Using MiddRAD-seq data to develop polymorphic microsatellite markers for an endangered yew species.
Using MiddRAD-seq data to develop polymorphic microsatellite markers for an endangered yew species.
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使用 MiddRAD-seq 数据开发濒危红豆杉物种的多态性微卫星标记
DOI：
10.1016/j.pld.2017.05.008
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发表时间：
2017-10
期刊：
影响因子：
4.8
通讯作者：
Gao L
中科院分区：
文献类型：
--
作者：
Qin H;Yang G;Provan J;Liu J;Gao L
微卫星是一种高度多态性的标记，已被广泛应用于遗传学研究。近年来，各种来源的下一代测序数据已被用于开发新的微卫星位点，但与更常见的鸟枪基因组测序或转录组数据相比，RAD-seq数据用于微卫星确定的潜在效用相对未被充分利用。在这项研究中，我们采用MiddleRAD-seq数据开发的多态性微卫星位点的濒危红豆杉物种佛罗里达红豆杉。在一个群体的10个个体产生的8，823，053个干净读段中，94，851个（0.11%）包含微卫星基序。这些位点对应于2993个独特的位点，其中526个（约18%）表现出多态性。其中237个位点适合设计微卫星引物对，随机选取128个位点进行PCR验证和微卫星筛选。在128对引物中，有16个位点给出了清晰的、可重复的模式，然后在来自两个种群的24个个体中进行筛选和表征。每个微卫星位点的等位基因数为2 ~ 10个（平均值为4.875），群体内期望杂合度为0 ~ 0.789（平均值为0.530），表明这些微卫星位点可用于弗氏锥虫的群体遗传学和物种形成研究。本研究是从ddRAD数据中挖掘多态性微卫星位点的少数几个例子之一。
Microsatellites are highly polymorphic markers which have been used in a wide range of genetic studies. In recent years, various sources of next-generation sequencing data have been used to develop new microsatellite loci, but compared with the more common shotgun genomic sequencing or transcriptome data, the potential utility of RAD-seq data for microsatellite ascertainment is comparatively under-used. In this study, we employed MiddRAD-seq data to develop polymorphic microsatellite loci for the endangered yew species Taxus florinii. Of 8,823,053 clean reads generated for ten individuals of a population, 94,851 (∼1%) contained microsatellite motifs. These corresponded to 2993 unique loci, of which 526 (∼18%) exhibited polymorphism. Of which, 237 were suitable for designing microsatellite primer pairs, and 128 loci were randomly selected for PCR validation and microsatellite screening. Out of the 128 primer pairs, 16 loci gave clear, reproducible patterns, and were then screened and characterized in 24 individuals from two populations. The total number of alleles per locus ranged from two to ten (mean = 4.875), and within-population expected heterozygosity from zero to 0.789 (mean = 0.530), indicating that these microsatellite loci will be useful for population genetics and speciation studies of T. florinii. This study represents one of few examples to mine polymorphic microsatellite loci from ddRAD data.
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