小麦骨干亲本矮孟牛衍生系主要农艺及品质性状的关联分析
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摘要
小麦(TriticumaestivumL.)是世界上主要粮食作物之一，小麦的许多重要性状是多基因控制的数量性状(Quantitativetraitlocus/loci，QTL)，数量性状的表型和基因型研究是育种工作的基础。
关联分析利用不同基因座等位变异(基因)间的连锁不平衡关系，进行标记与性状的相关性分析，它是一种十分有效的作图方法，可以鉴定特定目标性状基因(或染色体区段)。关联分析技术与传统的QTL相比，具有周期短、精确、鉴定位点多等优势。
“矮孟牛”是一个新确定的小麦骨干亲本，由其培育出一批大面积推广的品种，也衍生出许多具有广泛应用价值的亲本育种材料。本研究利用“矮孟牛”及其衍生系共109份材料构成一个研究群体，获得6个环境下的农艺及品质性状数据；选用覆盖小麦全基因组的971个DArT（DiversityArrayTechnology）标记扫描；分析群体的遗传多样性水平和选择牵连效应“V”字形谷区段；筛选矮孟牛3个亲本的特异标记位点（染色体区段），明确它们在衍生后代材料中的遗传频率和遗传贡献率；确定群体的遗传结构和连锁不平衡式样；最后，利用基于混合线性模型的TASSEL2.0.1软件，对株高、籽粒、穗部等重要农艺性状及面粉、面团特性、加工品质等主要品质性状进行关联分析，定位控制这些性状的位点。
对矮孟牛及其衍生系进行全基因组的高密度扫描，通过标记/性状关联分析，可以找到一些重要的基因组区段，定位一些骨干亲本所携带和传递的产量、品质相关基因。了解骨干亲本及其衍生系的基因组学基础，为品种分子设计、组合选配及后代分子标记选择提供重要的理论依据，进而为分子育种服务。本研究获得以下主要结果：
1.明确了该群体的遗传多样性水平。全基因组扫描确定全部109份小麦材料的多样性指数（PIC值）范围是0.054~0.5，平均值为0.408；绘制了21条染色体的PIC曲线变化趋势图，获得60多个发生选择牵连效应的“V”字形基因组区段。
2.明确了亲本特异标记位点的遗传特性。筛选到矮孟牛3个亲本的330个特异DArT位点，获得了它们在41份衍生后代（有详细系谱来源）中的遗传频率和遗传贡献率。结果发现3个原始亲本遗传差异较大；在对后代的影响方面，牛朱特影响最大，矮丰3号次之，孟县201最小；明确了对后代有较大贡献、高频率传递的染色体位点，其中7个位点效应显著。
3.获得关联群体的遗传结构和连锁不平衡（Linkagedisequilibrium，LD）状况。基于模型的STRUCTURE软件将该群体划分为5个亚群。整个群体中，7.03%的DArT位点之间存在显著的LD（P<0.01），在各亚群中存在显著LD的位点占0.501%~2.64%，在染色体上发现了许多LD块。整个群体的连锁不平衡衰减距离为23.6cM，各亚群的衰减距离为6~15cM。
4.对48个重要的农艺、品质性状进行6个环境下的关联分析，共确定了779个标记/性状关联（marker-traitassociations，MTAs）。这些关联分布在除4D、5A外的19条染色体上。其中，4个关联在4个环境中重复检测到，16个关联在3个环境中重复检测到，66个关联在两个环境中重复检测到。407个关联标记的变异解释率（R~2）较大（超过10%），14个关联标记的R~2超过20%。
4.1株高相关性状的关联分析。株高共检测到55个显著的关联，其中，6个关联在3个环境中重复检测到，3个关联在4个环境中重复检测到（标记的R~2平均为10.06%、14.29%和14.32%）。标记wPt-3457在4个环境下均检测到，R~2均大于10%，且具有最大R~2值（20.64%，p<0.0001），这可能是一个重要的QTL；穗下茎共检测到68个显著的关联，其中2个关联可在3个环境中重复检测到，1个关联可在4个环境中重复检测到。标记wPt-4744的R~2最大（24.26%，p<0.0001）；旗叶（长、宽及面积）共检测到61个显著的关联，各位点的R~2多小于10%。
4.2籽粒相关性状的关联分析。籽粒相关性状（千粒重、容重、粒径、籽粒硬度）共检测到76个显著的关联。其中，籽粒硬度的1个关联可在3个环境中重复检测到；标记wPt-2526、wPt-9613和wPt-8598都同时与千粒重、粒径关联，R~2平均为9.4%和12.44%。
4.3穗部相关性状的关联分析。穗部相关性状（穗长、总小穗数、有效小穗数、不育小穗数、穗密度、穗粒数、穗粒重）共检测到97个显著的关联。总小穗数的3个关联可在3个环境中重复检测到。其中穗长与穗密度的4个关联标记一致，尤其是标记wPt-9749、wPt-5737和wPt-9814的R~2都较高，在极显著水平下（p<0.0001）分别为15.19%和11.56%。
