Yang Xiaohong, Xu Yunbi, Shah Trushar, Li Huihui, Han Zhenhai, Li Jiansheng, Yan Jianbing
National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, No 2 Yuanmingyuan West Road, Haidian, Beijing 100193, China.
Genetica. 2011 Aug;139(8):1045-54. doi: 10.1007/s10709-011-9606-9. Epub 2011 Sep 9.
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.
高通量单核苷酸多态性（SNP）基因分型和基因组测序技术的进步，使得在剖析复杂数量性状的遗传基础时能够进行全基因组关联定位。在本研究中，使用了82个简单序列重复（SSR）标记和884个次要等位基因频率（MAF）超过0.20的SNP标记，来比较它们在一个由154个自交系组成的玉米关联群体中评估群体结构、主成分分析（PCA）和相对亲缘关系的能力。与SNP相比，SSR提供了更多关于遗传多样性的信息。在该群体中，SSR和SNP的期望杂合度（He）平均分别为0.65和0.44，这两种标记的多态信息含量分别为0.61和0.34。此外，使用STRUCTURE和PCA方法将所有品系聚类成组以及估计相对亲缘关系时，SSR表现更好。对于这两种标记系统，基于PCA观察到相同的聚类，并且前两个特征向量在该群体中占遗传变异的相似百分比。当特征向量从1变化到3时，SSR和SNP的每个特征向量的相关系数急剧下降，但当特征向量超过3时保持在0左右。基于SSR和SNP的亲缘关系估计呈中度相关（r (2) = 0.69）。所有这些结果表明，在玉米关联定位群体中评估遗传相关性时，中等密度的SSR标记比SNP标记更具信息性。
