Open Access Research article

Unraveling the genetic architecture of subtropical maize (Zea mays L.) lines to assess their utility in breeding programs

Nepolean Thirunavukkarasu1*, Firoz Hossain1, Kaliyugam Shiriga1, Swati Mittal1, Kanika Arora1, Abhishek Rathore2, Sweta Mohan1, Trushar Shah2, Rinku Sharma1, Pottekatt Mohanlal Namratha1, Amitha SV Mithra3, Trilochan Mohapatra3 and Hari Shankar Gupta1

Author Affiliations

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

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BMC Genomics 2013, 14:877  doi:10.1186/1471-2164-14-877

Published: 13 December 2013

Additional files

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.

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