Abstract
Although numerous linkage maps have been constructed in the genus Populus, they are typically sparse and thus have limited applications due to low throughput of traditional molecular markers. Restriction-site associated DNA sequencing (RADSeq) technology allows us to identify a large number of single nucleotide polymorphisms (SNP) across genomes of many individuals in a fast and cost-effective way, and makes it possible to construct high-density genetic linkage maps. We performed RADSeq for 299 progeny and their two parents in an F1 hybrid population generated by crossing the female Populus deltoides ‘I-69’ and male Populus simonii ‘L3’. A total of 2,545 high quality SNP markers were obtained and two parent-specific linkage maps were constructed. The female genetic map contained 1601 SNPs and 20 linkage groups, spanning 4,249.12 cM of the genome with an average distance of 2.69 cM between adjacent markers, while the male map consisted of 940 SNPs and also 20 linkage groups with a total length of 3,816.24 cM and an average marker interval distance of 4.15 cM. Finally, our analysis revealed that synteny and collinearity are highly conserved between the parental linkage maps and the reference genome of P. trichocarpa. We demonstrated that RAD sequencing is a powerful technique capable of rapidly generating a large number of SNPs for constructing genetic maps in outbred forest trees. The high-quality linkage maps constructed here provided reliable genetic resources to facilitate locating quantitative trait loci (QTLs) that control growth and wood quality traits in the hybrid population.
Highlights
The Populus genus has several attractive biological characteristics as a long-lived plant and possesses tremendous economic and ecological importance
142.0 Gb of 100-bp PE reads for the two parents and 150 progeny were produced from the sequencing experiment performed in Novogene Bioinformatics Institute (NBI), while the rest of 187.5 Gb 90-bp PE reads for the same two parents and other 149 progeny was produced by sequencing in Beijing Genomics Institute (BGI)
The two parent-specific linkage maps will serve as important genetic resources for identifying QTLs that contribute to growth and timber traits as well as resistance with different QTL mapping approaches implemented in such an F1 hybrid population of P. deltoides and P. simonii [46,47]
Summary
The Populus genus has several attractive biological characteristics as a long-lived plant and possesses tremendous economic and ecological importance. Because of its fast growth, asexual reproduction, small genome size (~480 Mbp) and easy genetic transformation, this genus was selected as a model system for forest trees [1, 2] and the species of P. trichocarpa and P. euphratica have had their genomes sequenced successively [3, 4]. Populus deltoides and P. simonii Linkage Maps design, data collection and analysis, decision to publish, or preparation of the manuscript
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