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

Thirunavukkarasu, N and Hossain, F and Shiriga, K and Mittal, S and Arora, K and Rathore, A and Mohan, S and Shah, T and Sharma, R and Namratha, P M and Mithra, A S V and Mohapatra, T and Gupta, H S (2013) Unraveling the genetic architecture of subtropical maize (Zea mays L.) lines to assess their utility in breeding programs. BMC Genomics, 14 (877). pp. 1-30. ISSN 1471-2164

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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 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. 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.

Item Type: Article
Divisions: UNSPECIFIED
CRP: UNSPECIFIED
Subjects: Others > Genetics and Genomics
Others > Agriculture-Farming, Production, Technology, Economics
Depositing User: Mr Sanat Kumar Behera
Date Deposited: 13 Dec 2013 06:47
Last Modified: 04 Sep 2017 08:30
URI: http://oar.icrisat.org/id/eprint/7284
Official URL: http://dx.doi.org/10.1186/1471-2164-14-877
Projects: National Agricultural Innovation Project (NAIP)-Component 4, ICAR Network Project on Transgenics in Crop Plants (Maize Functional Genomics Component)
Funders: Indian Council of Agricultural Research
Acknowledgement: We thank the breeders from AICRP (maize), India for contributing the seeds. This study was funded by the National Agricultural Innovation Project (NAIP)-Component 4 and the ICAR Network Project on Transgenics in Crop Plants (Maize Functional Genomics Component). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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