QTL Mapping And Genetic Basis Analysis For Growth Traits And Wood Chemical Compositions In Japanese Larch(Larix Kaempferi(Lamb.)Carr.)

Japanese larch(Larix kaempferi(Lamb.)Carr.)is a deciduous coniferous species in genus Larix with strong adaptability,fast growth in the early stage,fast forest establishment,hard timber and corrosion resistance.It is an important afforestation and timber tree species with huge growth potential and economic value in China.The genetic regulation mechanism of growth and wood traits in Japanese larch is still unclear,limiting its genetic improvement process.In this study an open-pollinated population was used to develop SNP markers with genotyping by sequencing(GBS)technology,and combined with EST-SSR markers for linkage-linkage disequilibrium mapping to construct a high-density genetic linkage map.QTL mapping and genetic structure analysis were carried out by linkage-linkage disequilibrium analysis,DNA genetic and non-DNA genetic effects analysis and functional mapping for growth and wood traits.The results not only help to reveal the genetic regulation mechanism of growth and wood traits,but also provide a theoretical basis for molecular marker-assisted selection breeding,new variety selection and germplasm resource creation of Japanese larch.The main research results and conclusions of this study are as follows:1.The Japanese larch genome is abundant with variation sites,which are widely distributed in the genome sequence,and there are many high-impact variation sites within the genes.A total of 60,799,116 variation sites were identified,which are distributed on 99% of Scaffolds in the whole genome with an average density of 299 bp per site.Mostly sites are biallelic(90.03%),and the average ratio of Ts/Tv is 1.5.The probability of GC variation to AT is higher than other types.Variation sites mostly occurred in intergenic regions(83.40%),introns(11.80%)and upstream or downstream regions(4.12%).91.6% of genome genes have variation sites.On average,each gene contains 10 SNPs,of which 5,999 genes(13%)contain high-impact variation sites.There are 2.82 high-impact variation sites per gene,which involves terminator,promoter and splicing variation sites,high-impact variation sites are mainly terminator gain type.2.A high-density genetic linkage map of Japanese larch was constructed,which contains12 linkage groups that including 6,022 SNPs and 75 SSR markers.The total map distance is13,840.46 c M,the average map distance is 2.36 c M,and the map coverage is 99.78%.LD decay analysis found that the LD decayed rapidly to 0.3 within the range of 0.50?29.99 c M in genomic regions,but some markers among different linkage groups still had higher LD coefficients.Results shown that the Japanese larch population has a long history of evolution,and some genomic regions have recently been affected by evolutionary factors.3.The growth traits and wood chemical compositions of Japanese larch are mainly controlled by minor-polygene and pleiotropic effects.Linkage-linkage disequilibrium mapping detected a total of 87 significant associated pairs between traits and markers,including 77 pairs associated with wood chemical compositions,with a maximum PVE of 9.54%,10 pairs associated with growth traits,with a maximum PVE of 7.67%.Analysis of genetic effects shows that the additive and dominant effects of different association sites occrur in various degree.All associations have significant additive effect,ranging from-2.51?1.75,of which 93% have a significant dominant effect and the intensity of action is-2.38?4.84.Compared with growth traits,the additive and dominant effects of wood properties are higher.Linkage-linkage disequilibrium mapping shows that 64 QTLs loci are in linkage equilibrium,indicating that these loci are stable in breeding.4.The growth traits and wood chemical compositions of Japanese larch are affected by epigenetics,which can explain the "missing heritability" in traditional quantitative genetic model.A total of 113 QTL loci were detected using unifying model,of which 4 loci had genetic,imprinting and maternal effects.96% QTL have traditional genetic effect with PVE between0.004% to 5.61%,while the QTL with epigenetic effects have higher PVE with range from5.48%?12.56%.5.The growth traits of Japanese larch have heterogeneity in growth trajectories and are genetically controlled by 3 QTL types.A total of 31 dynamic QTLs that significantly control the dynamic trait process were detected with functional mapping,of which 13 sites were related to tree height and 19 were related to DBH,including Permanent QTLs,Late QTLs and Inverse QTLs.Analysis of the heterochronic parameters of different genotypes showed that when there is no interaction between QTL and age,the duration of the fast-growing period is a key factor to determined which genotypes have growth advantage.On the contrary,when QTL interacts with age,growth trajectory would been changed by the time of genotype's maximum rate for growth.6.This study identified 68 key candidate genes related to growth traits and wood chemical compositions through functional analysis with QTL.14 genes which associated with growth are mainly involved in biological processes such as methylation modification,hormone metabolism,stress resistance,assimilation and cell wall formation.Such as Indole-3-acetate Omethyltransferase,N6-Adenosine methyltransferase,Microtubule EB1 C protein,HVA22-like protein,Photosystem I chlorophyll a/b-binding protein,glucuronosyltransferase,Glucan endo-1,3-beta-glucosidase and so on.Otherwise,54 genes include enzymes with known functions related to the synthesis of lignin,cellulose,and hemicellulose(hydroxycinnamoyl-Co A shikimate/quinate hydroxycinnamoyl transferase HCT,cellulose synthase-like A CSLA,polygalacturonase)and transcription factors(MYB),and also including some genes related to RNA transcription regulation(THO/TREX complex family,zinc finger structural proteins,eukaryotic transcription initiation factors,b HLH,b ZIP transcription factors)and protein phosphorylation(F-box/kelch repeat protein)with unknown functions during wood formation.In summary,this study revealed the complex genetic regulation mechanism of growth and wood formation in Japanese larch.Based on linkage-linkage disequilibrium analysis and functional mapping,QTLs which related to growth and wood chemical components traits were detected with diversified epigenetic effects.Candidate genes will provide research foundation for future study of molecular mechanism of quantitative traits,and also promote the process of molecular breeding and provide the theoretical support for the cultivate of industrial plantation in Japanese larch.