| Wheat (Triticum aestivum L.) is a major staple food in the world. Most traits in wheat are quantitative. Studies on the phenotype and genotypes for quantitative trait locus/loci (QTL) are the basis for breeding program.Association mapping is an important method to identify QTL contributing to phenotypic variation based on linkage disequilibrium (LD), which has obvious advantages compared with traditional linkage analysis." Aimengniu" is a newly identified founder parent in wheat, and a number of varieties and parental breeding materials were derived from it. In this study, founder parent "Aimengniu" and its derived progenies were planted in six environments, and a large number of phenotype data were obtained. Genetic diversity and hitchhiking effects "V" shaped bottom were preliminary analyzed by scanning the collection genome with DArT (Diversity Array Technology) markers;330special markers for parents were selected and their genetic contribution rates for derivatives were obtained; population structure and linkage disequilibrium were determined for the association population; association mapping for plant height, grain, spike related agronomic traits and quality traits on flour, dough, noodle quality were performed using mixed linear model in TASSEL2.0.1software in order to locate these quantitative trait locus.If the founder parent "Aimengniu" could be scanned high-densely, some of important genomic segments could be detected by association analysis, and genes related with yield and quality traits carried by founder parent could also be located. So the genomic base of founder parent could be clarified, and important theoretical basis for molecular breeding could be provided for molecular design, parental combination match, and molecular markers selection in wheat breeding program.The main results were as the following:1. Clarifying genetic diversity in the population. The PIC of109wheat collection by genome-wide scanning was0.054-0.5, and the mean value was0.408. The PIC curve of each chromosome was drew, and genomic regions with60"V" selection sweep were found by hitchhiking effect analysis.2. Defining the genetic characters of special markers in parents. Derivatives with detail pedigrees were selected from the total material. The special DArT markers for three parents (Aifeng3//Mengxian201/Neuzucht) were identified and their genetic contribution ratios and transmission frequencies were analyzed. The results indicated that three parents had large genetic differences. Neuzucht contributed more genetic components to their derivatives than other parents, followed by Aifeng3, Mengxian201did the least. Markers with high genetic contribution ratio and high frequency transmission were found,7markers of which had significant effect.3. Linkage disequilibrium (LD) and population structure were obtained in order to construct the association population. The population was derived into five subpopulations.7.03%of the DArT markers was in significant LD (p<0.01) in total, while the percentage was0.501%-2.64%in subpopulations, some LD blocks were found in chromosomes regions. LD extended23.6cM, subpopulations extended6-15cM.4. Association analysis for48important agronomic and quality traits (in6environments) were determined, and779significant associations were identified, which spread over19chromosomes except for4D and5A. In these associations,4association were detected repeatedly in four environments,16associations in three environments,66associations in two environments. R2for407associations was large (>10%), and R2for14associations exceeded20%.4.1Associations for plant height and related traits.55associations were identified for plant height. In these associations,6associations were detected repeatedly in three environments,3associations in four environments (R2was10.06%,14.29%and14.32%in average). The marker wPt-3457was detected in four environments with the maximum R2value (20.64%,p<0.0001).68associations were identified for the first interrnode length counted from the top. In these associations,2associations were detected repeatedly in three environments, and1association in four environments. The marker wPt-4744was with the maximum R2(24.26%,p<0.0001).61associations were identified for flag leaf (length, width and area), and R2of most markers was larger (>10%).4.2Association mapping for grain related traits.76associations for grain related traits (thousand kernel weight, test weight, grain diameter, grain hardness) were identified. In which,1association for grain diameter were detected repeatedly in two environments,1association for grain hardness in three environments. The marker wPt-2526, wPt-9613and wPt-8598were associated with both thousand kernel weight and grain diameter, R2was9.4%and12.44%.4.3Association for spike related traits.97associations for spike related traits (spike length, total spikelet number per spike, fertile spikelet number, sterile spikelet number, spike density, grain number per spike, grain weight per spike) were identified. In which,3associations for total spikelet number were detected repeatedly in three environments.4markers associated with spike length and spike density were the same, R2of wPt-9749, wPt-5737and wPt-9814were15.19%and11.56%(p<0.0001).4.4Association for flor feature.27associations were identified for flour color (L*, a*and b*). Two very significant associations (marker wPt-1196and wPt-669693) were found repeatedly in three environments, R2was14.26%and11.43%in average.45associations were identified for flour protein content.1association (wPt-7330) was repeatedly detected in three environments, wPt-0864had the maximum R2(18.12%).40associations were identified for gluten content and gluten index. The marker wPt-665169was associated with both traits, R2for gluten index was18.11%.46associations were identified for Zeleny sedimentation value, The markers wPt-6531and wPt-8393were repeatedly detected in two environments, R2was10.54%.130associations for RVA parameters (RPV, RTV, RBd, RFV, RSb and RPT) were identified.1association of RPT was repeatedly detected in three environments. There were5markers associated with three parameters,8markers associated with4parameters. The marker wPt-9423was associated with4parameters, R2was15.09%-23.27%very significantly.4.5Association for dough rheological properties.63associations were identified for Mixograph parameters (MPT, MPV, MPW, MPI and MTxV). The R2of wPt-0610associated with MPW was15.68%.4.6Association for noodle quality.30associations were identified for white water noodle score parameters (NCo, NAp, NFi, NSt, NSm, NTa and NTS). There were3markers such as wPt-3304associated with three parameters, with R2more than10%.33associations were identified for white water noodle TPA parameters (NHa, NAd, NSp, NCo, NGu, NChe and NRe). R2was0.4%-13.49%. There were3markers associated with three parameters, such as wPt-6854, R2was more or less10%.5. A total of30unmapped markers were located on chromosomes based on LD. In these markers, wPt-9280was in total linkage disequilibrium with wPt-4017(6A,20.7cM). Both the two markers were associated with PH and FIITL, and they could be seemed as the same locus.6. A total of103special DArT markers for3founder parents were selected from the markers associated with traits. On chromosome1A, wPt-2872associated with flour clour was derived from Aifeng3, wPt-3698associated with PH was derived from Mengxian201, and wPt-6005associated with TSN was derived from Neuzucht.7. Some important chromosome regions and locus were detected by association mapping based on hitchhiking effect analysis. The markers wPt-730408(1A,90.1cM), wPt-9423(2B,57.8cM), wPt-5836(3B,71.6cM), wPt-3457(5B,92.3cM), wPt-7576(6B,73.6cM) could be the focus in future study.
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