An Ultra-Dense Haploid Genetic Map for Evaluating the Highly Fragmented Genome Assembly of Norway Spruce (Picea abies)

Abstract

Norway spruce ( Picea abies (L.) Karst.) is a conifer species of substanital economic and ecological importance. In common with most conifers, the P. abies genome is very large (∼20 Gbp) and contains a high fraction of repetitive DNA. The current P. abies genome assembly (v1.0) covers approximately 60% of the total genome size but is highly fragmented, consisting of >10 million scaffolds. The genome annotation contains 66,632 gene models that are at least partially validated ( www.congenie.org ), however, the fragmented nature of the assembly means that there is currently little information available on how these genes are physically distributed over the 12 P. abies chromosomes. By creating an ultra-dense genetic linkage map, we anchored and ordered scaffolds into linkage groups, which complements the fine-scale information available in assembly contigs. Our ultra-dense haploid consensus genetic map consists of 21,056 markers derived from 14,336 scaffolds that contain 17,079 gene models (25.6% of the validated gene models) that we have anchored to the 12 linkage groups. We used data from three independent component maps, as well as comparisons with previously published Picea maps to evaluate the accuracy and marker ordering of the linkage groups. We demonstrate that approximately 3.8% of the anchored scaffolds and 1.6% of the gene models covered by the consensus map have likely assembly errors as they contain genetic markers that map to different regions within or between linkage groups. We further evaluate the utility of the genetic map for the conifer research community by using an independent data set of unrelated individuals to assess genome-wide variation in genetic diversity using the genomic regions anchored to linkage groups. The results show that our map is sufficiently dense to enable detailed evolutionary analyses across the P. abies genome.

Development of a highly efficient 50K single nucleotide polymorphism genotyping array for the large and complex genome of Norway spruce (Picea abies L. Karst) by whole genome resequencing and its transferability to other spruce species

“…This resulted in a final selection of 47,445 SNPs, covering 45,552 scaffolds and 19,794 gene models (Figure 3). To evaluate the genomic distribution of the selected ~50K SNPs, targeted scaffolds were compared to available genetic linkage maps (Bernhardsson et al., 2019 and our unpublished data), and the number of scaffolds positioned on the genetic maps, as well as the number of selected SNPs on that scaffold, were recorded for each linkage group. In total, 16,659 (35.2%) of the SNPs and 15,103 (33.3%) of the scaffolds could be positioned on the 12 LGs (Table 3), showing that the SNPs selected for the array have a genome‐wide distribution.…”

“…Finally, an additional 1,608 SNPs were randomly selected to bring the total number of selected SNPs up to 47,445, which could fit on the 50K Axiom array together with ~2,000 control probes to account for background noise during imaging analysis. A final investigation, to confirm that the selected SNPs were evenly distributed across the Norway spruce genome, was performed by comparing the targeted scaffolds to available genetic maps (Bernhardsson et al., 2019 and our unpublished data) by counting the number of SNPs and scaffolds positioned on different linkage groups (LGs).…”

Genome‐wide association study identified novel candidate loci affecting wood formation in Norway spruce

“…For the VQSR analysis two datasets were created, a training subset and an input file. The training dataset was derived from the Norway spruce genetic mapping population showing expected segregation patterns (Bernhardsson et al, 2019) and assigned a prior value of 15.0. The input file was derived from the raw sequence data using GATK with the following parameters: extended probe coordinates by +100 excluding INDELS, excluding LowQual sites, and keeping only bi-allelic sites.…”

Genome-Wide Variant Identification and High-Density Genetic Map Construction Using RADseq for Platycladus orientalis (Cupressaceae)

“…This nearly saturated linkage map is the first genetic map for P. orientalis , and to our knowledge is among the densest linkage maps available for conifer species. For example, maps with 21,056 markers spanning 3,556 cM for Picea abies (Bernhardsson et al 2019), 20,655 markers spanning 1,192 cM for Pinus balfouriana (Friedline et al 2015), 2,841 markers spanning 1,637 cM for Pinus taeda (Neves et al 2014), 2,560 markers spanning 1,266 cM for Cryptomeria japonica (Moriguchi et al 2016), and 4,284 markers spanning 1,033 cM for Callitris glaucophylla (Sakaguchi et al 2015). The average marker interval on the current map of P. orientalis is 0.2 cM, which is shorter than most of the maps aforementioned but comparable to the P. abies map (Figure 5).…”

“…Linkage map orders genetic markers and can link phenotypic traits with genomic regions to interpret population and quantitative genetics patterns of variation (Lynch and Walsh 1998). When available, linkage maps can be complementary to genome assembly in providing local fine-scale genomic information (Bernhardsson et al 2019). Construction of a single-tree linkage map in conifers is straightforward owing to the presence of the haploid megagametophyte tissue that is readily available from open-pollinated seed ( i.e.…”