Comparing RADseq and microsatellites for estimating genetic diversity and relatedness Implications for brown trout conservation
Comparing RADseq and microsatellites for estimating genetic diversity and relatedness Implications for brown trout conservation
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DOI：
10.1002/ece3.4905
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发表时间：
2019-02-01
影响因子：
2.6
通讯作者：
Vainikka, Anssi
中科院分区：
文献类型：
--
作者：
Lemopoulos, Alexandre;Prokkola, Jenni M.;Vainikka, Anssi
保护和管理濒危物种需要关于它们的遗传多样性、亲缘关系和种群结构的信息。应用于这些问题的主要遗传标记是微卫星和单核苷酸多态(SNPs)，后者在大多数情况下仍然是更需要资源的方法。在这里，我们比较了两种方法，即通过限制性内切酶相关DNA测序(RADseq)获得的SNPs和16个DNA微卫星座位，用于估计三个地理位置相近的小型野生褐鲑鱼种群和一个地区使用的孵化品系的遗传多样性、亲缘关系和遗传分化。用16个微卫星和4876个SNPs测量F-ST的遗传分化是相似的。根据这两种标记类型，每个褐鲑鱼种群代表着一个不同的基因库，具有较低的杂交水平。与基于微卫星的分析相比，SNPs分析识别半同胞和全同胞的概率更高，并且在估计个体水平的多位点杂合性方面，SNPs优于微卫星。总体而言，结果表明，来自RADseq的中等多态微卫星和SNPs在中等分化的小种群中对种群遗传结构的估计一致，但在需要个体水平的基因信息的应用方面，如量化亲缘关系和个体水平的杂合度，RADseq优于微卫星。这一结果也适用于其他遗传多样性水平较低或中等的小种群。
The conservation and management of endangered species requires information on their genetic diversity, relatedness and population structure. The main genetic markers applied for these questions are microsatellites and single nucleotide polymorphisms (SNPs), the latter of which remain the more resource demanding approach in most cases. Here, we compare the performance of two approaches, SNPs obtained by restriction-site-associated DNA sequencing (RADseq) and 16 DNA microsatellite loci, for estimating genetic diversity, relatedness and genetic differentiation of three, small, geographically close wild brown trout (Salmo trutta) populations and a regionally used hatchery strain. The genetic differentiation, quantified as F-ST, was similar when measured using 16 microsatellites and 4,876 SNPs. Based on both marker types, each brown trout population represented a distinct gene pool with a low level of interbreeding. Analysis of SNPs identified half- and full-siblings with a higher probability than the analysis based on microsatellites, and SNPs outperformed microsatellites in estimating individual-level multilocus heterozygosity. Overall, the results indicated that moderately polymorphic microsatellites and SNPs from RADseq agreed on estimates of population genetic structure in moderately diverged, small populations, but RADseq outperformed microsatellites for applications that required individual-level genotype information, such as quantifying relatedness and individual-level heterozygosity. The results can be applied to other small populations with low or moderate levels of genetic diversity.