Genetic Variation Analysis And Wood Traits Association Study Of Multi-generation Eucalyptus Pellita Based On Whole Genome Resequencing

China has a large demand for timber and a high proportion of imports.Developing fast-growing plantation is one of the important ways to solve the contradiction between supply and demand.Eucalyptus pellita is an excellent species,which can be used as pulp wood and solid wood.The improvement of its wood traits is the key to improve its utilization value.At present,the improvement of E.pellita was in the 2^ndgeneration in China.Before constructing the 3^rdgeneration population of E.pellita,we need to have a deep understanding of the first two generations of E.pellita population.Based on the whole genome re-sequencing（WGR）technology,the variation loci of 196families from 23 provenances of the 1^stgeneration population and 220 families from the 2^ndgeneration population were analyzed.The aim of this study was to analyze the population genetic structure and intergenerational variation of two generations;to analyze genotypic changes and evolution of two generations of E.pellita populations under selection pressure;the performance of wood traits in the 2^ndgeneration of E.pellita population was obtained,and the genome wide association study（GWAS）of wood traits was performed based on re-sequencing to find the associated loci of wood traits.In order to achieve the above purpose,the following research was carried out:（1）The whole genome of 416 families of two generations of E.pellita was re-sequenced,the sequencing quality was analyzed,the genome was compared,the SNP and In Del of each family were obtained,the composition of SNP and In Del was analyzed,and the function of SNP and In Del was annotated.（2）Based on the obtained variation sites,phylogenetic trees of two generations were constructed to analyze the population structure,principal component analysis and phylogenetic relationship analysis,and near infrared spectroscopy（NIRs）was used to verify the population structure,so as to understand the population structure and genetic changes between the two generations of E.pellita.（3）Based on the obtained variation sites,using selective sweep to analyze the genetic evolution of E.pellita;The selected loci and genes were annotated to analyze the genotype changes under selection.（4）Using the 2^ndgeneration E.pellita population,17 wood traits data were measured and genetic analysis was carried out.（5）Based on the re-sequencing data,genome wide association study of wood traits in the 2^ndgeneration was carried out,the association results were analyzed,and the associated genes were annotated.The main results in this study were as following:（1）The sequencing quality of 416 E.pellita samples reached 91.41%;The comparison rate with reference genome was 93.55%;The average sequencing depth was 14.34×,the sequencing quality is high.A total of 6.3267 million SNPs were detected in 416 samples,with an average of 1.6486 million SNPs per sample.The average Ti/Tv was 1.96,and the average heterozygosity ratio was 36.81%;The SNPs in CDS accounted for 14.60%.A total of 2.1525million In Dels were detected in 416 samples,including 0.9872 million insertions.A total of47251 In Dels were detected in CDS,accounting for 2.41%,including 19522 insertions.（2）The phylogenetic tree,cluster analysis and principal component analysis of 23provenances of the 1^stgeneration E.pellita showed that they could be divided into three groups.The division of these three groups was not completely consistent with QLD,PNG and IDN,but there was a strong correlation between them.The 2^ndgeneration of E.pellita population could also be divided into three groups,but there was no significant correlation between the three groups and the three sources of E.pellita,that was,the genotype of the 2^ndgeneration of E.pellita population experienced recombination.（3）The 1^stgeneration population of E.pellita had high genetic diversity,the He,Nei DI,SHI,PIC were 0.29,0.46,0.24 and 0.29 respectively.The genetic diversity of the 2^ndgeneration was higher than that of the 1^stgeneration,and the He,Nei DI,SHI,PIC were 0.30,0.30,0.46 and 0.25 respectively,this was related to the abundance of materials in the 2^ndgeneration.Nucleic acid polymorphism（π）of the 2^ndgeneration E.pellita population higher than the 1^stgeneration.（4）The neutral test showed that there were selective sweep between the two generations,but they were not strong.The Fst provided the basis for previous scholars’conjecture that there were two natural origin centers（QLD and PNG）of E.pellita.At the same time,we infer that the source PNG1 of PNG,was transmitted from QLD,which was one of the important conclusions of this study.（5）Based on selective sweep analysis,the average number of selected genes in QLD and PNG2 of the 1^stgeneration population was largest,reaching 66.4,which was consistent with the results of genetic distance and Fst,indicating that there were significant differences between QLD and PNG2 provenances.The analysis of the number of selected genes in the 2^ndgeneration population showed that there was selective elimination.（6）The average basic density of E.pellita was 0.518 g/cm³,and the fiber length and width were 590.9μm and 28.9μm,fiber length-width ratio was 20.34,fiber kink index was 0.29,MOE was 13.49Gpa,cellulose was 43.10%,and KYP was 48.07%.According to the analysis of growth and wood properties of E.pellita,it was suitable for pulpwood and solid wood.Comprehensive comparison showed that A20659 was a good provenance.（7）The GWAS of E.pellita revealed 6 loci and 92 genes,which were related to DBH,Extract Content,Total Lignin,KYP.The GO annotation of genes related to each trait involved protein phosphorylation,ion transmembrane transport,organophosphate ester transport and negative regulation of cell population proliferation.This study had significant theoretical significance and potential application value for genetic improvement and molecular breeding of E.pellita.