An ultra-dense haploid genetic map for evaluating the highly fragmented genome assembly of Norway spruce(Picea abies)

Abstract

27Norway spruce (Picea abies (L.) Karst.) is a conifer species of substanital 28 economic and ecological importance. In common with most conifers, the P. abies 29 genome is very large (~20 Gbp) and contains a high fraction of repetitive DNA. The 30 current P. abies genome assembly (v1.0) covers approximately 60% of the total 31 genome size but is highly fragmented, consisting of >10 million scaffolds. The 32 genome annotation contains 66,632 gene models that are at least partially validated 33 (www.congenie.org), however, the fragmented nature of the assembly means that 34 there is currently little information available on how these genes are physically 35 distributed over the 12 P. abies chromosomes. By creating an ultra-dense genetic 36 linkage map, we anchored and ordered scaffolds into linkage groups, which 37complements the fine-scale information available in assembly contigs. Our ultra-38 dense haploid consensus genetic map consists of 21,056 markers derived from 14,336 39 scaffolds that contain 17,079 gene models (25.6% of the validated gene models) that 40we have anchored to the 12 linkage groups. We used data from three independent 41 component maps, as well as comparisons with previously published Picea maps to 42 evaluate the accuracy and marker ordering of the linkage groups. We demonstrate that 43 approximately 3.8% of the anchored scaffolds and 1.6% of the gene models covered 44 by the consensus map have likely assembly errors as they contain genetic markers that 45 map to different regions within or between linkage groups. We further evaluate the 46 3 utility of the genetic map for the conifer research community by using an independent 47 data set of unrelated individuals to assess genome-wide variation in genetic diversity 48 using the genomic regions anchored to linkage groups. The results show that our map 49 is sufficiently dense to enable detailed evolutionary analyses across the P. abies 50 genome. 51

Environmental Genome-Wide Association Reveals Climate Adaptation Is Shaped by Subtle to Moderate Allele Frequency Shifts in Loblolly Pine

“…These results represent the most complete and dense map ever built for the species [previous map had 3,856 markers in Westbrook et al. (2015)], and one of the few ultradense linkage maps available to date in gymnosperms (others include Norway spruce, Bernhardsson et al. 2019; and Ginkgo biloba , Liu et al.…”

Genomic data provide new insights on the demographic history and the extent of recent material transfers in Norway spruce

“…Mapping to paralog sequences could also distort the distributions of quality scores. Instead of hard filtering based on arbitrary cutoffs, we applied a protocol of variant quality score recalibration, parameters of which were trained using set of SNPs discovered in a pedigree study (Baison et al, ; Bernhardsson et al, ). This should help reduce false‐positive discovery but may also bias toward shared SNPs and less private ones in P. obovata and P. omorika .…”

“…HaplotypeCaller was used for individual genotype identification, and joint SNP calling was performed across all samples using GenotypeGVCFs. We then applied the same variant quality score recalibration protocols as Baison et al (), which were trained on a set of ~21,000 SNPs identified from a pedigree study (Bernhardsson et al, ). This resulted in 2,406,289 SNPs after recalibration.…”

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 ., ) 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.…”