CN112852989B - 一种与大豆农艺性状相关的snp位点组合、液相基因芯片及应用 - Google Patents
一种与大豆农艺性状相关的snp位点组合、液相基因芯片及应用 Download PDFInfo
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Abstract
本发明涉及一种与大豆农艺性状相关的SNP位点组合、液相基因芯片及应用,与大豆农艺性状相关的SNP位点组合,包括223个SNP位点,每个SNP位点包含两个不同碱基变异位点,用于检测该位点的等位基因变化,所述223个SNP位点的物理位置是基于大豆品种Williams82的全基因组序列比对确定的,所述大豆品种Williams82的全基因组序列的版本号为Glycine max Wm82.a2.v1。本发明所采用的223个SNP位点与大豆的重要农艺性状相关,可通过测定大豆植株DNA中这223个SNP位点的基因型来评估大豆植株的农艺性状,将其应用于大豆的分子辅助育种或全基因组育种时,加快了育种进程。
Description
技术领域
本发明属于分子植物育种领域,具体涉及一种与大豆农艺性状相关的SNP位点组合、液相基因芯片及应用。
背景技术
SNP标记的开发是以DNA测序为基础的,自从2005年454测序仪问世以来的十多年时间,二代测序技术不断完善,基因组测序效率得到极大提高,测序成本也大幅度下降,大量物种的全基因组序列完成,极大地推进了功能基因组研究的进展。
大豆作为全球最重要的经济作物,同时也是全球最重要的粮食作物,目前在大豆的遗传育种过程中,仍旧采用的是传统的表型性状评估方法,其需要对种子进行种植后,通过观察其株高、测定蛋白含量等方式来获得其性状指标,周期较长,而随着SNP标记技术的快速发展,对不同的品种进行重测序,利用重测序发现的SNP标记,利用全基因组关联分析(Genome-wide Association Mapping,GWAS)对重要农艺性状进行关联分析,确定重要农艺性状相关的候选基因位点,建立起一套高效快速、成熟稳定、成本低、通量高的基因型鉴定方法,是分子生物学研究人员优先考虑的方向。
发明内容
本发明的目的在于克服现有技术的缺陷,提供一种与大豆农艺性状相关的SNP位点组合、基因芯片及应用。
为了实现上述目的,本发明采取的技术方案如下:
一种与大豆农艺性状相关的SNP位点组合,其特征在于,包括223个SNP位点,每个SNP位点包含两个不同碱基变异位点,用于检测该位点的等位基因变化,所述223个SNP位点的物理位置是基于大豆品种Williams82的全基因组序列比对确定的,所述大豆品种Williams82的全基因组序列的版本号为Glycine max Wm82.a2.v1,所述大豆品种Williams82的全基因组序列的获取网址为:https://phytozome.jgi.doe.gov.;所述SNP位点的变异信息采用染色体编号_物理位置参考基因型/等位基因型的形式进行表示,所述223个SNP位点的变异信息如下:
Chr01_01533882 A/G;Chr01_04026903 G/A;Chr01_04050717 A/T;Chr01_04092615 G/A;Chr01_39860894 C/T;Chr01_49903973 A/G;Chr01_50602779 A/C;Chr01_50653236 T/G;Chr01_51315364 A/G;Chr01_53509482 G/A;Chr01_54065323 C/T;Chr01_55547694 T/A;Chr02_05225452 C/T;Chr02_06300927 C/T;Chr02_38935935 A/G;Chr02_43559616 G/A;Chr02_44953925 G/C;Chr02_45012265 C/T;Chr02_45106877 G/A;Chr02_45225277 A/T;Chr02_45460408 A/G;Chr03_00155260 C/T;Chr03_00333082 G/C;Chr03_00558044 C/G;Chr03_01404553 G/A;Chr03_18107159 G/A;Chr03_25891807 T/G;Chr03_36421392 A/G;Chr03_36426626 T/C;Chr03_36451021 G/A;Chr03_36504983 C/A;Chr03_36789422 G/C;Chr03_37027494 C/A;Chr03_37706557 T/A;Chr03_38305381 G/A;Chr04_01886636 G/A;Chr04_03350250 C/A;Chr04_08569889 T/A;Chr04_16473219 A/G;Chr04_45658472 T/G;Chr04_46878018 G/A;Chr04_50850178 G/A;Chr04_51554352 C/A;Chr04_51579450 G/A;Chr05_05558466 C/T;Chr05_05575650 A/G;Chr05_05613716 T/C;Chr05_18929941 T/C;Chr05_22058564 A/G;Chr05_32075424 C/T;Chr05_33844667 