed a 594 bp coding fragment of the antifreeze protein gene (AnAFP) in one wild population and two ex situ collections maintained under active versus passive management contexts. Only two variable sites were detected across 75 individuals, both represented by single-base indels near the 5′ end of the coding region. The wild population contained both rare variants, the actively managed ex situ collection retained one of them at low frequency, and the passively maintained collection was monomorphic across the analyzed fragment. Rarefaction analysis indicated that the absence of variation in the passive collection is unlikely to be explained by sample-size disparity alone at this targeted locus. Because only one locus was analyzed, these results are interpreted as locus-specific patterns rather than evidence of genome-wide diversity change. Nevertheless, the observed pattern is consistent with reduced retention of rare sequence variants in the passive ex situ collection and with the possibility that a narrow founder base, together with the absence of subsequent genetic supplementation, contributed to this outcome. These results support the view that ex situ conservation of A. nanus may benefit from maximizing founder representation, maintaining sufficiently large managed collections, and combining neutral marker approaches with targeted monitoring of ecologically relevant loci. Targeted loci such as AnAFP should, however, be regarded as complementary indicators rather than stand-alone proxies for broader genetic diversity or adaptive potential.