Abstract

BackgroundRestriction site associated DNA sequencing (RAD-seq), a next-generation sequencing technology, has greatly facilitated genetic linkage mapping studies in outbred species. RAD-seq is capable of discovering thousands of genetic markers for linkage mapping across many individuals, and can be applied in species with or without a reference genome. Although several analytical tools are available for RAD-seq data, alternative strategies are necessary for improving the marker quality and hence the genetic mapping accuracy.ResultsWe demonstrate a strategy for constructing dense genetic linkage maps in hybrid forest trees by combining RAD-seq and whole-genome sequencing technologies. We performed RAD-seq of 150 progeny and whole-genome sequencing of the two parents in an F1 hybrid population of Populus deltoides × P. simonii. Two rough references were assembled from the whole-genome sequencing reads of the two parents separately. Based on the parental reference sequences, 3442 high-quality single nucleotide polymorphisms (SNPs) were identified that segregate in the ratio of 1:1. The maternal linkage map of P. deltoides was constructed with 2012 SNPs, containing 19 linkage groups and spanning 4067.16 cM of the genome with an average distance of 2.04 cM between adjacent markers, while the male map of P. simonii consisted of 1430 SNPs and the same number of linkage groups with a total length of 4356.04 cM and an average interval distance of 3.09 cM. Collinearity between the parental linkage maps and the reference genome of P. trichocarpa was also investigated. Compared with the result on the basis of the existing reference genome, our strategy identified more high-quality SNPs and generated parental linkage groups that nicely match the karyotype of Populus.ConclusionsThe strategy of simultaneously using RAD and whole-genome sequencing technologies can be applied to constructing high-density genetic maps in forest trees regardless of whether a reference genome exists. The two parental linkage maps constructed here provide more accurate genetic resources for unraveling quantitative trait loci and accelerating molecular breeding programs, as well as for comparative genomics in Populus.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3003-9) contains supplementary material, which is available to authorized users.

Highlights

  • Restriction site associated DNA sequencing (RAD-seq), a next-generation sequencing technology, has greatly facilitated genetic linkage mapping studies in outbred species

  • We found that the optimal assemblies of the two parents both corresponded to a k-mer length of 37, which resulted in N50 length of 586 bp and average contig length of 441 bp for the female ‘I-69’, and N50 length of 873 bp and average contig length of 532 bp for the male ‘L-3’

  • The two single nucleotide polymorphism (SNP) genotype datasets each based on one parental reference can confirm each other to generate a high-quality genotype dataset for linkage mapping

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Summary

Introduction

Restriction site associated DNA sequencing (RAD-seq), a next-generation sequencing technology, has greatly facilitated genetic linkage mapping studies in outbred species. The availability of genome sequence information is essential for studying genomic architecture and evolution as well as for comparative genomics. For those tree species without a reference genome sequence, investigations on genome structure have to resort to genetic linkage maps that show the order and distance of a set of genome-wide genetic markers. Genetic linkage maps are prerequisites for identifying quantitative trait loci (QTLs) that control growth, wood quality, and other economically important traits, and thereby facilitating the genetic improvement of cultivated trees through marker-assisted selection and breeding

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