Unlocking local adaptation: harnessing the genetic diversity of Italian traditional maize landraces through landscape genomics

Climate change is the greatest challenge of modern agriculture significantly impacting agricultural systems through an increased frequency and intensity of extreme environmental events. Maize, a vital crop for global food security, is particularly vulnerable to these changes, highlighting the urgent need to develop resilient varieties. Maize landraces can represent a valuable germplasm source where breeders may acquire adaptation alleles. Through landscape genomics this study identifies significant genes for adaptation to environmental conditions and represents a starting point for breeding programs to improve maize crop under climate change. The present research aims to identify genetic markers associated to specific environmental factors in 140 individuals derived from 28 Italian maize landraces by a landscape genomics approach to support the development of resilient maize genotypes. Landraces were genotyped-by-sequencing and the resulting genetic matrix was used to represent the collection's diversity. Population genetic studies were conducted on the genomic dataset to investigate the genetic diversity and structure of the collection. Subsequently, partial redundancy analysis (pRDA) was employed to analyze the relationship existing between climate and genetic variation of our materials. Within the 12 ancestral population detected, well-defined populations as well as completely admixed groups were observed; this high degree of genetic fragmentation was reflected in the phylogenetic and PCA analysis, although clear differentiation of individual populations was exhibited. Partial redundancy analysis revealed that 30% of the genetic variance in our collection was explained together by climate (45%), geography (11%), and genetic structure (31%). Three significantly associated SNPs were identified and two of these localized in two distinct genes. Finally, we found a gene encoding the AP2-EREBP-transcription factor in the LD-window of one significant SNP. Results highlight significant intra-landrace variability within the examined germplasm and reveal unique landraces tied to ancestral lineages. Most notably, we identify distinct genetic markers strongly correlated with environmental factors. This discovery opens new avenues for potential genetic improvement in maize cultivation. Landraces preserve vital traits for maize's adaptation to environmental stresses, making them sources for breeding programs to improve stress tolerance and ensure stable yields under climate change. The work is part of NODES project, receiving funds from MUR–M4C2 1.5 of PNRR, grant agreement nECS00000036