A/G;Chr05_34000026 G/A;Chr05_34977447 C/T;Chr05_36371924 C/T;Chr05_39604331 C/T;Chr05_39788521 C/T;Chr05_40075652 T/C;Chr05_42019019 G/T;Chr06_01756279 A/C;Chr06_02636926 T/C;Chr06_03286909 C/T;Chr06_04134589 A/T;Chr06_04351486 G/A;Chr06_10505562 T/A;Chr06_13105258 A/T;Chr06_13432800 C/A;Chr06_13481784 T/G;Chr06_15231313 G/T;Chr06_15968336 A/C;Chr06_17382650 T/C;Chr06_17582094 G/A;Chr06_17602402 T/C;Chr06_17626369 T/A;Chr06_19781007 C/T;Chr06_27625128 A/G;Chr06_28928355 G/T;Chr06_42252843 C/T;Chr06_48428377 C/T;Chr06_50163774 G/A;Chr06_50975144 T/G;Chr07_01952143 T/C;Chr07_05575080 C/T;Chr07_05825087 T/C;Chr07_15480093 T/C;Chr07_19025998 C/T;Chr07_42689775 C/T;Chr07_42700692 G/T;Chr07_42732051 A/G;Chr07_42782332 A/T;Chr07_42836543 T/A;Chr08_00776002 C/T;Chr08_01028572 C/A;Chr08_07805605 A/C;Chr08_09185800 C/G;Chr08_22078860 G/A;Chr09_00458254 G/A;Chr09_00475009 G/A;Chr09_00500375 T/C;Chr09_04283906 A/C;Chr09_06653411 T/A;Chr09_35879535 G/A;Chr09_38843968 T/A;Chr09_40052962 A/T;Chr09_41676859 G/A;Chr09_45975341 C/A;Chr09_46200899 C/A;Chr09_46308505 G/A;Chr09_46478149 T/A;Chr09_46836433 A/G;Chr10_02750802 G/C;Chr10_02870996 G/T;Chr10_02887410 A/T;Chr10_02927284 T/A;Chr10_31900041 T/C;Chr10_45082937 A/G;Chr10_45127748 T/C;Chr10_45175769 G/A;Chr10_48926597 G/A;Chr10_49256007 A/G;Chr10_49302884 T/C;Chr10_49343783 C/T;Chr11_02104739 T/C;Chr11_02167163 T/G;Chr11_02630521 T/G;Chr11_04153990 C/T;Chr11_04306322 T/C;Chr11_09896347 G/T;Chr11_32376132 G/A;Chr11_32506058 C/T;Chr11_32929777 C/T;Chr11_33857564 G/A;Chr12_03951770 G/A;Chr12_08916858 T/C;Chr12_35265460 G/A;Chr12_35289582 G/T;Chr12_35578344 A/G;Chr12_36595459 C/A;Chr12_36704530 G/C;Chr12_36736475 G/A;Chr12_36765947 T/G;Chr13_16484275 T/C;Chr13_18615062 A/C;Chr13_19460489 T/C;Chr13_21768219 C/G;Chr13_29215285 G/T;Chr13_29550344 G/A;Chr13_30388748 A/G;Chr13_41775097 G/A;Chr13_42028098 A/C;Chr13_42050209 T/A;Chr13_42150995 C/T;Chr13_42216053 C/T;Chr13_42383660 C/A;Chr13_42410927 A/G;Chr13_44483438 A/G;Chr13_45066236 G/T;Chr13_45794372 C/T;Chr14_02226559 C/T;Chr14_04785275 A/C;Chr14_04978437 A/G;Chr14_09234257 T/C;Chr14_45860975 A/T;Chr14_46525690 A/G;Chr14_46614414 A/G;Chr14_47779860 A/T;Chr14_48354923 C/T;Chr15_00207098 A/G;Chr15_00282154 T/C;Chr15_00474286 T/C;Chr15_03989240 