Comparative SNP and Haplotype Analysis Reveals a Higher Genetic Diversity and Rapider LD Decay in Tropical than Temperate Germplasm in Maize

Lu, Y and et al, . (2011) Comparative SNP and Haplotype Analysis Reveals a Higher Genetic Diversity and Rapider LD Decay in Tropical than Temperate Germplasm in Maize. PLoS ONE, 6 (9). pp. 1-8. ISSN 1932-6203

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Understanding of genetic diversity and linkage disequilibrium (LD) decay in diverse maize germplasm is fundamentally important for maize improvement. A total of 287 tropical and 160 temperate inbred lines were genotyped with 1943 single nucleotide polymorphism (SNP) markers of high quality and compared for genetic diversity and LD decay using the SNPs and their haplotypes developed from genic and intergenic regions. Intronic SNPs revealed a substantial higher variation than exonic SNPs. The big window size haplotypes (3-SNP slide-window covering 2160 kb on average) revealed much higher genetic diversity than the 10 kb-window and gene-window haplotypes. The polymorphic information content values revealed by the haplotypes (0.436–0.566) were generally much higher than individual SNPs (0.247–0.259). Cluster analysis classified the 447 maize lines into two major groups, corresponding to temperate and tropical types. The level of genetic diversity and subpopulation structure were associated with the germplasm origin and post-domestication selection. Compared to temperate lines, the tropical lines had a much higher level of genetic diversity with no significant subpopulation structure identified. Significant variation in LD decay distance (2–100 kb) was found across the genome, chromosomal regions and germplasm groups. The average of LD decay distance (10–100 kb) in the temperate germplasm was two to ten times larger than that in the tropical germplasm (5–10 kb). In conclusion, tropical maize not only host high genetic diversity that can be exploited for future plant breeding, but also show rapid LD decay that provides more opportunity for selection.

Item Type: Article
Subjects: Others > Genetics and Genomics
Others > Maize
Depositing User: Mr Sanat Kumar Behera
Date Deposited: 16 Feb 2012 09:24
Last Modified: 16 Feb 2012 09:24
Official URL:
Funders: Rockefeller Foundation, Bill and Melinda Gates Foundation, Generation Challenge Programme, European Community, Education Department of Sichuan Province
Acknowledgement: The SNP chips used in this study were developed through a collaborative project between Cornell University (Ed Buckler and Tim Setter) and the International Maize and Wheat Improvement Center (CIMMYT) (Marilyn Warburton and Jianbing Yan). Some of the maize germplasm used in this study was obtained from the CIMMYT's Global Maize Program.
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