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

Semagn K, Magorokosho C, Vivek BS, Makumbi D, Beyene Y, Mugo S, Prasanna BM, Warburton ML - BMC Genomics (2012)

Bottom Line: Our results demonstrated large differences among the SNP markers in terms of reproducibility, ease of scoring, polymorphism, minor allele frequency and polymorphic information content.There 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: International Maize and Wheat Improvement Center (CIMMYT), Village Market 00621, Nairobi, Kenya. k.semagn@cgiar.org

ABSTRACT

Background: Knowledge 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.

Results: Genetic 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.

Conclusions: There 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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Principal component (PC) analysis of 450 maize germplasm genotyped with 1065 SNPs. PC1 (5.3%) and PC2 (3.4%) separated the lines into 3 major groups. The groups from PCA supports the presence of population structure at K = 3. Individuals that were assigned in to a mixed group in the population structure analysis are indicated in red color.
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Figure 6: Principal component (PC) analysis of 450 maize germplasm genotyped with 1065 SNPs. PC1 (5.3%) and PC2 (3.4%) separated the lines into 3 major groups. The groups from PCA supports the presence of population structure at K = 3. Individuals that were assigned in to a mixed group in the population structure analysis are indicated in red color.

Mentions: Roger's genetic distance between pairwise comparisons of all the 450 lines ranged from 0.003 to 0.450, and the overall average distance was 0.353; however, the vast majority (94.2%) fell between 0.300 and 0.400 (Figure 4a). Relative kinship coefficients between pairs of samples varied from 0 to 1.97 (Figure 4b), with an overall average of 0.370, but most (79%) values were from 0.050 to 0.500. The neighbor-joining (NJ) tree generated from Roger's genetic distance matrix grouped the 450 lines into 3 major groups and 6 subgroups (Figure 5; Additional file 1: Table S1). Group 1 consisted of 288 very diverse lines, including early maturing lines (1A); MSV resistant, extra-early, and QPM lines (1B); and MSV resistant lines (1 C). Group 2 consisted of 123 lines, including 16 weevil resistant, 24 multiple borer resistant and 18QPM lines (2A). Nearly half (25 out of 51) of the lines in group 2B were QPM lines. Group 3 consisted of mainly drought tolerant lines from La Posta Sequia population, MSV resistant lines extracted from populations 100 and 300, and some early-intermediate maturing lines. There was low concordance between the neighbor-joining clustering and model-based population partition in assigning lines into the different groups or populations. The first two principal components (PCs) from principal component analysis explained 8.7% of the total SNP variations among samples. A plot of PC1 (5.3%) and PC2 (3.4%) revealed 4 major groups (Figure 6) and the pattern of groupings was basically the same as that of the model-based population partition at K = 3. Nearly all individuals assigned to a population at K = 3 were in the same group in the principal component analysis, with the mixed group being intermediate between the 3 populations.


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

Semagn K, Magorokosho C, Vivek BS, Makumbi D, Beyene Y, Mugo S, Prasanna BM, Warburton ML - BMC Genomics (2012)

Principal component (PC) analysis of 450 maize germplasm genotyped with 1065 SNPs. PC1 (5.3%) and PC2 (3.4%) separated the lines into 3 major groups. The groups from PCA supports the presence of population structure at K = 3. Individuals that were assigned in to a mixed group in the population structure analysis are indicated in red color.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3362765&req=5

Figure 6: Principal component (PC) analysis of 450 maize germplasm genotyped with 1065 SNPs. PC1 (5.3%) and PC2 (3.4%) separated the lines into 3 major groups. The groups from PCA supports the presence of population structure at K = 3. Individuals that were assigned in to a mixed group in the population structure analysis are indicated in red color.
Mentions: Roger's genetic distance between pairwise comparisons of all the 450 lines ranged from 0.003 to 0.450, and the overall average distance was 0.353; however, the vast majority (94.2%) fell between 0.300 and 0.400 (Figure 4a). Relative kinship coefficients between pairs of samples varied from 0 to 1.97 (Figure 4b), with an overall average of 0.370, but most (79%) values were from 0.050 to 0.500. The neighbor-joining (NJ) tree generated from Roger's genetic distance matrix grouped the 450 lines into 3 major groups and 6 subgroups (Figure 5; Additional file 1: Table S1). Group 1 consisted of 288 very diverse lines, including early maturing lines (1A); MSV resistant, extra-early, and QPM lines (1B); and MSV resistant lines (1 C). Group 2 consisted of 123 lines, including 16 weevil resistant, 24 multiple borer resistant and 18QPM lines (2A). Nearly half (25 out of 51) of the lines in group 2B were QPM lines. Group 3 consisted of mainly drought tolerant lines from La Posta Sequia population, MSV resistant lines extracted from populations 100 and 300, and some early-intermediate maturing lines. There was low concordance between the neighbor-joining clustering and model-based population partition in assigning lines into the different groups or populations. The first two principal components (PCs) from principal component analysis explained 8.7% of the total SNP variations among samples. A plot of PC1 (5.3%) and PC2 (3.4%) revealed 4 major groups (Figure 6) and the pattern of groupings was basically the same as that of the model-based population partition at K = 3. Nearly all individuals assigned to a population at K = 3 were in the same group in the principal component analysis, with the mixed group being intermediate between the 3 populations.

Bottom Line: Our results demonstrated large differences among the SNP markers in terms of reproducibility, ease of scoring, polymorphism, minor allele frequency and polymorphic information content.There 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: International Maize and Wheat Improvement Center (CIMMYT), Village Market 00621, Nairobi, Kenya. k.semagn@cgiar.org

ABSTRACT

Background: Knowledge 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.

Results: Genetic 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.

Conclusions: There 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.

Show MeSH
Related in: MedlinePlus