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

BMC Genomics

Research Article

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

[1] Division of Genetics, Indian Agricultural Research Institute, Pusa, 110012, New Delhi, India;International Crops Research Institute for the Semi-Arid Tropics, 502324, Patancheru, Andhra Pradesh, India;National Research Centre on Plant Biotechnology, 110012, Pusa, New Delhi, India;

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

DOI  :  10.1186/1471-2164-14-877

 received in 2013-08-21, accepted in 2013-12-10,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundMaize 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.ResultsWe 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.ConclusionsThe 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.

【 授权许可】

CC BY   
© Thirunavukkarasu et al.; licensee BioMed Central Ltd. 2013