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：
10.1101/2021.06.29.450162
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发表时间：
2021-06
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通讯作者：
Chedly Kastally;Alina K. Niskanen;A. Perry;S. Kujala;K. Avia;Sandra Cervantes;M. Haapanen;Robert Kesälahti;T. Kumpula;Tiina M. Mattila;D. I. Ojeda;J. Tyrmi;W. Wachowiak;S. Cavers;K. Kärkkäinen;O. Savolainen;T. Pyhäjärvi
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作者：
Chedly Kastally;Alina K. Niskanen;A. Perry;S. Kujala;K. Avia;Sandra Cervantes;M. Haapanen;Robert Kesälahti;T. Kumpula;Tiina M. Mattila;D. I. Ojeda;J. Tyrmi;W. Wachowiak;S. Cavers;K. Kärkkäinen;O. Savolainen;T. Pyhäjärvi
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(如关联研究和基因组选择)带来了挑战。我们提出了一种新的50K SNP基因分型阵列，用于樟子松的研究、育种计划和其他应用。为了选择SNP集合，我们首先在407540个SNP筛选阵列上对480个苏格兰松树样本进行了基因分型，并为最终的阵列(称为‘PiSy50k’)鉴定了47712个高质量的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以及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繁殖种群样本验证了PiSy50k阵列的性能。总体而言，39678个(83.2%)SNPs的错误率较低(平均为0.92%)。基于阵列基因型的亲缘关系估计与预期的家系一致，孟德尔误差可以忽略不计。此外，阵列基因型别成功地区分了不同地理来源的苏格兰松种群。PiSy50k阵列将是未来基因研究和林业应用的宝贵工具。意义说明樟子松是一种进化的、经济的和生态上令人印象深刻的针叶树种，但其巨大的基因组限制了对其功能性状变异的遗传基础的研究。我们开发了一种基因分型阵列，用于促进樟子松的遗传研究，并将其特征变异与整个基因组的遗传多态和基因表达水平联系起来。
Scots pine (Pinus sylvestris) is the most widespread coniferous tree in the boreal forests of Eurasia and has major economic and ecological importance. However, its large and repetitive genome presents a challenge for conducting genome-wide analyses such as association studies and genomic selection. We present a new 50K SNP genotyping array for Scots pine research, breeding programs, 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 breeding populations from Finland and Scotland. Overall, 39 678 (83.2%) SNPs showed low error rates (mean = 0.92%). Relatedness estimates based on array genotypes were consistent with the expected pedigrees, and the amount of Mendelian error was negligible. In addition, array genotypes successfully discriminate Scots pine populations from different geographic origins. The PiSy50k array will be a valuable tool for future genetic studies and forestry applications. Significance statement Scots pine is an evolutionary, economically and ecologically impressive coniferous species but its gigantic genome has limited studying e.g. the genetic basis of its functional trait variation. We have developed a genotyping array that facilitates Scots pine genetic research and linking its trait variation to genetic polymorphisms and gene expression levels across the genome.