Genetic diversity and population structure of temperate maize (Zea mays L.) inbred lines from a public breeding program in Argentina

Abstract

Background: Understanding and effectively leveraging the genetic diversity present in breeding programs is decisive for increasing genetic gain and rapidly responding to changes in breeding objectives. In this work, a set of 472 representative lines from the Argentine National Institute of Agricultural Technology (INTA) temperate maize (Zea mays L.) breeding program was genotyped with a mid-density DArTag panel to assess genetic diversity, degree of linkage disequilibrium (LD) and population structure. In addition, a breeding core set that captured the program’s genetic diversity was selected to facilitate future functional studies. Results: After curation of the genotypic matrix, 461 lines and 2,199 single nucleotide polymorphisms (SNPs) remained in the analysis. SNPs were highly informative, with an average polymorphic information content of 0.32. Inbred lines exhibited low heterozygosity (1.6% average) and kinship coefficients indicated low redundancy among them. Rogers’ genetic distances (RD) presented values greater than 0.35 in 92.6% of the comparisons, showing high allelic diversity. LD decay was estimated to be 158,609 bp at r2 half-decay distance. Two levels of population structure were detected using Bayesian inference at k=2 and k=12, mainly pinpointing Argentine Flint (AF) and Iowa Stiff Stalk Synthetic (BSSS) origins. These results were consistent with both Principal Component Analysis and cluster analysis based on RD. Additionally, a breeding core set (n=138) that retained 100% of alleles (allele coverage, CV=1) present in this panel of INTA breeding lines was selected using Core Hunter 3. Core set representativeness was validated through multiple quality metrics, including a low mean difference percentage (MD=11%), a high coincidence rate of range (CR=100%), and appropriate variance difference percentage (VD=30%) and variable rate of coefficient of variation (VR=114%). Conclusions: Implementation of mid-density SNP genotyping enabled the characterization of a public panel of temperate maize inbred lines, revealing an intricate population structure with high genetic diversity and low redundancy. These findings provide a foundational framework for germplasm reorganization and the potential development of genomic prediction models. The selected multipurpose breeding core set effectively preserved the program’s allelic diversity and represents a versatile genomic resource for future functional studies.