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Comparison of SSRs and SNPs in assessment of genetic relatedness in maize

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Relation http://oar.icrisat.org/5524/
http://dx.doi.org/10.1007/s10709-011-9606-9
 
Title Comparison of SSRs and SNPs in assessment of genetic relatedness in maize
 
Creator Yang, X
et al, .
 
Subject Maize
 
Description Advances in high-throughput SNP genotyping
and genome sequencing technologies have enabled genome-
wide association mapping in dissecting the genetic
basis of complex quantitative traits. In this study, 82 SSRs
and 884 SNPs with minor allele frequencies (MAF) over
0.20 were used to compare their ability to assess population
structure, principal component analysis (PCA) and relative
kinship in a maize association panel consisting of 154
inbred lines. Compared to SNPs, SSRs provided more
information on genetic diversity. The expected heterozygosity
(He) of SSRs and SNPs averaged 0.65 and 0.44, and the polymorphic information content of these two markers
was 0.61 and 0.34 in this panel, respectively. Additionally,
SSRs performed better at clustering all lines into groups
using STRUCTURE and PCA approaches, and estimating
relative kinship. For both marker systems, the same clusters
were observed based on PCA and the first two eigenvectors
accounted for similar percentage of genetic
variations in this panel. The correlation coefficients of each
eigenvector from SSRs and SNPs decreased sharply when
the eigenvector varied from 1 to 3, but kept around 0 when
the eigenvector were over 3. The kinship estimates based
on SSRs and SNPs were moderately correlated (r2 = 0.69).
All these results suggest that SSR markers with moderate
density are more informative than SNPs for assessing
genetic relatedness in maize association mapping panels.
 
Publisher Springer Netherlands
 
Date 2011
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
Rights —
 
Identifier http://oar.icrisat.org/5524/1/Genetica_139_8_1045%E2%80%931054_2011.pdf
Yang, X and et al, . (2011) Comparison of SSRs and SNPs in assessment of genetic relatedness in maize. Genetica, 139 (8). 045-1054. ISSN 1573-6857