Abstract
BackgroundNorway spruce [Picea abies (L.) Karst.] is ecologically and economically one of the most important conifer worldwide. Our main goal was to develop a large catalog of annotated high confidence gene SNPs that should sustain the development of genomic tools for the conservation of natural and domesticated genetic diversity resources, and hasten tree breeding efforts in this species.ResultsTargeted sequencing was achieved by capturing P. abies exome with probes previously designed from the sequenced transcriptome of white spruce (Picea glauca (Moench) Voss). Capture efficiency was high (74.5%) given a high level of exome conservation between the two species. Using stringent criteria, we delimited a set of 61,771 high-confidence SNPs across 13,543 genes. To validate SNPs, a high-throughput genotyping array was developed for a subset of 5571 predicted SNPs representing as many different gene loci, and was used to genotype over 1000 trees. The estimated true positive rate of the resource was 84.2%, which was comparable with the genotyping success rate obtained for P. abies control SNPs recycled from previous genotyping efforts. We also analyzed SNP abundance across various gene functional categories. Several GO terms and gene families involved in stress response were found over-represented in highly polymorphic genes.ConclusionThe annotated high-confidence SNP catalog developed herein represents a valuable genomic resource, being representative of over 13 K genes distributed across the P. abies genome. This resource should serve a variety of population genomics and breeding applications in Norway spruce.
Highlights
Norway spruce [Picea abies (L.) Karst.] is ecologically and economically one of the most important conifer worldwide
Given that the P. abies exome capture was conducted with P. glauca probes, the success of the Single nucleotide polymorphism (SNP) detection and distribution Burrows-Wheeler Alignment (BWA) mapped about 18.5 millions of captured sequences against the paired homologous contigs (Fig. 1)
We found 238,666 SNPs that were not in the intersection of the data generated by both PLATYPUS and Genomic selection (GS) REFERENCE MAPPER but were detected by either of the two softwares, and 68,004 SNPs predicted simultaneously by the two methods, that represented roughly 60% and 35% of the SNP datasets predicted by PLATYPUS and GS REFERENCE MAPPER, respectively
Summary
Norway spruce [Picea abies (L.) Karst.] is ecologically and economically one of the most important conifer worldwide. It first included ~ 12 K high-confidence nonsingleton SNPs encompassing ~ 6.5 K genes [42], which was further extended to ~ 212 K high-confidence nonsingleton SNPs in ~ 13.5 K expressed genes with a true positive rate of 92% [27] Exome sequencing is another efficient approach to identify gene SNPs in non-model species with large genomes such as spruces [3, 43]. This approach was successfully used in black spruce (Picea mariana) to generate a catalog of ~ 97 K high-confidence SNPs encompassing ~ 15 K genes with true positive rate of 96% [41]. In Norway spruce, two SNP resources have been published to date, but their annotation was rather limited and their true positive rate has not been estimated yet [44, 45]
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