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ARS Home » Southeast Area » Mississippi State, Mississippi » Crop Science Research Laboratory » Corn Host Plant Resistance Research » Research » Publications at this Location » Publication #242814

Title: Genetic Characterization and Linkage Disequilibrium Estimation of a Global Maize Collection Using SNP Markers

item YAN, JIANBING - International Maize & Wheat Improvement Center (CIMMYT)
item SHAH, TRUSHAR - International Maize & Wheat Improvement Center (CIMMYT)
item Warburton, Marilyn
item Buckler, Edward - Ed
item McMullen, Michael
item CROUCH, JONATHAN - International Maize & Wheat Improvement Center (CIMMYT)

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/15/2009
Publication Date: 12/24/2009
Citation: Yan, J., Shah, T., Warburton, M.L., Buckler IV, E.S., McMullen, M.D., Crouch, J. 2009. Genetic Characterization and Linkage Disequilibrium Estimation of a Global Maize Collection Using SNP Markers. PLoS One. 4:1-14.

Interpretive Summary: The characterization of 632 maize inbred lines using 1536 SNP markers was used to study genetic diversity levels and relationships within the collection. In addition, linkage disequilibrium breakdown was measured and factors that affect linkage disequilibrium was studied, including chromosome, genetic distance, and characteristics of the markers and inbred lines themselves. The information gained here will make future association mapping studies and targeted introgression of useful traits into new maize varieties more efficient.

Technical Abstract: A newly developed maize Illumina GoldenGate Assay with 1536 SNPs from 582 candidate genes was used to genotype a highly diverse global maize collection of 632 inbred lines from temperate, tropical, and subtropical public breeding programs. A total of 1229 informative SNPs and 1785 haplotypes were used to estimate the genetic diversity, population structure, and familial relatedness. No obvious structure was evident, but complex familial relationships were identified among the global collection. Linkage disequilibrium (LD) was measured overall and within chromosomes, allelic frequency groups, and subgroups of different sample sizes and relationships were analyzed. The LD decay distance differed among chromosomes and ranged between <1kb to 5-10kb. The LD distance increased with the increase of minor allelic frequency (MAF), and with smaller sample sizes, encouraging caution when using too few lines in a study. The LD decay distance was much higher in temperate than in tropical and subtropical lines, because tropical and subtropical lines are more diverse and contain more rare alleles than temperate lines. A core sets of inbreds were defined based on haplotypes, and 60 lines capture 90% of haplotype diversity of the entire panel. The defined core sets with the largest diversity and the entire collection can be used widely in the future for different research targets.