Construction And Application Of Integrated Genetic Linkage Map Of Populus Deltoides And Populus Simonii

Genetic linkage maps are the foundation of genetic research and have important applications in forest tree breeding.They are often used for identifying quantitative trait loci（QTL）and molecular marker assisted breeding.Due to the long growth cycle and high heterozygosity of forest trees,hybrid F₁ generations are often used as the mapping population,and the"pseudo-testcross"strategy is used for map construction,ultimately obtaining genetic maps of two parents.Such a map only contains genetic information from a single parent,which has great limitations in genetic breeding and other researches.Therefore,it is of great significance to study how to construct an integrated genetic linkage map of forest trees that includes parental genetic information.Based on the next generation sequencing technology,this study proposes novel strategies for constructing integrated genetic maps of forest trees using hybrid F₁ and F₂populations.The integrated genetic maps of Populus deltoides and P.simonii were constructed for the first time,and the recombination rate and interference of the two poplar trees were compared.QTLs were also mapped for growth traits of poplar trees.The main conclusions are as follows:（1）A new strategy for constructing an integrated genetic map of forest trees based on the next generation sequencing data from the F₁ generation of forest hybridization has been proposed.This strategy first obtains SNP genotype data of the population based on sequencing data,and then selects molecular tags containing two different types of SNPs,one of which is a heterozygous site only in the maternal parent and the other is a heterozygous site only in the paternal parent.This molecular tag contains both parental genetic information,and after appropriate adjustments or transformations to SNP genotype data,existing genetic mapping software can be used to construct a parental integrated genetic map.On this basis,using reduced-representation genome sequencing data from the F₁ hybrid of P.deltoides and P.simonii,an integrated genetic map of both parents was successfully constructed,with a total length of 2953.8c M and an average distance of 2.73 c M between adjacent markers.The collinearity analysis showed that the collinearity between the integrated map and the reference genome was higher than that of the genetic map of two single parents,and the heat map of marker recombination rate also showed that the integrated map had higher quality.（2）An analysis method for constructing integrated genetic maps using F₂ population of forest hybridization was proposed.Firstly,select SNPs that are heterozygous on both parents,consider multiple possible linkage information,transform SNP genotype data based on two-point linkage analysis,and use existing mapping software to construct an integrated genetic map.At the same time,a F₂ hybrid population of P.deltoides and P.simonii was established,and the entire genome was re-sequenced on 162 offspring and 2 parents.The total sequencing data file size for all samples was 5.23 Tb,with an average sequencing depth of 80.69×.On this basis,a large amount of specific SNP genotype data was identified,thus constructing an integrated genetic linkage map for F₂ generation.The map contains a total of 3645 high-quality SNP loci,with a total length of 3146 c M and an average distance of 0.863 c M between markers.（3）Genetic analysis and QTL mapping were performed for seedling growth traits in the F₂generation population of a cross between P.deltoides and P.simonii.The continuous two-year traits of height,diameter,branch angle of the first branch,and branch number showed significant trait segregation in the F₂ generation,with large coefficients of variation.Through the mixed major gene and polygene inheritance model analysis,the results showed that most traits fit the two pairs of major genes with additive-dominant effect model.Taken together,the additive and dominant effects of the main genes of each trait were considered,indicating the presence of Heterosis in the progeny.Based on the information from the genetic map of the F₂ generation constructed in this study,a total of 10 QTL loci were identified for seedling traits using the composite interval mapping method.could the QTLs explained 6.77～16.14%of the phenotypic variation,including three QTL controlling height,two QTL controlling diameter,three QTL controlling branch angle and two QTL controlling branch number.Most of the QTLs had additive effects greater than dominant effects,indicating that the first year traits were dominated by additive effects.（4）Combined with the two integrated genetic maps,the recombination rate and crossover interference were compared between the maternal P.deltoides and the paternal P.simonii,as well as the two progeny used to construct the F₂ generation.It is found that the maternal P.deltoides had a smaller recombination rate than the paternal P.simonii,and that the crossover interference was higher than that of the paternal P.simonii.The recombination rate of the two progeny used to construct the F₂ generation population was the same as the average recombination rate of the parents,but there were obvious differences in the recombination distribution patterns in the individual chromosomes,and their crossover interference was also much higher than that of the parents,suggesting some differences in the genetic mechanism between the progeny from the cross and the parents.In addition,a very pronounced negative interference phenomenon was found in both parents and in the progeny.In this study,we proposed two novel strategies for constructing an integrated genetic linkage map for forest trees using the F₁ and F₂ generations,which is of great importance for further studies such as QTL mapping,comparative genomics,and genome assembly in forest trees.Especially,we demonstrated that combined use of the next-generation sequencing technology and the hybrid F₁ and F₂ generation populations can construct an integrated genetic linkage map of P.deltoides and P.simonii.In addition,we demonstrated that using the integrated genetic map not only can simultaneously estimate the additive effect and dominant effect of QTL for growth traits in poplars,but also compare and analyze the similarities and differences in recombination rate between two poplars and their hybrids,providing an example for the construction and application of integrated genetic linkage maps in other forest trees.