title: Unraveling the genetic architecture of subtropical maize (Zea mays L.) lines to assess their utility in breeding programs.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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 r(2) ≤ 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.
  
  
  CONCLUSIONS
  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.
authors: Division of Genetics, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India. tnepolean@gmail.com.
authors: Nepolean
authors: N
authors: Thirunavukkarasu
authors: Firoz
authors: F
authors: Hossain
authors: Kaliyugam
authors: K
authors: Shiriga
authors: Swati
authors: S
authors: Mittal
authors: Kanika
authors: K
authors: Arora
authors: Abhishek
authors: A
authors: Rathore
authors: Sweta
authors: S
authors: Mohan
authors: Trushar
authors: T
authors: Shah
authors: Rinku
authors: R
authors: Sharma
authors: Pottekatt Mohanlal
authors: PM
authors: Namratha
authors: Amitha S V
authors: AS
authors: Mithra
authors: Trilochan
authors: T
authors: Mohapatra
authors: Hari Shankar
authors: HS
authors: Gupta
mesh_terms: D032461:Chromosomes, Plant; D016000:Cluster Analysis; D019143:Evolution, Molecular; D014644:Genetic Variation; D005828:Genetics, Population; D018745:Genome, Plant; D023281:Genomics; D005838:Genotype; D006239:Haplotypes; D007178:Inbreeding; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D015203:Reproducibility of Results; D003313:Zea mays / Q000235:genetics*