Development And Evaluation Of Introgression Lines From Two Feral Landraces Into Gossypium Hirsutumacc TM-1

Using unadapted stocks to introgress novel genes into elite cultivars is one of the mostimportant avenues for breeders to broaden cultivar's genetic base.Unadapted stocks havebeen demonstrated to be useful to improve disease resistance,salt tolerance and agronomictraits.Unfortunately,the introduction of exotic genes into an elite genome can often lead toa decrease of desirable agronomic characteristics due to the linkage drag of genes withundesirable effects from the wild species.By using molecular markers and suitablestatistical methods the chromosomal location of quantitative trait locus(QTL)involved inthe character under study can be determinated and selected,allowing the breeder to discardother regions with undesirable effects after relatively few generations of marker-assistedselection.TX-256(G.hirsutum race richmondii)and TX-1046(G.hirsutum raceyucatanense)are highly resistant to Verticillium wilt.These two feral landraces wereemployed to develop introgression lines from into Gossypium hirsutum acc TM-1.1.Construction of integrated genetic mapIn total,7080 pairs of SSR primers available in our institute were first used to screen forpolymorphisms in the three parents.Markers found to be polymorphic were then used tosurvey the two BC1 mapping populations.There were 281(4.08%)and 430(6.60%)pairsof SSR markers found to be polymorphic between the parents in TM-1 xTX-256(popl)and TM-1×TX-1046(pop2),respectively.In addition,200 pairs of SSR primers(H)weremined from the DNA sequence of G.raimondii reported by Paterson et al.(2012)andused to screen the polymorphisms found in the three parents.The results indicated thatthere were 28(14%)and 38(19%)pairs of polymorphic primers screened in popl and pop2,respectively.In total,there were 309 and 468 pairs of markers that produced 344 and 537loci in the two populations,respectively.There were 89 common markers between the twopopulations,bridging for integrating the genetic maps.According to mapped loci from theprevious studies,all 89 common markers were affirmatory loci.A total of 622 SSRs wereidentified in the genetic map.These produced 713 loci that were employed to construct a genetic linkage map using JoinMap 3.0,and these loci were mapped onto 37 linkage groups which were assigned to 26 chromosomes of the cotton AD genome.The total recombination length of the map was 3594.70 cM,covering approximately 87.78%of the total recombination length of the cotton genome,based on estimates of the genetic distance of the 4450 cM cotton genome,and the average distance of 5.04 cM between the adjacent markers.The At-subgenome covered 1870.48 cM of the cotton genome and the average distance between adjacent markers was 5.92 cM,while the Dt-subgenome covered 1724.22 cM,with an average distance between adjacent markers of 4.34 cM.The densities of markers varied between chromosomes;ranging from 2.41 cM(D6)to 8.93 cM(A12).There were 50 markers on Chr.D8,representing the greatest abundance of markers of the 26 chromosomes.The chromosomes with the fewest markers were Chrs.A4 and D4;each only with 10 polymorphic loci.Chr.A5 had the greatest length,covering 256.67 cM,and the shortest genetic distance was 59.51 cM,which related to Chr.D4.The largest gap between two adjacent loci was 32.56 cM on Chr.A12.A total of 191 segregation-distorted loci,accounting for 26.79%(191/713)of the mapped loci,were unevenly distributed on the 26 cotton chromosomes with 1 to 23 loci on each chromosome.The distorted rates ranged from 9.68 to 62.16%.Fewer distorted loci were located on the At-subgenome than on the Dt-subgenome(72 vs 119,respectively).2.Introgression analysisThe total length of the introgressed segments spanned 3887.75 cM,with an average length of 11.15 cM between the segments,and represented 71.55%of the tetraploid cotton genome.The introgression percentages of the At-and Dt-subgenomes were 76.77%and 65.88%,respectively.The introgressed segments in each line varied in length,ranging from 1.1 cM to 58.80 cM.The average length of the introgressed segments per chromosome was 148.80 cM and ranged from 39.70 cM on Chr.D4 to 330.20 cM on Chr.A9.The largest coverage of introgressed segments was 177.37 cM in length on Chr.A9,and the shortest was 35.49 cM on Chr.D4,with an average coverage of 98.92 cM.The percentage of chromosomal introgression length was highest on Chr.A12(97.04%)and lowest on Chr.D8(42.19%).The coverage rates on Chrs.A3,A8,A9,A10,A12,A13,and D10 were all greater than 80%.The average length of introgression segments of the ILs derived from TX-256 was 10.74 cM and with a total length of 1104.15 cM,which accounted for 28.40%of the whole introgression fragment.The length of introgression fragment from TX-1046 was 2783.60 cM and 11.32 cM on average,accounting for 71.60%of the whole introgression fragment.3.Association mapping of yield and fiber quality related traitsThe TASSEL package was used to analyze molecular marker data and yield-relatedand fiber quality related traits in different different environments individually through the Q+K+MLM model.A total of 37 markers were associated with BW,and the PVE rangedfrom 1.02 to 13.23%.Among them,14 markers were detected in more than oneenvironment.Sixteen markers and 21 markers were found in At-and