Development of a single nucleotide polymorphism array for population genomic studies in four European pine species.
Development of a single nucleotide polymorphism array for population genomic studies in four European pine species.
复制标题
开发用于四种欧洲松树种群基因组研究的单核苷酸多态性阵列。
DOI：
10.1111/1755-0998.13223
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发表时间：
2020
影响因子：
7.7
通讯作者：
Perry A
中科院分区：
文献类型：
--
作者：
Perry A
松树是世界上一些最具生态和经济价值的树种，许多树种具有巨大的自然分布或被广泛种植。然而，缺乏快速基因分型能力阻碍了对这些物种遗传变异的分子基础的理解。在这里，我们提供了一个有效的工具，可以对基因组中数千个单核苷酸多态(SNP)标记进行基因分型，这些标记可以应用于松树的遗传学研究。重新测序的候选基因和转录组序列的多态。、西尔维斯特里斯(P.mugo)、尖顶侧耳(P.uncinata)、尖顶侧耳(P.uliginosa.)用辐射设计了49,829个SNP阵列(Axiom_PineGAP，Thermo Fisher)。超过1/3(34.68%)的单胞菌被鉴定出来。该阵列用于筛选四种松树的样本。阵列在所有样本上的转化率为42%(N=0.20795个SNPs)，来自重新测序的候选基因和转录组序列的SNPs的转化率相似。基因本体论术语由包含转换后的SNPs的单基因广泛表示，反映了它们在整个转录组中的覆盖面。超过四分之一的成功转化的SNPs在所有物种中是多态的，这些数据成功地区分了物种和一些个体群体。SNP阵列为推进这些物种的遗传研究提供了一个有价值的新工具，并证明了该技术在拥有大型和复杂基因组的物种中快速基因分型的有效性。
Pines are some of the most ecologically and economically important tree species in the world, and many have enormous natural distributions or have been extensively planted. However, a lack of rapid genotyping capability is hampering progress in understanding the molecular basis of genetic variation in these species. Here, we deliver an efficient tool for genotyping thousands of single nucleotide polymorphism (SNP) markers across the genome that can be applied to genetic studies in pines. Polymorphisms from resequenced candidate genes and transcriptome sequences ofP. sylvestris,P. mugo,P. uncinata, P. uliginosaandP. radiatawere used to design a 49,829 SNP array (Axiom_PineGAP, Thermo Fisher). Over a third (34.68%) of the unigenes identified from theP. sylvestristranscriptome were represented on the array, which was used to screen samples of four pine species. The conversion rate for the array on all samples was 42% (N= 20,795 SNPs) and was similar for SNPs sourced from resequenced candidate gene and transcriptome sequences. The broad representation of gene ontology terms by unigenes containing converted SNPs reflected their coverage across the full transcriptome. Over a quarter of successfully converted SNPs were polymorphic among all species, and the data were successful in discriminating among the species and some individual populations. The SNP array provides a valuable new tool to advance genetic studies in these species and demonstrates the effectiveness of the technology for rapid genotyping in species with large and complex genomes.