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dc:title "HTML Summary of #5524 \n\nComparison of SSRs and SNPs in assessment of genetic relatedness in maize\n\n";
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bibo:abstract "Advances in high-throughput SNP genotyping\r\nand genome sequencing technologies have enabled genome-\r\nwide association mapping in dissecting the genetic\r\nbasis of complex quantitative traits. In this study, 82 SSRs\r\nand 884 SNPs with minor allele frequencies (MAF) over\r\n0.20 were used to compare their ability to assess population\r\nstructure, principal component analysis (PCA) and relative\r\nkinship in a maize association panel consisting of 154\r\ninbred lines. Compared to SNPs, SSRs provided more\r\ninformation on genetic diversity. The expected heterozygosity\r\n(He) of SSRs and SNPs averaged 0.65 and 0.44, and the polymorphic information content of these two markers\r\nwas 0.61 and 0.34 in this panel, respectively. Additionally,\r\nSSRs performed better at clustering all lines into groups\r\nusing STRUCTURE and PCA approaches, and estimating\r\nrelative kinship. For both marker systems, the same clusters\r\nwere observed based on PCA and the first two eigenvectors\r\naccounted for similar percentage of genetic\r\nvariations in this panel. The correlation coefficients of each\r\neigenvector from SSRs and SNPs decreased sharply when\r\nthe eigenvector varied from 1 to 3, but kept around 0 when\r\nthe eigenvector were over 3. The kinship estimates based\r\non SSRs and SNPs were moderately correlated (r2 = 0.69).\r\nAll these results suggest that SSR markers with moderate\r\ndensity are more informative than SNPs for assessing\r\ngenetic relatedness in maize association mapping panels."^^xsd:string;
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dct:date "2011";
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skos:prefLabel "Maize"@en .
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