Construction of High-Density Linkage Maps of Populus deltoides × P. simonii Using Restriction-Site Associated DNA Sequencing

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.

High-quality genetic mapping with ddRADseq in the non-model tree Quercus rubra

“…Even with the aid of a good framework map and using only those SNPs remaining after application of the premapping filters, we found that map inflation was best minimized using the strict criterion of 5% missing data, a lower value than the 10–25% typically reported for genetic maps constructed with RRS technologies [3, 31, 73, 74]. Improvements in sequencing technologies and methods of library construction could address the problem of missing data, as long as the calling accuracy (the number of times a variant is detected when it is present) is part of the quality control process.…”

Constructing a high-density linkage map to infer the genomic landscape of recombination rate variation in European Aspen(Populus tremula)

“…On the other hand, our framework genetic maps are similar in size to the ca. 4200 cM and 3800 cM maps presented by Tong et al (2016) for the more distantly related species…”

“…Populus deltoides and Populus simonii, respectively. The large size of these maps led Tong et al (2016) to suggest that their maps were suffering from inflation due to the difficulty of properly ordering a large number of markers within a linkage group. While we likely also suffer from such size inflation, these issues appear to be less severe in our P. tremula parental maps, which contain between 8-14 times the number of markers used in the P. deltoides (1601) and P. simonii (940) maps and yet yield linkage maps of similar size.…”

“…trichocarpa could at least partly stem from differences in the effective population size (N e ) of two species (Wang et al 2016). In light of this, it would be interesting to perform further comparisons of recombination rates in P. tremula with other Populus species that have wide distribution ranges and large N e , such as P. deltoides (Tong et al 2016) or P. tremuloides (Wang et al 2016).…”

“…Similarly, linkage maps have been produced for many of the species in the genus (e.g. Paolucci et al 2010, Tong et al 2016, including Populus tremula (Zhigunov et al 2017). However, these maps have been relatively coarse, utilizing a few hundred up to a few thousand markers and typically employing mapping populations consisting of fewer than 300 progenies.…”