G/C;Chr15_06834700 G/T;Chr15_08981420 C/T;Chr15_09077137 C/G;Chr15_09108212 G/A;Chr15_09138650 T/C;Chr15_09176525 G/A;Chr15_09325304 C/T;Chr15_09632956 A/G;Chr15_09950434 A/G;Chr15_10109864 T/G;Chr15_10128698 T/G;Chr15_10605120 G/A;Chr15_15854711 A/T;Chr15_49558739 A/C;Chr15_50357591 A/G;Chr15_50377398 T/C;Chr15_50532317 A/G;Chr16_04075059 A/T;Chr16_06026215 A/C;Chr16_18681277 C/T;Chr16_32911332 G/C;Chr17_08312752 G/A;Chr17_12475327 A/G;Chr17_38307270 A/G;Chr17_38350306 T/G;Chr17_39257059 C/A;Chr18_00453852 T/C;Chr18_01331239 T/A;Chr18_05957508 T/C;Chr18_06825701 A/T;Chr18_08671202 A/G;Chr18_09165638 C/A;Chr18_48017092 T/C;Chr18_48056177 T/C;Chr18_48125071 G/A;Chr18_48153620 C/T;Chr18_50326879 G/A;Chr18_50526685 G/A;Chr18_50554508 T/C;Chr18_51200487 C/A;Chr18_54703004 C/G;Chr18_55727744 C/T;Chr18_55800924 A/G;Chr18_56182068 G/C;Chr19_00005221 C/T;Chr19_34475899 A/G;Chr19_34574726 C/T;Chr19_34843169 C/T;Chr19_36797568 G/A;Chr20_08076579 A/G;Chr20_39493065 T/A;Chr20_39531946 A/C;Chr20_39680045 G/A。
一种与大豆农艺性状相关的SNP位点组合,所述农艺性状包括株高、百粒重、底荚高度、脂肪含量、蛋白含量、单株粒数、单株荚数、荚粒数、百粒重和分枝数。
一套用于检测所述与大豆农艺性状相关的SNP位点组合的探针。
一种用于检测所述与大豆农艺性状相关的SNP位点组合的基因芯片,所述基因芯片采用液相芯片,所述基因芯片含有一套用于检测所述与大豆农艺性状相关的SNP位点组合的核苷酸探针。
进一步,所述液相芯片的溶液体系为无核酸酶的水,所述溶液体系中探针的浓度为60ng/μL。
一种所述的与大豆农艺性状相关的SNP位点组合在分子辅助育种或全基因组育种中的应用。
一种所述的探针在制备与大豆农艺性状相关的SNP位点组合的基因芯片上的应用。
一种所述探针在分子辅助育种或全基因组育种中的应用。
一种所述基因芯片在分子辅助育种或全基因组育种中的应用。
与现有技术相比,本发明所取得的有益效果如下:
1、本发明所采用的223个SNP位点与大豆的重要农艺性状相关,可通过测定大豆植株DNA中这223个SNP位点的基因型来评估大豆植株的农艺性状,将其应用于大豆的分子辅助育种和全基因组育种时,加快了育种进程。此外,223个SNP位点其数量相对较少,其不仅降低了基因型检测的成本,较2193个SNP位点组合而言,更适用于大量样本的粗筛,且较2193个SNP位点组合而言在对综合性状的评估上更具优势。
2、本发明基因芯片采用最新标记基因型检测的GBTS靶向测序基因型检测技术,具有成本低,准确度高,检测灵敏度高等优点。
附图说明
图1为20648个SNP位点在大豆全基因组中的分布图;
图2为综合育种指数与与农艺性状相关的优势位点数目的相关性分析图。
具体实施方式
下面结合实施例对本发明进行进一步的阐述。
实施例1:
一种与大豆农艺性状相关的SNP标记位点组合,包括223个SNP位点,每个SNP位点包含两个不同碱基变异位点,用于检测该位点的等位基因变化,所述223个SNP位点的物理位置是基于大豆品种Williams82的全基因组序列比对确定的,所述大豆品种Williams82的全基因组序列的版本号为Glycine max Wm82.a2.v1,所述大豆品种Williams82的全基因组序列的获取网址为:https://phytozome.jgi.doe.gov.;所述223个SNP位点的变异信息如下:
