A Novel Strategy for Constructing an Integrated Linkage Map in an F1 Hybrid Population of Populus deltoides and Populus simonii

Abstract

The genetic linkage maps of the traditional F₂ population in inbred lines were estimated from the frequency of recombination events in both parents, providing full genetic information for genetic and genomic studies. However, in outbred forest trees, it is almost impossible to generate the F₂ population because of their high heterozygosity and long generation times. We proposed a novel strategy to construct an integrated genetic linkage map that contained both parental recombination information, with restriction-site-associated DNA sequencing (RADSeq) data in an F1 hybrid population of Populus deltoides and Populus simonii. We selected a large number of specific RAD tags to construct the linkage map, each of which contained two SNPs, one heterozygous only in the female parent and the other heterozygous only in the male. Consequently, the integrated map contained a total of 1154 RAD tags and 19 linkage groups, with a total length of 5255.49 cM and an average genetic distance of 4.63 cM. Meanwhile, the two parent-specific linkage maps were also constructed with SNPs that were heterozygous in one parent and homozygous in the other. We found that the integrated linkage map was more consensus with the genomic sequences of P. simonii and P. deltoides. Additionally, the likelihood of the marker order in each linkage group of the integrated map was greater than that in both parental maps. The integrated linkage map was more accurate than the parent-specific linkage maps constructed in the same F₁ hybrid population, providing a powerful genetic resource for identifying the quantitative trait loci (QTLs) with dominant effects, assembling genomic sequences, and performing comparative genomics in related Populus species. More importantly, this novel strategy can be used in other outbred species to build an integrated linkage map.

Keywords: F1 hybrid population; Populus; genetic linkage map; next-generation sequencing; outbred species.

Figure 1

Recombination fraction between two RAD tags: (A) each RAD tag contains two SNPs, one segregating in the type of ab×aa and the other in aa×ab; (B) the genotype counts at SNPs 1 and 3 in the progeny are used to estimate the female recombination fraction, while the counts at SNPs 2 and 4 are for estimating the male recombination fraction; (C) under the assumption of the SNP linkage phases in coupling, the formulas are given for calculating the recombination fractions of the female (r_f), the male (r_m), and the combination of both (r).

Figure 2

Transformation of progeny genotype data at two linked SNPs in an F₁ outbred population: (A) the linkage phase of the maternal parent is repulsion with haplotypes as ab/ba, where the same letters at different sites represent different alleles; (B) at the second SNP site in the maternal parent, allele “a” is transformed into “b” and “b” into “a”. Correspondingly, the genotype of “aa” is transformed into “ab” and “ab” into “aa” in the progeny.

Figure 3

The integrated genetic linkage map of the female P. deltoides and the male P. simonii. The map included 19 linkage groups from LG1 to LG19 with the LG length presented in cM.