Genetic Diversity within a Collection of Italian Maize Inbred Lines: A Resource for Maize Genomics and Breeding

Author:

Mastrangelo Anna Maria1ORCID,Hartings Hans2,Lanzanova Chiara2,Balconi Carlotta2,Locatelli Sabrina2ORCID,Cassol Helga2,Valoti Paolo2,Petruzzino Giuseppe1,Pecchioni Nicola12ORCID

Affiliation:

1. CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, SS 673 Metri 25200, 71122 Foggia, Italy

2. CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, Via Stezzano 24, 24126 Bergamo, Italy

Abstract

Genetic diversity is fundamental for studying the complex architecture of the traits of agronomic importance, controlled by major and minor loci. Moreover, well-characterized germplasm collections are essential tools for dissecting and analyzing genetic and phenotypic diversity in crops. A panel of 360 entries, a subset of a larger collection maintained within the GenBank at CREA Bergamo, which includes the inbreds derived from traditional Italian maize open-pollinated (OP) varieties and advanced breeding ones (Elite Inbreds), was analyzed to identify SNP markers using the tGBS® genotyping-by-sequencing technology. A total of 797,368 SNPs were found during the initial analysis. Imputation and filtering processes were carried out based on the percentage of missing data, redundant markers, and rarest allele frequencies, resulting in a final dataset of 15,872 SNP markers for which a physical map position was identified. Using this dataset, the inbred panel was characterized for linkage disequilibrium (LD), genetic diversity, population structure, and genetic relationships. LD decay at a genome-wide level indicates that the collection is a suitable resource for association mapping. Population structure analyses, which were carried out with different clustering methods, showed stable grouping statistics for four groups, broadly corresponding to ‘Insubria’, ‘Microsperma’, and ‘Scagliolino’ genotypes, with a fourth group composed prevalently of elite accessions derived from Italian and US breeding programs. Based on these results, the CREA Italian maize collection, genetically characterized in this study, can be considered an important tool for the mapping and characterization of useful traits and associated loci/alleles, to be used in maize breeding programs.

Publisher

MDPI AG

Reference56 articles.

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