Original paper 63 ~ M15 Open Access Maydica electronic publication - 2018 Maydica Introduction The development and application of various DNA marker technologies has contributed signifcantly to genetic research in maize in the last decades (Yan et al., 2009) and the use of molecular markers for the detection and exploitation of DNA polymorphism has made a signifcant contribution to the feld of molecu- lar genetics (Semagn et al., 2006). DNA-based or mo- lecular markers are tools that can be used effectively for genetic diversity analysis of many crop species. Unlike morphological markers, these markers are not infuenced by environmental factors (Smith and Smith, 1992; Westman and Kresovich, 1997); and they are a refection of the actual level of genetic difference exist- ing between genotypes. SNP markers have been found to be abundant and evenly distributed throughout the genomes of most plant species. It is considered to be an ideal marker system for genetic research in many crops (Yan et al., 2009). Several high throughput platforms have been developed that allow rapid and simultaneous genotyp- ing of up to a million SNP markers (Yan et al., 2009), and SNP-based genetic diversity among few-branched-1 (Fbr1) maize lines and its relationship with heterosis, combining ability and grain yield of testcross hybrids Shorai Dari 1* , John MacRobert 2 , Adré Minnaar-Ontong 3 , Maryke.T.Labuschagne 3 1 Department of Crop Science, University of Zimbabwe, Harare, Zimbabwe 2 International Maize and Wheat Improvement Centre (CIMMYT), Harare, Zimbabwe 3 Department of Plant Sciences, University of the Free State, Bloemfontein, South Africa *Corresponding author: E-mail: shoraidari@yahoo.co.uk Abstract Single nucleotide polymorphism (SNP) markers are regarded as effcient, compared to other marker types in genetic characterization of maize (Zea mays L.) germplasm because of their vast coverage of the maize genome. The objectives of this study were to (a) genetically fngerprint ‘few-branched-1’ (Fbr1) and normal tasselled CIMMYT elite lines using SNP markers, to assess their relatedness and level of homozygosity and (b) to determine SNP-based genetic distance among these maize lines and to fnd association of genetic distances with specifc combining ability (SCA), mid-parent heterosis (MPH), high-parent heterosis (HPH) and mean grain yield of the hybrids. Twenty-six CIMMYT maize lines (12 with the Fbr1 gene, and 14 normal-tasselled) were genotyped using 1074 SNP marker loci. Fifteen of these lines were used in two separate diallel mating designs: a 9x9 and 6x6 crossing set-up, to make hybrids for yield evaluation. Average residual heterozygosity of SNP loci ranged from 0.2-36.1%, with an average of 8.2%, well above the expected ranges for residual heterozygosity found in maize inbred lines. The polymorphic information content (PIC) for the 1074 SNP loci ranged from 0.015-0.50, with an average of 0.25. Mean genetic distance for all pair wise comparisons of lines was lower (0.30) suggesting a high level of relatedness among lines. A number of elite CIMMYT lines were successfully converted to Fbr1, and were homozygous for the 1074 SNP loci, thus could be used in breeding programmes involving these new tassel mutants. The unweighted paired group method using arithmetic averages (UPGMA) cluster analysis revealed two discrete clusters for the inbred lines, refecting heterotic groups used by CIMMYT. In the principal component (PC) analysis, PC1 and PC2 explained 10.87 and 9.08% respectively, of the molecular variance in tassel size for the 1074 SNPs. The results confrmed molecular markers as a powerful complement for use in genetic characterization, in assigning lines into defned heterotic groups and in examining the relationships among inbred lines at deoxyribonucleic acid (DNA) level. Marker-based genetic distances were positively correlated with hybrid performance, SCA and heterosis indicating that they could accurately predict hybrid performance in this set of germplasm. Grain yield for the hybrids ranged from 0.49-2.48 kg/plot, with an average of 1.80 kg/plot. Hybrids from closely related parental lines (according to SNP-based genetic distances) had the lowest mean grain yield, lowest SCA effects for grain yield, and had the lowest heterosis values. Thus, SNP-based genetic distance information would be useful for effective selection by avoiding genetically similar lines when selecting parents for breeding programmes that require genetically diverse lines as parents. KeyWords Maize (Zea mays L.); SNP markers; genetic diversity; Fbr1 tassel mutation CORE Metadata, citation and similar papers at core.ac.uk