Construction Of A High-density Linkage Map Of P. Deltoids×p. Simonii Using Restriction-site Associated DNA Sequencing

The genus Populus is one of the most popular planted forest species in the world. Beacuse ofits small genome size and economic importance, this specie was selected as a model system inperennial forest trees. Meanwile, the genome of Populus trcichocarpa has been sequenced andthe data is available to the community. Although there are many reports on the research of geneticlinkage maps in poplar, the studies of quantitative trait loci (QTL) locating and marker-assistedbreeding are limited due to the lack of a large number of genetic markers on the linakge maps.Restriction site-associated DNA sequencing (RAD-seq) techonology, which is a new andpowerful sequencing approach, can provide thousands of SNP markers in a mapping population,and hence make it possible to construct high-density genetic linkage maps in poplar.In this study, an F1mapping population was produced by hybredizing P. deltoids (♀) with P.simonii (♂). RAD libraries were constructed using genomic DNA from both parents and150individuals in the progeny, which were digensted with the restriction enzyme EcoRI. Weperformed RAD sequencing with Illumina Hiseq2000platform and obtained a total of65Gbpdata with average sequencing depth2.6x in parents and0.86x in the progeny. A total number of298,863SNPs were identified in P. deltoids and269,508SNPs in P. simonii through mapping theRAD reads to the reference genome of P. trcichocarpa. Totally, there are509,155SNPs from thefemale or male parent,59,216of which are common for the both. Then, RAD sequences of eachprogeny were aligned to these parental SNP loci so that the genotypes were determined. Atfer arigorous filtering process, we developed2,457high quality SNP markers that follow Mendel’ssegregation ratio for all of the individuals currently studied. With these molecular markers, twoparental genetic linkage maps were constructed separately. The female linkage map of P. deltoidscontains1,457maternal inherited markers, constituting25linkage groups and spanning thegenome of5481.84cM with an average map distance of4.00cM, whereras the male linkage mapof P. simonii has942paternal inherited markers, also consisting of25linkage groups andcovering the genome of4670.07cM with an average distance of5.67cM.The result demonstrates that RAD-seq is a powerful technique capable of rapidly generatinga large number of SNPs for constructing genetic linkage maps in outbred forest trees. Thehigh-density linkage maps of P. deltoids and P. simonii provide reliable genetic resources tofacilitate mapping QTLs that control growth and wood quality traits in the hybrid population.