Unraveling the genetic architecture of subtropical maize (Zea mays L.) lines to assess their utility in breeding programs
1 Division of Genetics, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
2 International Crops Research Institute for the Semi-Arid Tropics, Patancheru, 502324, Andhra Pradesh, India
3 National Research Centre on Plant Biotechnology, Pusa, New Delhi 110012, India
BMC Genomics 2013, 14:877 doi:10.1186/1471-2164-14-877Published: 13 December 2013
Additional file 1: Table S1:
Attributes of genotypes used in the genotyping panel. Maturity groups: E, early; M, medium; L, late. Kernel color: Y, yellow; W, white; SD: Semi-dent; SF: Semi-Flint.
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Additional file 2: Figure S1:
GenTrain (GT) and cluster separation (CS) scores for 56,110 SNPs. Each SNP had an individual GT and CS score across the subtropical panel.
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Additional file 3: Figure S2:
SNP coverage across all chromosomes. The average number of SNPs/chromosome across the whole genome was 2962.
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Additional file 4: Figure S3:
Characteristics of 29,619 high-quality SNPs. Gene diversity (GD), polymorphic information content (PIC), and minor allelic frequency (MAF) averaged for 240 individuals.
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Additional file 5: Table S2:
Characteristics of haplotype blocks obtained from three different models using 10-Mb and 20-Mb windows.
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Additional file 6: Figure S4:
Effects of minor allelic frequency (MAF) on LD decay. Comparison of mean r2 values at MAF levels of 0%, ≥ 5%, and ≥ 10% across the subtropical panel.
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Additional file 7: Figure S5:
Graphical representation of genotype grouping based on allele frequency at different K levels. Each of the 240 genotypes is represented by vertical lines partitioned into the respective clusters denoted by K (range, 2–7).
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Additional file 8: Table S3:
Membership value of the genotypes of the association mapping panel generated by ADMIXTURE.
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Additional file 9: Figure S6:
Genetic dissimilarity coefficient of all pairwise genotypes. The genetic dissimilarity matrix was calculated between 240 individuals using 29,619 SNPs and Roger’s modified distance.
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Additional file 10: Table S4:
Genotype pairs selected on the basis of genetic dissimilarity (> 0.35) and other traits for various breeding purposes. Note: Maturity groups: E, early; M, medium; L, late. Kernel color: Y, yellow; W, white.
Format: XLSX Size: 18KB Download file