Genomic selection incorporates all the available marker information into a model to predict genetic values of breeding progenies for selection. The objective of this study was to estimate genetic gains in grain yield from genomic selection (GS) in eight bi‐parental maize populations under managed drought stress environments. In each population, 148 to 300 F2:3 (C0) progenies were derived and crossed to a single‐cross tester from a complementary heterotic group. The resulting testcrosses of each population were evaluated under two to four managed drought stress and three to four well‐watered conditions in different locations and genotyped with 191 to 286 single nucleotide polymorphism (SNP) markers. The top 10% families were selected from C0 using a phenotypic selection index and were intermated to form C1. Selections both at C1 and C2 were based on genomic estimated breeding values (GEBVs). The best lines from C0 were also advanced using a pedigree selection scheme. For genetic gain studies, a total of 55 entries representing the eight populations were crossed to a single‐cross tester, and evaluated in four managed drought stress environments. Each population was represented by bulk seed containing equal amounts of seed of C0, C1, C2, C3, parents, F1s, and lines developed via pedigree selection. Five commercial checks were included for comparison. The average gain from genomic selection per cycle across eight populations was 0.086 Mg ha–1. The average grain yield of C3–derived hybrids was significantly higher than that of hybrids derived from C0. Hybrids derived from C3 produced 7.3% (0.176 Mg ha–1) higher grain yield than those developed through the conventional pedigree breeding method. The study demonstrated that genomic selection is more effective than pedigree‐based conventional phenotypic selection for increasing genetic gains in grain yield under drought stress in tropical maize.

Characterization of genetic diversity is of great value to assist breeders in parental line selection and breeding system design. We screened 770 maize inbred lines with 1,034 single nucleotide polymorphism (SNP) markers and identified 449 high-quality markers with no germplasm-specific biasing effects. Pairwise comparisons across three distinct sets of germplasm, CIMMYT (394), China (282), and Brazil (94), showed that the elite lines from these diverse breeding pools have been developed with only limited utilization of genetic diversity existing in the center of origin. Temperate and tropical/subtropical germplasm clearly clustered into two separate groups. The temperate germplasm could be further divided into six groups consistent with known heterotic patterns. The greatest genetic divergence was observed between temperate and tropical/subtropical lines, followed by the divergence between yellow and white kernel lines, whereas the least divergence was observed between dent and flint lines. Long-term selection for hybrid performance has contributed to significant allele differentiation between heterotic groups at 20% of the SNP loci. There appeared to be substantial levels of genetic variation between different breeding pools as revealed by missing and unique alleles. Two SNPs developed from the same candidate gene were associated with the divergence between two opposite Chinese heterotic groups. Associated allele frequency change at two SNPs and their allele missing in Brazilian germplasm indicated a linkage disequilibrium block of 142 kb. These results confirm the power of SNP markers for diversity analysis and provide a feasible approach to unique allele discovery and use in maize breeding programs.

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.

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