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



Maize is an increasingly important food crop in southeast Asia. The elucidation of its genetic architecture, accomplished by exploring quantitative trait loci and useful alleles in various lines across numerous breeding programs, is therefore of great interest. The present study aimed to characterize subtropical maize lines using high-quality SNPs distributed throughout the genome.


We genotyped a panel of 240 subtropical elite maize inbred lines and carried out linkage disequilibrium, genetic diversity, population structure, and principal component analyses on the generated SNP data. The mean SNP distance across the genome was 70 Kb. The genome had both high and low linkage disequilibrium (LD) regions; the latter were dominant in areas near the gene-rich telomeric portions where recombination is frequent. A total of 252 haplotype blocks, ranging in size from 1 to 15.8 Mb, were identified. Slow LD decay (200–300 Kb) at r2 ≤ 0.1 across all chromosomes explained the selection of favorable traits around low LD regions in different breeding programs. The association mapping panel was characterized by strong population substructure. Genotypes were grouped into three distinct clusters with a mean genetic dissimilarity coefficient of 0.36.


The genotyped panel of subtropical maize lines characterized in this study should be useful for association mapping of agronomically important genes. The dissimilarity uncovered among genotypes provides an opportunity to exploit the heterotic potential of subtropical elite maize breeding lines.

Subtropical maize; Genome-wide SNPs; Linkage disequilibrium; Population structure; Association mapping; Genetic diversity