Construction Of Transcriptome Maps And QTL Analyses Of Some Complex Traits By Integrating Genomics And Transcriptomics For Populus Tomentosa Carr. And P. Tomentosa×P. Bolleana

For years,genetics of complex traits is always situated in the most difficult center of genetics because most economic traits are quantitative nature and are the most significant targets for improvement which needs more understanding of the genetic mechanisms underlying the complex traits.However,the facts that hundreds of gene networks contribute to the formation of phenotype lead to a worse situation.The success of QTL mapping and major QTL cloning built a theoretical and practical foundation for research on genetics of complex traits.Recently,linkage mapping and QTL analysis involving with woody plants have been developed rapidly,and plenty of tree species established dense genomic DNA linkage maps and abundant QTLs controlling the important traits had been located on the genetic maps.However,the nature of long reproductive cycle and high heterozygous genomic background for perennial plants blocks the development of positional-cloning the QTLs in practical phase.Populus L.which had been full-sequenced and accumulated abundant informative resources is a model species for genetic research on woody plants.In this study,a F₁ backcross population of(Populus tomentosa×Populus bolleana)×Populus tomentosa was used for constructing the first transcriptome maps for woody plants and QTLs analysis was carried out for 28 traits related to growth, photosynthetic traits and wood quality.Furthermore,gene contents within QTL genomic intervals had been deeply analyzed and some most potential QTL candidate genes had been screened out by introducing the genomic and transcriptomic tools.This study is first try to identify QTL in woody plant genome by focusing on the candidate gene selection with gene co-expression prediction approach which can dramatically shrink the primary candidate gene pool and efficiently picking up the most potential genes for further research.In detail,as follow:1) Two separate transcriptome maps were constructed with developing xylem for P. tomentosa and its hybrid P.tomentosa×p.bolleana.For P.tomentosa(male parent),the map comprised of 18 linkage groups which is a total of 1536cM in length,for P.tomentosa×p.bolleana(female parent),13 linkage groups in length of 1030cM made of the map.The coverage of deduced genome is 72.3%and 67.1%for both parents,respectively.To improve the quality of the transcriptome maps,another transcriptome maps for parents had been constructed with the whole plant of sucker seedling(without root) collecting from the juvenilized population.Afterward,two set of transeriptome maps had been compared and integrated into combined maps which had an obvious improvement in map length,marker density and average marker intervals.2) QTL analysis was carried out for 28 traits with these 3 sets of transcriptome maps (combined maps included) and QTL results had been drawn a comparison.With single marker mapping method,402 associated markers had been detected for all traits,including 127 markers for 7 growth traits,166 for 10 photosynthetic traits and 109 for wood quality traits.By using interval mapping,118 QTLs were detected at LOD>1.0,only 10 QTLs existed when LOD>3.0.For each QTL,contribution to the phenotype variation was limited under 10 percents,but also some major QTLs with over 30 percents contribution for some phenotypes had been discovered.3) Fourteen QTL intervals had been transferred from genetic maps into the Populus genome by anchoring the boundary markers covering the QTLs into the whole sequence of Populus.Analysis had been done on the gene contents within each QTL including gene number,gene frequency and gene function.What had been found is every index varied dramatically depending on different QTLs,for example,the gene number varied from 34 to 284 and the physical length of QTLs ranged from 500Kb to 3500Kb.It can be drawn a conclusion that recombination frequency within hotspot and cold spot changed according to the different chromosome segments.4) A gene co-expression model had been constructed with 668 public Populus cDNA chips data which had been used to predict the potential novel genes required in the process of wood formation.Of the top potential genes required in cellulose synthesis and lignin synthesis,some had been testified for their function in this biological process which also was a guarantee for the prediction with this model.5) With this co-expression model in use,the candidate genes within two QTLs controlling cellulose content and one QTL controlling lignin content had been searched in order to deduce the gene mumber for selection.The results showed that 3 mostly highly co-expressed with two cellulose synthesis enzymes had been discovered including gene model estExt_Genewisel_vl.C_LG_XI2954(PU07734),fgenesh4_pg.C LG_XI000690 (PU05329) and grail3.0062007201(PU01733).Using the same methods,corresponding candidate genes had been selected for another two QTLs.