Dt-subgenome,respectively.Eighteen QTLs for BW were present in El,with the PVE ranging from 1.02%to 2.84%;13 were present in E2,with the PVE ranging from 3.91%to 8.67%;9 werepresent in E3,with the PVE ranging from 4.83 to 9.25%;and 12 were present in E4,withthe PVE ranging from 6.27%to13.23%.Chrs.A1,A4,A10,A11,A13,D8,and D10 werefound to have one marker each,while Chrs.A5,D5,and D9 were found to have twomarkers each.Three markers each were detected on Chrs.A3,A9,A12,and D13,and Chrs.Dl,D3,and D7 were found to have four markers each.There were 33 markers associated with LP in the four environments,and the PVEranged from 1.00 to 12.23%.Nine markers associated with QTLs were detected in morethan one environment.Fourteen markers and 19 markers were found in the At-and Dt-subgenomes,respectively.Twenty QTLs for LP were present in E1,with a PVE range of1.00 to 2.14%,8 were present in E2 with a PVE range of 3.63 to 12.23%,5 were present inE3 with a PVE range of 3.51 to 6.18%,and 11 were present in E4 with a PVE range of 3.52to 7.31%.Nine markers were anchored on Chrs.A5,A7,All,D1,D2,D4,D5,D8,andD11.Chrs.A3,A9,A12,A13,and D7,had two markers each,Chrs.A10 and D9 had threemarkers each,and Chrs.D3 and D10 had four markers each.Thirty-eight markers were associated with S1,with a PVE range of 1.09 to 8.19%.Tenmarkers associated with QTLs were detected in more than one environment.Eighteenmarkers and 20 markers were found in the At-and Dt-subgenomes,respectively.Twenty-two QTLs for SI were present in E1,with a PVE range of 1.09 to 2.75%,10 werepresent in E2 with a PVE range of 4.02 to 7.56%,12 were in E3 with a PVE range of 3.56to 8.19%,and 8 were present in E4 with a PVE range of 3.57 to 6.48%.Nine markers wereanchored on Chrs.A6,A7,A8,A11,D2,D4,D5,D6,and D11 respecitively.Chrs.Al,A5,A9 and D3 had two markers each,Chrs.D7,D9,and D10 had three markers each,and Chrs.A12,A13,and D1 had four markers each.A total of 15 markers were associated with FE,and the PVE ranged from 2.14 to 14.77%.Among them,4 markers were detected in more than one environment.Eightmarkers and 7 markers were found in At-and Dt-subgenome,respectively.Ten QTLs forFE were present in E1,with the PVE ranging from 2.14 to 9.45%;3 were present in E2,with the PVE ranging from 10.77 to 14.44%;6 were present in E3,with the PVE rangingfrom 9.67 to 14.06%.Chrs.D3,D9,D11,D12,and D13 were found to have one markereach,while Chrs.A13,and D5 were found to have two markers each.Three markers eachwere detected on Chrs.Al,and A7.A total of 17 markers were associated with FL,and the PVE ranged from 2.53 to14.34%.Among them,4 markers were detected in more than one environment.Sevenmarkers and 10 markers were found in At-and Dt-subgenome,respectively.ThirteenQTLs for FL were present in E1,with the PVE ranging from 2.53 to 7.92%;3 were presentin E2,with the PVE ranging from 9.22 to 12.66%;6 were present in E3,with the PVEranging from 10.33 to 14.34%.Chrs.D5,D6,D8,and D10 were found to have one markereach,while Chrs.A9,A13,D9,D11,and D12 were found to have two markers each.Threemarkers each were detected on Chrs.A7.A total of 17 markers were associated with FS,and the PVE ranged from 2.45 to15.49%.Among them,6 markers were detected in more than one environment.Ninemarkers and 8 markers were found in At-and Dt-subgenome,respectively.Seven QTLsfor FS were present in E1,with the PVE ranging from 2.45 to 4.18%;7 were present in E2,with the PVE ranging from 8.48 to 15.49%;9 were present in E3,with the PVE rangingfrom 9.00 to 14.86%.Chrs.A7,A8,A9,A11,A13,D2,D4,D11,and D13 were found tohave one marker each,while Chrs.Al,A6,D8,and D9 were found to have two markerseach.A total of 16 markers were associated with FU,and the PVE ranged from 2.58 to17.24%.Among them,1 marker was detected in more than one environment.Eight markersand 8 markers were found in At-and Dt-subgenome,respectively.Three QTLs for FUwere present in E1,with the PVE ranging from 2.58 to 7.70%;7 were present in E2,withthe PVE ranging from 9.34 to 16.56%;7 were present in E3,with the PVE ranging from10.11 to 17.24%.Chrs.A1,A3,A8,A9,D6,and D10 were found to have one marker each,while Chrs.A6,A7,and D11 were found to have two markers each.Three markers eachwere detected on Chrs.D9.A total of 12 markers were associated with MIC,and the PVE ranged from 5.70 to14.42%.Among them,4 markers were detected in more than one environment.Seven markers and 5 markers were found in At-and Dt-subgenome,respectively.Four QTLs for MIC were present in E1,with the PVE ranging from 5.70 to 6.58%;7 were present in E2,with the PVE ranging from 9.16 to 11.96%;5 were present in E3,with the PVE ranging from 9.16 to 14.42%.Chrs.A1,A2,A6,A9,A11,D9,and D11 were found to have one marker each,while Chrs.A7 was found to have two markers each.Three markers each were detected on Chrs.D8.4.Evaluation of the yield-related,fiber quality related traits,drought-resistance and verticillium wilt-resistanceAccording to the result of QTL mapping and variation analysis,we detected three ILs(IL-A1-1,IL-D9-1 and IL-D10-2)that have significant difference in yield and fiber quality related traits compared with TM-1.Five ILs(IL-D2-3,IL-D2-2,IL-D7-1,IL-A8-1 and IL-A9-1)with much lower relative disease index than TM-1 were found by resistance of verticillium wilt.Three ILs(IL-A11-1,IL-A13-1 and IL-D5-1)showd higher drought-resistance than TM-1.