Unveiling the genetic diversity and landscape genomics of maize landraces: insight into adaptation and conservation

Climate change poses a formidable challenge to modern agriculture, exerting notable effects on agricultural systems through global warming, altered rainfall patterns, and increased occurrence of extreme events. Maize, being a vital crop worldwide, is projected to face substantial vulnerability to climate change across Europe. Addressing this concern necessitates the development of a more resilient cropping system and the cultivation of genotypes that can withstand these challenges. However, current maize hybrids exhibit limited genetic diversity, making them inadequate for such endeavours. In contrast, maize landraces, which have adapted to various agroecological conditions, harbour valuable indigenous germplasm that holds promise for future genetic improvements. The primary objectives of this research are twofold: to conduct a comprehensive study and genotype analysis of 28 Italian landraces and to identify genetic markers associated with environmental factors. In the spring of 2022, carefully selected landracesfrom Lombardia, Emilia Romagna, Trentino-Alto Adige, Veneto, Toscana, Valle d’Aosta and Friuli Venezia Giulia were cultivated at the experimental farm of Università Cattolica del Sacro Cuore in Piacenza. Phenotypic characterization followed the UPOV protocol, with the apex of the final leaf sampled from five individuals per variety. Genotyping was performed using the GBS technique, and subsequent population studies based on sequencing data unveiled 12 ancestral populations in the admixture analysis. Noteworthy populations, including Nostrano Val Tidone, Châtillon, and Entrebin, displayed distinct and well-defined genetic profiles. Conversely, there were completely admixed groups consisting of varieties from Trentino, Emilia Romagna, and Tuscany, which posed challenges in identifying a singular reference population. The high degree of genetic fragmentation was evident in the phylogenetic tree structure, which did not conform to regional patterns but effectively differentiated individual varieties. Of particular interest, the Ottofile Mantovano variety exhibited the most distinct genetic profile, aligning with its unique field phenotype. Principal Component Analysis (PCA) also revealed clear differentiation among individual populations, although specific varietal groups were not readily discernible. Subsequently, a comprehensive analysis was conducted to investigate local adaptation in relation to the environment, using climatic variables spanning a 30-year period (1970-2000). Preliminary findings from this ongoing investigation identified two specific Single Nucleotide Polymorphisms (SNPs) strongly correlated with the environmental factor of wind, indicating promising prospects for genetic improvement. These SNPs were located on chromosome 3 and 8, respectively, within the region of protein-coding genes. While the function of the second SNP's encoded protein remains unknown, the first SNP encodes a mitochondrial carrier, thiamine diphosphate carrier 2, involved in metabolic pathways not yet fully characterized in maize. In conclusion, the analyses consistently demonstrate significant intra-population variability in the germplasm under study. Additionally, this collection comprises unique populations derived from ancestral lineages that have not interbred with others. The presence of completely admixed materials aligns with historical cultivation practices prior to hybridization, wherein farmers cultivated diverse maize varieties without territorial continuity, facilitating easier cross-pollination between distinct materials. This work is part of the project NODES which has received funding from the MUR–M4C2 1.5 of PNRR with grant agreement nECS00000036