SNP-Based Evaluation of Genetic Diversity and Purity in Elite hybrid Maize breeding in Ethiopia

In maize breeding, cultivar release, and multiplication of the seed, verifying the genetic diversity and uniformity of inbred lines and the resulting commercial hybrid is a crucial technique of quality control. Two thousand two hundred and ninety-four single-nucleotide polymorphism (SNP) markers were used to assess 87 genotypes. Bi-allelic SNP data was processed using R software to assess genetic purity and genotype variation. Polymorphism information content (PIC) values greater than 0.2 were observed in 89% of highly polymorphic SNPs. The parental lines genetic distances varied from 0.004 to 0.548, with CML395/CML202 seed producer5 (SP5) and KIT21XW32XKIT seed producer1 (SP1) showing the largest distance (0.548) and CML495 and CML202 the smallest (0.004). Heterozygosity above 5% was found in 64% of lines, indicating poor purity and the need for additional inbreeding. The lines were divided into three distinct genetic clusters by cluster analysis, which may improve breeding efficiency and provide advantageous alleles to maize breeding programs. Out of the 56 parental lines (36%) that passed the parent offspring test. However, 64% of inbred lines purity % less than 95% which were not pure need to be purified by further inbreeding. The lines were separated into three categories, which might offer useful alleles for breeding maize. This study provides molecular quality control for preserving genetically pure parental lines by evaluating and confirming the genetic purity of inbred lines using genome-wide SNP markers. In order to identify genetic variation, contamination, or residual heterogeneity that could impact hybrid seed quality and breeding efficiency, it also compares lines from various seed producers.