SSR等位变异数对普通野生稻居群遗传结构分析的影响

Minimum Number of SSR Alleles Needed for Genetic Structure Analysis of Oryza rufipogon Populations

运用矩阵相关检测及聚类分析比较相结合的方法,在对广西玉林普通野生稻居群进行遗传结构分析中,从260至60每降低20个等位变异进行梯度取样,研究了不同SSR等位变异相似系数矩阵与总等位变异相似系数矩阵之间的相关关系。结果表明:1)当等位变异数为200时,居群内个体间的遗传关系与总变异数为277时个体间遗传关系的相关系数高达99.5%,达到极显著标准;如果将等位变异数梯度降低到10,则所有4个群体分别在等位变异数为180、190、210和200时与总变异数为277时个体间遗传关系的相关系数达到99.5%。2)当等位变异数减少到60时,其相关系数也达到95.0%的显著相关。3)所有4个群体在其相似系数达到99.5%时的聚类图与总变异数为277时的聚类图基本一致,只有个别样品在聚类图中的位置略有变化,但其相似系数为95.0%时聚类图与总变异数为277时的聚类图差异非常明显。因此,在进行普通野生稻居群遗传结构分析时,选择均匀分布于基因组的SSR引物并得到200个左右的等位变异时就能精确地获得居群内个体间的遗传关系。由于水稻SSR引物在野生稻居群遗传结构分析中的平均等位基因数约为4,所以,50对引物即能反映居群内个体间的遗传关系。

One original population of Oryza rufipogen with 113 individuals (P) and three derivative populations (P1, P2, P3) randomly sampled from the original population were applied by the methods of Mantel correlation test and NTSYS clustering. For each population, the similarity matrix of the total alleles (277) and those of different numbers of alleles from 260 to 60 with the difference of 20 alleles were compared. The correlations of the matrices decreased with the reduction of alleles. When the numbers of alleles were about 200, the correlation coefficients of all the four populations were about 99.5%, meaning the best fit. If the difference of alleles was lessened to 10, the numbers of alleles were 180, 190, 210 and 200 while the correlation coefficients of the four populations (P, P1, P2, P3) all reached 99.5%. When the numbers of alleles continuously reduced to 60, the correlation coefficients of all the four populations were about 95.0%, also meaning good fit. The clustering dendrograms of the four populations with the correlation coefficient of 99.5% were almost the same as those of the toual alleles. However, those dendrograms with the correlation coefficient of 95.0% were obviously different from those of the total alleles. Therefore, the minimum number of SSR alleles needed for genetic structure analysis of O. rufipogon is between 190 and 210. Considering the mean number of alleles per SSR locus in O. rufipogon populations is about 4, fifty pairs of SSR primers could be enough to reveal genetic relationship among the individuals within O. rufipogon populations.