Genomic early growth mechanisms of two endangered Mexican spruces

This study elucidated the genomic basis of family-level growth variance in the critically endangered endemic Mexican spruces Picea martinezii and P. mexicana by: (i) analyzing family- and population-level variations in seedling basal diameter and height after 12 months of growth under common garden conditions and seed weight as maternal provisioning trait; and (ii) identifying genomic loci (SNPs) associated with these traits. Despite limited sample sizes (77 and 74 families representing all known populations of both species), 32 and 10 outlier SNPs were identified yielding 17 and six annotated candidate genes in P. martinezii and P. mexicana, respectively. These genes showed contrasting multivariate associations suggesting species-specific hypothesized growth strategies at the family level: defense-oriented framework in P. martinezii and plasticity-driven response in P. mexicana. Notably, several candidate genes encode key components of growth hormone pathways, including a gibberellin-regulated protein, a cytokinin hydroxylase and the AP2-like transcription factor ANT, providing valuable insights into how maternal genetic variation corresponds to the hormonal pathways that govern cell proliferation and organ size in the progeny. Integration of these findings with the contrasting demographic histories of both species revealed that population bottlenecks enhance the detectability of growth-associated variants by reducing background genetic variation. These genomic resources provide actionable information for prioritizing conservation measures, implementing assisted gene flow to maintain adaptive potential under climate change and designing future breeding programs. With 80.9–99.6% sequence identity to conserved Picea abies homologs, these findings may extend across the genus.