caa a22 4500 445845546 CHVBK 20180317145357.0 cr unu---uuuuu 170323e20110801xx s 000 0 eng 10.1007/s10709-011-9606-9 doi (NATIONALLICENCE)springer-10.1007/s10709-011-9606-9 Comparison of SSRs and SNPs in assessment of genetic relatedness in maize [Elektronische Daten] [Xiaohong Yang, Yunbi Xu, Trushar Shah, Huihui Li, Zhenhai Han, Jiansheng Li, Jianbing Yan] 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 (r 2=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. Springer Science+Business Media B.V., 2011 SSR nationallicence SNP nationallicence Population structure nationallicence Kinship nationallicence PCA nationallicence Yang Xiaohong National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, No 2 Yuanmingyuan West Road, 100193, Haidian, Beijing, China aut Xu Yunbi International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, D.F., Mexico aut Shah Trushar International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, Hyderabad, Andhra Pradesh, India aut Li Huihui Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081, Beijing, China aut Han Zhenhai College of Agriculture and Biotechnology, China Agricultural University, No 2 Yuanmingyuan West Road, 100193, Beijing, China aut Li Jiansheng National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, No 2 Yuanmingyuan West Road, 100193, Haidian, Beijing, China aut Yan Jianbing National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, No 2 Yuanmingyuan West Road, 100193, Haidian, Beijing, China aut Genetica Springer Netherlands 139/8(2011-08-01), 1045-1054 0016-6707 139:8<1045 2011 139 10709 https://doi.org/10.1007/s10709-011-9606-9 text/html Onlinezugriff via DOI 1 research-article jats NATIONALLICENCE 856 40 https://doi.org/10.1007/s10709-011-9606-9 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Yang Xiaohong National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, No 2 Yuanmingyuan West Road, 100193, Haidian, Beijing, China aut NATIONALLICENCE 700 1- Xu Yunbi International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, D.F., Mexico aut NATIONALLICENCE 700 1- Shah Trushar International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, Hyderabad, Andhra Pradesh, India aut NATIONALLICENCE 700 1- Li Huihui Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081, Beijing, China aut NATIONALLICENCE 700 1- Han Zhenhai College of Agriculture and Biotechnology, China Agricultural University, No 2 Yuanmingyuan West Road, 100193, Beijing, China aut NATIONALLICENCE 700 1- Li Jiansheng National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, No 2 Yuanmingyuan West Road, 100193, Haidian, Beijing, China aut NATIONALLICENCE 700 1- Yan Jianbing National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, No 2 Yuanmingyuan West Road, 100193, Haidian, Beijing, China aut NATIONALLICENCE 773 0- Genetica Springer Netherlands 139/8(2011-08-01), 1045-1054 0016-6707 139:8<1045 2011 139 10709 Metadata rights reserved Springer special CC-BY-NC licence nationallicence BK010053 XK010053 XK010000 NATIONALLICENCE NATIONALLICENCE NL-springer