We evaluated genetic diversity and population structure in 32 Canadian maize inbred lines and performed association analysis for five agronomical traits and 50 simple sequence repeat (SSR) markers. Genetic diversity analysis revealed a total of 381 alleles at the 50 SSR loci. The average number of alleles per locus was 7.6. The average genetic diversity and polymorphic information content values were 0.709 and 0.676, respectively. The average major allele frequency was 0.414. Population structure analysis indicated that these maize inbred lines were comprised of four major groups and one admixed group based on a membership probability threshold of 0.80. A general linear model showed 20 marker-trait associations involving 12 SSR markers associated with the four agronomic traits except for leaf length. For these marker-trait associations, phi056, mmc0022, bnlg1621, bnlg1695, phi116, and bnlg1028 were associated with only one trait. The other nc005, bnlg1012, phi065, and umc1982 were associated with two traits. Two SSR markers, mmc0111 and umc1038, were associated with three traits. These results will help in optimizing the choice of parents for crossing combinations, as well as in selecting markers for marker-assisted selection for maize improvement.
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