4.4面粉特性的关联分析。面粉色泽（L*、a*和b*）共检测到27个显著的关联。色泽a*有两个极显著的关联（p<0.0001）（标记wPt-1196和wPt-669693）可在3个环境中重复检测到，R~2分别平均为14.26%和11.43%。面粉蛋白质含量，共检测到45个显著的关联，标记wPt-7330在3个环境中重复检测到，wPt-0864的R~2最大（18.12%）。湿面筋含量和指数，共检测到40个显著的关联，标记wPt-665169同时与两性状关联，在极显著水平下对湿面筋指数的变异解释率R~2为11.89%。Zeleny沉淀值，检测到46个显著的关联。wPt-6531和wPt-8393在2个环境中重复检测到，对性状的变异解释率最高，平均R~2为10.54%。淀粉糊化特性（RVA）的六个参数(糊化温度、峰值黏度、衰减值、回升值、最终黏度和低谷黏度)共检测到130个显著的关联。糊化温度的1个关联（wPt-9277）在3个环境中重复检测到。5个标记同时与3个参数关联，8个标记同时与4个参数关联。尤其是标记wPt-9423与4个参数关联且都在极显著水平下R~2为15.09%~23.27%。
4.5面团流变学特性的关联分析。面团揉混Mixograph参数（峰值时间、峰值高度、峰值宽度、达到峰值时间总功量和8分钟带宽）共检测到63个显著的关联。标记wPt-0610对峰值宽度的R~2最高（15.86%，p<0.0001）。
4.6加工品质的关联分析。面条品尝测试的七个参数（色泽、表现状态、硬度、粘弹性、光滑性、食味、品尝打分）共检测到30个显著的关联。wPt-3304等3个标记同时与3个参数关联，R~2都大于10%。面条TPA测试的七个参数（硬度、黏着性、弹性、黏聚性、胶着性、咀嚼性、回复性）共检测到33个显著的关联，wPt-6854等3个标记同时与3个参数关联，且R~2为10%左右。
5.定位了30个新的性状关联标记。其中，与株高和穗下茎极显著关联的标记wPt-9280（R~2分别为13.74%和10.89%）与相同关联的定位标记wPt-4017（6A，20.7cM）存在完全连锁不平衡，可视为同一位点。
6.在与性状关联的标记中，确定了103个来源于三个亲本的特异标记。其中，1A染色体上与色泽等性状关联的标记位点wPt-2872来自亲本矮丰3号，与株高等关联的标记位点wPt-3698来源于孟县201，与小穗数等关联的标记位点wPt-6005来源于牛朱特。
7.综合考虑亲本特异性、选择牵连效应、连锁不平衡程度、关联显著性及重复性和效应大小，获得一批重要的染色体区段和位点。其中，标记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）等具有重要意义，可作为以后研究的重点。
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.
关联分析利用不同基因座等位变异(基因)间的连锁不平衡关系，进行标记与性状的相关性分析，它是一种十分有效的作图方法，可以鉴定特定目标性状基因(或染色体区段)。关联分析技术与传统的QTL相比，具有周期短、精确、鉴定位点多等优势。
“矮孟牛”是一个新确定的小麦骨干亲本，由其培育出一批大面积推广的品种，也衍生出许多具有广泛应用价值的亲本育种材料。本研究利用“矮孟牛”及其衍生系共109份材料构成一个研究群体，获得6个环境下的农艺及品质性状数据；选用覆盖小麦全基因组的971个DArT（DiversityArrayTechnology）标记扫描；分析群体的遗传多样性水平和选择牵连效应“V”字形谷区段；筛选矮孟牛3个亲本的特异标记位点（染色体区段），明确它们在衍生后代材料中的遗传频率和遗传贡献率；确定群体的遗传结构和连锁不平衡式样；最后，利用基于混合线性模型的TASSEL2.0.1软件，对株高、籽粒、穗部等重要农艺性状及面粉、面团特性、加工品质等主要品质性状进行关联分析，定位控制这些性状的位点。
对矮孟牛及其衍生系进行全基因组的高密度扫描，通过标记/性状关联分析，可以找到一些重要的基因组区段，定位一些骨干亲本所携带和传递的产量、品质相关基因。了解骨干亲本及其衍生系的基因组学基础，为品种分子设计、组合选配及后代分子标记选择提供重要的理论依据，进而为分子育种服务。本研究获得以下主要结果：
1.明确了该群体的遗传多样性水平。全基因组扫描确定全部109份小麦材料的多样性指数（PIC值）范围是0.054~0.5，平均值为0.408；绘制了21条染色体的PIC曲线变化趋势图，获得60多个发生选择牵连效应的“V”字形基因组区段。
2.明确了亲本特异标记位点的遗传特性。筛选到矮孟牛3个亲本的330个特异DArT位点，获得了它们在41份衍生后代（有详细系谱来源）中的遗传频率和遗传贡献率。结果发现3个原始亲本遗传差异较大；在对后代的影响方面，牛朱特影响最大，矮丰3号次之，孟县201最小；明确了对后代有较大贡献、高频率传递的染色体位点，其中7个位点效应显著。
3.获得关联群体的遗传结构和连锁不平衡（Linkagedisequilibrium，LD）状况。基于模型的STRUCTURE软件将该群体划分为5个亚群。整个群体中，7.03%的DArT位点之间存在显著的LD（P<0.01），在各亚群中存在显著LD的位点占0.501%~2.64%，在染色体上发现了许多LD块。整个群体的连锁不平衡衰减距离为23.6cM，各亚群的衰减距离为6~15cM。