Chr01_01533882 A/G;Chr01_04026903 G/A;Chr01_04050717 A/T;Chr01_04092615 G/A;Chr01_39860894 C/T;Chr01_49903973 A/G;Chr01_50602779 A/C;Chr01_50653236 T/G;Chr01_51315364 A/G;Chr01_53509482 G/A;Chr01_54065323 C/T;Chr01_55547694 T/A;Chr02_05225452 C/T;Chr02_06300927 C/T;Chr02_38935935 A/G;Chr02_43559616 G/A;Chr02_44953925 G/C;Chr02_45012265 C/T;Chr02_45106877 G/A;Chr02_45225277 A/T;Chr02_45460408 A/G;Chr03_00155260 C/T;Chr03_00333082 G/C;Chr03_00558044 C/G;Chr03_01404553 G/A;Chr03_18107159 G/A;Chr03_25891807 T/G;Chr03_36421392 A/G;Chr03_36426626 T/C;Chr03_36451021 G/A;Chr03_36504983 C/A;Chr03_36789422 G/C;Chr03_37027494 C/A;Chr03_37706557 T/A;Chr03_38305381 G/A;Chr04_01886636 G/A;Chr04_03350250 C/A;Chr04_08569889 T/A;Chr04_16473219 A/G;Chr04_45658472 T/G;Chr04_46878018 G/A;Chr04_50850178 G/A;Chr04_51554352 C/A;Chr04_51579450 G/A;Chr05_05558466 C/T;Chr05_05575650 A/G;Chr05_05613716 T/C;Chr05_18929941 T/C;Chr05_22058564 A/G;Chr05_32075424 C/T;Chr05_33844667 A/G;Chr05_34000026 G/A;Chr05_34977447 C/T;Chr05_36371924 C/T;Chr05_39604331 C/T;Chr05_39788521 C/T;Chr05_40075652 T/C;Chr05_42019019 G/T;Chr06_01756279 A/C;Chr06_02636926 T/C;Chr06_03286909 C/T;Chr06_04134589 A/T;Chr06_04351486 G/A;Chr06_10505562 T/A;Chr06_13105258 A/T;Chr06_13432800 C/A;Chr06_13481784 T/G;Chr06_15231313 G/T;Chr06_15968336 A/C;Chr06_17382650 T/C;Chr06_17582094 G/A;Chr06_17602402 T/C;Chr06_17626369 T/A;Chr06_19781007 C/T;Chr06_27625128 A/G;Chr06_28928355 G/T;Chr06_42252843 C/T;Chr06_48428377 C/T;Chr06_50163774 G/A;Chr06_50975144 T/G;Chr07_01952143 T/C;Chr07_05575080 C/T;Chr07_05825087 T/C;Chr07_15480093 T/C;Chr07_19025998 C/T;Chr07_42689775 C/T;Chr07_42700692 G/T;Chr07_42732051 A/G;Chr07_42782332 A/T;Chr07_42836543 T/A;Chr08_00776002 C/T;Chr08_01028572 C/A;Chr08_07805605 A/C;Chr08_09185800 C/G;Chr08_22078860 G/A;Chr09_00458254 G/A;Chr09_00475009 G/A;Chr09_00500375 T/C;Chr09_04283906 A/C;Chr09_06653411 T/A;Chr09_35879535 G/A;Chr09_38843968 T/A;Chr09_40052962 A/T;Chr09_41676859 G/A;Chr09_45975341 C/A;Chr09_46200899 C/A;Chr09_46308505 G/A;Chr09_46478149 T/A;Chr09_46836433 A/G;Chr10_02750802 G/C;Chr10_02870996 G/T;Chr10_02887410 A/T;Chr10_02927284 T/A;Chr10_31900041 T/C;Chr10_45082937 A/G;Chr10_45127748 T/C;Chr10_45175769 G/A;Chr10_48926597 G/A;Chr10_49256007 A/G;Chr10_49302884 T/C;Chr10_49343783 C/T;Chr11_02104739 T/C;Chr11_02167163 T/G;Chr11_02630521 T/G;Chr11_04153990 C/T;Chr11_04306322 T/C;Chr11_09896347 G/T;Chr11_32376132 G/A;Chr11_32506058 C/T;Chr11_32929777 C/T;Chr11_33857564 G/A;Chr12_03951770 G/A;Chr12_08916858 