Molecular characterization of diverse CIMMYT maize inbred lines from eastern and southern Africa using single nucleotide polymorphic markers

Abstract

BackgroundKnowledge of germplasm diversity and relationships among elite breeding materials is fundamentally important in crop improvement. We genotyped 450 maize inbred lines developed and/or widely used by CIMMYT breeding programs in both Kenya and Zimbabwe using 1065 SNP markers to (i) investigate population structure and patterns of relationship of the germplasm for better exploitation in breeding programs; (ii) assess the usefulness of SNPs for identifying heterotic groups commonly used by CIMMYT breeding programs; and (iii) identify a subset of highly informative SNP markers for routine and low cost genotyping of CIMMYT germplasm in the region using uniplex assays.ResultsGenetic distance for about 94% of the pairs of lines fell between 0.300 and 0.400. Eighty four percent of the pairs of lines also showed relative kinship values ≤ 0.500. Model-based population structure analysis, principal component analysis, neighbor-joining cluster analysis and discriminant analysis revealed the presence of 3 major groups and generally agree with pedigree information. The SNP markers did not show clear separation of heterotic groups A and B that were established based on combining ability tests through diallel and line x tester analyses. Our results demonstrated large differences among the SNP markers in terms of reproducibility, ease of scoring, polymorphism, minor allele frequency and polymorphic information content. About 40% of the SNPs in the multiplexed chip-based GoldenGate assays were found to be uninformative in this study and we recommend 644 of the 1065 for low to medium density genotyping in tropical maize germplasm using uniplex assays.ConclusionsThere were high genetic distance and low kinship coefficients among most pairs of lines, clearly indicating the uniqueness of the majority of the inbred lines in these maize breeding programs. The results from this study will be useful to breeders in selecting best parental combinations for new breeding crosses, mapping population development and marker assisted breeding.

Genetic diversity analysis in tropical maize germplasm for stem borer and storage pest resistance using molecular markers and phenotypic traits

“…This is in agreement with the results of genetic diversity studies from previous research on maize populations (Semagn et al, 2012;Wen et al, 2012). In addition it has been reported that most variation in maize populations is partitioned within, rather than between populations, because maize is an out-crossing species a factor that lead to reduced population differentiation (Hamrick and Godt 1997).…”

“…Overall mean Roger's genetic distance of 0.353 among pairwise comparisons of inbred lines, with the vast majority (94.2 %) showing distances between 0.300 and 0.400 have been reported (Semagn et al, 2012). This slightly differs from the average distance (0.3012) obtained from the current study.…”

“…Earlier studies have shown that principal component analysis as well as population structure are good predictors of grouping patterns and they can be used to complement the clustering method analysis, since different combinations of genetic distance matrices and clustering algorithms can give rise to somewhat different groups Semagn et al, 2012).…”

Effect of enriched farmyard manure and inorganic fertilizers on grain yield and harvest index of hybrid maize (bh-140) at Chiro, eastern Ethiopia

“…In Eastern Africa, for instance, 3.9% of the cultivated land is under maize production with grain yields of 700 to 1800 kg /ha as opposed to 7437 kg /ha in the USA . In general, maize in Africa is grown on a small-scale by farmers for local consumption, and yields tend to be low, averaging less than half that of Asia and Latin America (Soboksa et al, 2008;Semagn et al, 2012).…”

Molecular and phenotypic characterisation of diverse temperate maize inbred lines in Southeast Europe

“…The growing number of SNP-based maize genetic diversity studies due to decreasing costs per data point, high throughput application and large abundance of SNPs in the maize genome, do not necessarily presume the absolute supremacy of SNPs over SSRs. A recent study demonstrated the suitability of 1065 SNP markers to group 450 diverse maize inbreds according to their pedigrees using different multivariate methods, but it also showed their failure to clearly distinguish between two main maize heterotic groups (Semagn et al, 2012). Comparing the discriminating power of SSR and SNP markers in assessing maize diversity, Wu et al (2016) indicated that the better genome coverage of SNPs contributed to their better performance.…”