4.对48个重要的农艺、品质性状进行6个环境下的关联分析，共确定了779个标记/性状关联（marker-traitassociations，MTAs）。这些关联分布在除4D、5A外的19条染色体上。其中，4个关联在4个环境中重复检测到，16个关联在3个环境中重复检测到，66个关联在两个环境中重复检测到。407个关联标记的变异解释率（R~2）较大（超过10%），14个关联标记的R~2超过20%。
4.1株高相关性状的关联分析。株高共检测到55个显著的关联，其中，6个关联在3个环境中重复检测到，3个关联在4个环境中重复检测到（标记的R~2平均为10.06%、14.29%和14.32%）。标记wPt-3457在4个环境下均检测到，R~2均大于10%，且具有最大R~2值（20.64%，p<0.0001），这可能是一个重要的QTL；穗下茎共检测到68个显著的关联，其中2个关联可在3个环境中重复检测到，1个关联可在4个环境中重复检测到。标记wPt-4744的R~2最大（24.26%，p<0.0001）；旗叶（长、宽及面积）共检测到61个显著的关联，各位点的R~2多小于10%。
4.2籽粒相关性状的关联分析。籽粒相关性状（千粒重、容重、粒径、籽粒硬度）共检测到76个显著的关联。其中，籽粒硬度的1个关联可在3个环境中重复检测到；标记wPt-2526、wPt-9613和wPt-8598都同时与千粒重、粒径关联，R~2平均为9.4%和12.44%。
4.3穗部相关性状的关联分析。穗部相关性状（穗长、总小穗数、有效小穗数、不育小穗数、穗密度、穗粒数、穗粒重）共检测到97个显著的关联。总小穗数的3个关联可在3个环境中重复检测到。其中穗长与穗密度的4个关联标记一致，尤其是标记wPt-9749、wPt-5737和wPt-9814的R~2都较高，在极显著水平下（p<0.0001）分别为15.19%和11.56%。
4.4面粉特性的关联分析。面粉色泽（L*、a*和b*）共检测到27个显著的关联。色泽a*有两个极显著的关联（p<0.0001）（标记wPt-1196和wPt-669693）可在3个环境中重复检测到，R~2分别平均为14.26%和11.43%。面粉蛋白质含量，共检测到45个显著的关联，标记wPt-7330在3个环境中重复检测到，wPt-0864的R~2最大（18.12%）。湿面筋含量和指数，共检测到40个显著的关联，标记wPt-665169同时与两性状关联，在极显著水平下对湿面筋指数的变异解释率R~2为11.89%。Zeleny沉淀值，检测到46个显著的关联。wPt-6531和wPt-8393在2个环境中重复检测到，对性状的变异解释率最高，平均R~2为10.54%。淀粉糊化特性（RVA）的六个参数(糊化温度、峰值黏度、衰减值、回升值、最终黏度和低谷黏度)共检测到130个显著的关联。糊化温度的1个关联（wPt-9277）在3个环境中重复检测到。5个标记同时与3个参数关联，8个标记同时与4个参数关联。尤其是标记wPt-9423与4个参数关联且都在极显著水平下R~2为15.09%~23.27%。
4.5面团流变学特性的关联分析。面团揉混Mixograph参数（峰值时间、峰值高度、峰值宽度、达到峰值时间总功量和8分钟带宽）共检测到63个显著的关联。标记wPt-0610对峰值宽度的R~2最高（15.86%，p<0.0001）。
4.6加工品质的关联分析。面条品尝测试的七个参数（色泽、表现状态、硬度、粘弹性、光滑性、食味、品尝打分）共检测到30个显著的关联。wPt-3304等3个标记同时与3个参数关联，R~2都大于10%。面条TPA测试的七个参数（硬度、黏着性、弹性、黏聚性、胶着性、咀嚼性、回复性）共检测到33个显著的关联，wPt-6854等3个标记同时与3个参数关联，且R~2为10%左右。
5.定位了30个新的性状关联标记。其中，与株高和穗下茎极显著关联的标记wPt-9280（R~2分别为13.74%和10.89%）与相同关联的定位标记wPt-4017（6A，20.7cM）存在完全连锁不平衡，可视为同一位点。
6.在与性状关联的标记中，确定了103个来源于三个亲本的特异标记。其中，1A染色体上与色泽等性状关联的标记位点wPt-2872来自亲本矮丰3号，与株高等关联的标记位点wPt-3698来源于孟县201，与小穗数等关联的标记位点wPt-6005来源于牛朱特。
7.综合考虑亲本特异性、选择牵连效应、连锁不平衡程度、关联显著性及重复性和效应大小，获得一批重要的染色体区段和位点。其中，标记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）等具有重要意义，可作为以后研究的重点。
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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