T/C;Chr12_35265460 G/A;Chr12_35289582 G/T;Chr12_35578344 A/G;Chr12_36595459 C/A;Chr12_36704530 G/C;Chr12_36736475 G/A;Chr12_36765947 T/G;Chr13_16484275 T/C;Chr13_18615062 A/C;Chr13_19460489 T/C;Chr13_21768219 C/G;Chr13_29215285 G/T;Chr13_29550344 G/A;Chr13_30388748 A/G;Chr13_41775097 G/A;Chr13_42028098 A/C;Chr13_42050209 T/A;Chr13_42150995 C/T;Chr13_42216053 C/T;Chr13_42383660 C/A;Chr13_42410927 A/G;Chr13_44483438 A/G;Chr13_45066236 G/T;Chr13_45794372 C/T;Chr14_02226559 C/T;Chr14_04785275 A/C;Chr14_04978437 A/G;Chr14_09234257 T/C;Chr14_45860975 A/T;Chr14_46525690 A/G;Chr14_46614414 A/G;Chr14_47779860 A/T;Chr14_48354923 C/T;Chr15_00207098 A/G;Chr15_00282154 T/C;Chr15_00474286 T/C;Chr15_03989240 G/C;Chr15_06834700 G/T;Chr15_08981420 C/T;Chr15_09077137 C/G;Chr15_09108212 G/A;Chr15_09138650 T/C;Chr15_09176525 G/A;Chr15_09325304 C/T;Chr15_09632956 A/G;Chr15_09950434 A/G;Chr15_10109864 T/G;Chr15_10128698 T/G;Chr15_10605120 G/A;Chr15_15854711 A/T;Chr15_49558739 A/C;Chr15_50357591 A/G;Chr15_50377398 T/C;Chr15_50532317 A/G;Chr16_04075059 A/T;Chr16_06026215 A/C;Chr16_18681277 C/T;Chr16_32911332 G/C;Chr17_08312752 G/A;Chr17_12475327 A/G;Chr17_38307270 A/G;Chr17_38350306 T/G;Chr17_39257059 C/A;Chr18_00453852 T/C;Chr18_01331239 T/A;Chr18_05957508 T/C;Chr18_06825701 A/T;Chr18_08671202 A/G;Chr18_09165638 C/A;Chr18_48017092 T/C;Chr18_48056177 T/C;Chr18_48125071 G/A;Chr18_48153620 C/T;Chr18_50326879 G/A;Chr18_50526685 G/A;Chr18_50554508 T/C;Chr18_51200487 C/A;Chr18_54703004 C/G;Chr18_55727744 C/T;Chr18_55800924 A/G;Chr18_56182068 G/C;Chr19_00005221 C/T;Chr19_34475899 A/G;Chr19_34574726 C/T;Chr19_34843169 C/T;Chr19_36797568 G/A;Chr20_08076579 A/G;Chr20_39493065 T/A;Chr20_39531946 A/C;Chr20_39680045 G/A。。
在本实施例中,所述与大豆农艺性状相关的SNP标记位点组合(即223个SNP位点)来源于270份栽培大豆品种的全基因组重测序信息及相关GWAS位点,其获得方法,包括如下步骤:
1、获得20k大豆全基因组的SNP标记位点
1)样本的采集与获得:270份大豆核心种质资源于2018年播种于中国科学院东北地理与农业生态研究所实验田,正常田间管理;并获得株高、百粒重、底荚高度、单株粒数、单株荚数、单株粒重、主茎节数、分枝数、脂肪含量、蛋白含量这10个重要农艺性状的数值。
2)SNP检测:取V4期大豆幼嫩叶片,利用CTAB法提取高质量的大豆基因组DNA。用于基因组重测序,测序获得高质量的clean data数据量为8100Gb,平均每个样品30G,测序深度约为30倍;将测序数据利用BWA软件将数据比对到大豆参考基因组(版本号为Glycinemax Wm82.a2.v1),PICARD软件去除重复,GATK软件获得高质量的SNPS;利用ANNORVAR软件对SNP检测结果进行注释。
3)全基因组关联分析:对获得的SNP标记位点与测定的表型信息进行全基因组关联分析,分析软件为TASSEL,采用混合线性模型进行分析。
