Taming the massive genome of Scots pine with PiSy50k, a new genotyping array for conifer research.
Taming the massive genome of Scots pine with PiSy50k, a new genotyping array for conifer research.
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DOI：
10.1111/tpj.15628
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发表时间：
2022-03
期刊：
影响因子：
7.2
通讯作者：
Pyhajarvi, Tanja
中科院分区：
文献类型：
--
作者：
Kastally, Chedly;Niskanen, Alina K.;Perry, Annika;Kujala, Sonja T.;Avia, Komlan;Cervantes, Sandra;Haapanen, Matti;Kesalahti, Robert;Kumpula, Timo A.;Mattila, Tiina M.;Ojeda, Dario, I;Tyrmi, Jaakko S.;Wachowiak, Witold;Cavers, Stephen;Karkkainen, Katri;Savolainen, Outi;Pyhajarvi, Tanja
樟子松是欧亚大陆北部针叶林中分布最广的针叶树种，具有重要的经济和生态价值。然而，其庞大和重复的基因组给进行全基因组分析带来了挑战，如关联研究、遗传图谱和基因组选择。我们提出了一种新的50K单核苷酸多态(SNP)基因分型阵列，用于樟子松的研究、育种和其他应用。为了选择SNP集合，我们首先在407PiSys540SNP筛选阵列上对480个苏格兰松树样本进行了基因分型，并为最终阵列(称为‘ 50k’)鉴定了47个高质量的 712 SNP。在这里，我们提供了设计和测试的细节，以及来自发现小组的等位基因频率估计、功能注释、组织特定的表达模式和SNPs或相应基因的表达水平信息(如果可用)。我们使用来自芬兰和苏格兰的样本验证了PiSy50k阵列的性能。总体而言，39个 678(83.2%)SNP的错误率较低(平均 = 为0.9%)。基于阵列基因型的亲缘关系估计与预期的家系一致，孟德尔误差水平可以忽略不计。此外，阵列基因型别成功地区分了芬兰和苏格兰起源的苏格兰松树种群。PiSy50k SNP阵列将成为未来各种遗传学研究和林业应用的宝贵工具。在基因组时代，针叶树基因组的巨大规模仍然阻碍着应用科学和基础科学的广泛领域的进步。为了促进樟子松遗传研究和现代育种方法，我们开发了50K SNP基因分型阵列，并提供将阵列标记与组织中的遗传多样性和基因表达水平联系起来的信息。
Pinus sylvestris (Scots pine) is the most widespread coniferous tree in the boreal forests of Eurasia, with major economic and ecological importance. However, its large and repetitive genome presents a challenge for conducting genome‐wide analyses such as association studies, genetic mapping and genomic selection. We present a new 50K single‐nucleotide polymorphism (SNP) genotyping array for Scots pine research, breeding and other applications. To select the SNP set, we first genotyped 480 Scots pine samples on a 407 540 SNP screening array and identified 47 712 high‐quality SNPs for the final array (called ‘PiSy50k’). Here, we provide details of the design and testing, as well as allele frequency estimates from the discovery panel, functional annotation, tissue‐specific expression patterns and expression level information for the SNPs or corresponding genes, when available. We validated the performance of the PiSy50k array using samples from Finland and Scotland. Overall, 39 678 (83.2%) SNPs showed low error rates (mean = 0.9%). Relatedness estimates based on array genotypes were consistent with the expected pedigrees, and the level of Mendelian error was negligible. In addition, array genotypes successfully discriminate between Scots pine populations of Finnish and Scottish origins. The PiSy50k SNP array will be a valuable tool for a wide variety of future genetic studies and forestry applications. In the genomic era, the gigantic size of conifer genomes still hampers advances in a wide range of fields of applied and fundamental sciences. To facilitate Scots pine genetic research and modern breeding methods, we developed a 50K SNP genotyping array and provide information that links the array markers to genetic diversity and gene expression levels across tissues.
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通过整个基因组重新配置的挪威云杉（picea abies L. karst）的大型且复杂的基因组的高效50K单核苷酸多态性基因分型阵列及其转移到其他云杉物种。
影响因子：
7.7
作者：
Bernhardsson C;Zan Y;Chen Z;Ingvarsson PK;Wu HX
通讯作者：
Wu HX
影响因子：
9.2
作者：
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通讯作者：
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影响因子：
7.2
作者：
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通讯作者：
Troggio, Michela
影响因子：
4.4
作者：
Howe, Glenn T.;Jayawickrama, Keith;McEvoy, Susan
通讯作者：
McEvoy, Susan
影响因子：
4.1
作者：
Isabel, Nathalie;Holliday, Jason A.;Aitken, Sally N.
通讯作者：
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