Evaluation Of Genetic Diversity And Genome-wide Association Studies Of Important Traits In Chinese Fir

Chinese fir[Cunninghamia lanceolata(Lamb.)Hook]is an important indigenous tree species in China,which is widely cultivated in southern China with more than 9.11 × 106 hm2 of artificial planting area.Research on the genetic improvement of Chinese fir has been performed since 1957,and thus a large number of excellent plant resources were collected,that can provide good materials for breeding program.It is significant to evaluate and use of them.In addition,the genome of Chinese fir is large and highly heterozygous,with most important economic characters of it are quantitative traits,which hindered the breeding process of Chinese fir.While molecular marker assisted breeding can accelerate it.In this study,a set of 700 well-conserved Chinese fir clones from six provinces in southern China in the ex situ gene bank of Longshan State Forest,was analyzed using phenotypic traits and 21 simple sequence repeat markers,with the aim of assessing the genetic diversity of these germplasm resources.Then a core collection of 300 accessions,representative of this germplasm,was established,based on genotypic and phenotypic data.To facilitate marker developed and molecular breeding in Chinese fir,we have first developed a large number of single nucleotide polymorphisms(SNPs)using specific-length amplified fragment sequencing(SLAF-seq)in the core collection.To identify loci underlying variation in major phenotype traits,we performed genome-wide association studies(GWAS)on 10 growth traits and wood properties of this resource based on the high density SNP marker.The main results were as follows:1.Abundant phenotypic variation was found among this resource,and clonal variation is the main source of phenotypic variation.The phenotypic variation coefficients all exceeded 10%,and the largest was for volume of timber(70.47%).The high value of repeatability suggested moderate genetic control of the measured traits.The 10 traits were strongly correlated with each other;strong positive correlations(p<0.01)were observed between growth traits,while significant negative correlations(p<0.01 or 0.05)were found between the density of wood and all of the growth traits,and most other property traits,except for heartwood ratio and ratio of tracheid length to tracheid diameter.Using growth traits and density of wood as criteria,98 relatively fast-growing genotypes with relatively high wood basic density were identified,with 61 had higher volume of timber than average2.Genetic analyses using 21 simple sequence repeat markers revealed extensive genetic variation among the accessions.In total,there were 181 alleles,with an average of 8.31 alleles per locus,a mean Shannon index of 1.331,and a mean polymorphism information content of 0.57,suggesting all the site has high polymorphism.Excluding loci with null alleles,three clusters were identified by Structure,which did not match the individuals' geographical provenances.The low level of genetic differentiation among provinces and among subpopulations was obtained,consistent with the intrapopulation genetic variation3.Screening large collections for multiple-trait selective breeding programs is laborious and expensive;a core collection of 300 accessions,representative of the germplasm,was established,based on genotypic and phenotypic data using M strategy.There was no significant difference between the core collection and the whole collection.All of these quantitative traits are normally distributed.The identified small,but diverse,collections will be useful for further genome-wide association studies4.To facilitate marker developed and molecular breeding in Chinese fir,we have characterized 166,646 high-quality single nucleotide polymorphisms(SNPs)using specific-length amplified fragment sequencing(SLAF-seq)in 300 plus accessions.Using this genome-wide SNP marker,we quantified variation for this resource,and revealed modified genetic variation among the accessions,with an average ? of 0.00554 and a mean 0 of 0.00466.Using these SNPs,two clusters were identified by Admixture,but not distinct among the accessions,consistent with the NJ clustering,as well as the similar classification result identified by the first few principal components.To identify loci underlying variation in major phenotype traits,we performed genome-wide association studies(GWAS)on 10 growth traits and wood properties of this resource.Both of the general linear model(GLM)and the compressed mixed linear model(MLM)were fit for association in this population,with 144 and 52 significant associations(p<1E-5),respectively.The percentage of variance explained by each SNP was small,which ranged from 7.59%to 28.45%,and 8.25%to 27.27%,respectively.Pleiotropic effects of loci were found among these associations,and some SNPs were significantly associated with more than one trait,that consistent with the strong phenotypic correlation between the traits.This genome-wide analysis of SNP variation in Chinese fir provides a basis for select growth and wood property of Chinese fir through marker-assisted breeding.