SNP-based genetic diversity among few-branched-1 (Fbr1) maize lines and its relationship with heterosis, combining ability and grain yield of testcross hybrids
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Single nucleotide polymorphism (SNP) markers are regarded as efficient, 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 fingerprint '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 find association of genetic distances with specific 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, reflecting 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 confirmed molecular markers as a powerful complement for use in genetic characterization, in assigning lines into defined 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.
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