4)20K位点的获取:20K标记位点的获取要求在270个栽培大豆中,基因型缺失小于20%,杂合基因型小于30%,最大等位基因频率小于95%,最小等位基因频率大于5%,优先选择GWAS标记位点,其次选择基因编码区的标记,每25kb选择一个标记,若连续75kb无上述两种标记,则选择非编码区标记;最终得到所述的20648个大豆全基因组SNP标记位点,其中17096个标记位于功能基因上,覆盖31%的大豆编码基因,SNP分子标记分布均匀,标记平均间距为46kb。
2、将获得的20648个大豆全基因组SNP标记位点与大豆的表型性状进行关联分析;
1)检测基因型
利用靶向测序基因型检测(genotyping by target sequencing,GBTS)技术的液态芯片检测270个主栽品种的20648个SNP标记位点,分析20648个SNP标记位点在染色体上的分布密度,结果见图1,将20648个SNP标记位点作为构建基因组选择模型的基因型文件。
2)、检测表型
检测270个大豆主栽品种包括株高、百粒重、底荚高度、单株粒数、单株荚数、单株粒重、主茎节数、分枝数、脂肪含量、蛋白含量在内的10个性状,作为构建基因组选择模型的表型输入文件:10个性状的检测方法如下:
株高:测量地面到主茎顶端生长点的长度。
百粒重:随机取100粒发育良好的种子,准确称重至0.01克,并换算为水分含量为13%时的重量。
底荚高度:测量地面到第一个有效荚的长度。
单株粒数:计数单株有效粒数。
单株荚数:计数单株有效荚数。
单株粒重:计数单株有效籽粒重量。
主茎节数:从子叶节算起,至主茎顶端(不包括顶端花序)的实际节数。
分枝数:计数,具有1个或以上节且结有豆荚的一级分枝方计入分枝数。
脂肪含量:利用近红外技术检测大豆粗脂肪含量。
蛋白含量:利用近红外技术检测大豆粗蛋白含量。
3)、构建全基因组选择模型以及获得标记效应
利用20648个SNP标记位点作为基因型与检测的10个大豆性状表型值构建针对每个性状全基因组选择模型,进而分析获得20648个SNP标记位点中每个SNP标记位点对各个性状的效应值;
4)、筛选与各表型性状相关的优势等位基因,获得表型性状与优势等位基因之间的关联情况
利用全基因组选择,分析获得所述10个性状中每个性状关联的标记效应值的绝对值排名靠前的25个SNP标记位点的基因型,即每个表型性状获得与其相关的25个优势等位基因,10个表型性状共计获得250个优势等位基因,关联结果如下:
所述优势等位基因以染色体编号_物理位置_优势基因型的形式表示;
获得的与蛋白含量相关的25个优势等位基因如下:
Chr01_49903973_A;Chr01_54065323_T;Chr02_6300927_C;Chr03_18107159_G;Chr04_3350250_A;Chr04_8569889_T;Chr05_18929941_T;Chr05_22058564_G;Chr06_17382650_T;Chr06_17582094_G;Chr06_17602402_T;Chr06_17626369_T;Chr06_27625128_G;Chr06_28928355_T;Chr06_42252843_T;Chr09_40052962_A;Chr09_6653411_A;Chr10_31900041_C;Chr14_48354923_C;Chr14_4978437_G;Chr16_4075059_A;Chr18_55727744_C;Chr18_55800924_G;Chr19_34843169_C;Chr19_5221_C。
与单株荚数相关的25个优势等位基因如下:
Chr01_39860894_T;Chr01_4026903_G;Chr01_4092615_G;Chr02_43559616_G;Chr03_38305381_A;Chr04_16473219_G;Chr04_45658472_G;Chr06_3286909_T;Chr06_50975144_G;Chr07_19025998_T;Chr08_776002_T;Chr09_38843968_T;Chr11_32929777_C;Chr12_36704530_C;Chr12_36736475_A;Chr14_4785275_A;Chr15_207098_A;Chr15_282154_T;Chr15_474286_T;Chr16_18681277_C;Chr17_8312752_A;Chr18_50326879_G;Chr18_50526685_G;Chr18_50554508_T;Chr18_5957508_T;
获得的与株高相关的25个优势等位基因如下:
Chr01_55547694_A;Chr03_155260_C;Chr03_558044_C;Chr04_50850178_G;Chr05_34977447_C;Chr05_40075652_T;Chr06_15231313_G;Chr06_15968336_A;Chr10_2750802_G;Chr10_2870996_G;Chr10_2887410_A;Chr10_2927284_T;Chr10_45082937_A;Chr10_45127748_C;Chr10_48926597_A;Chr10_49256007_G;Chr10_49302884_C;Chr11_4153990_C;Chr11_4306322_T;Chr13_29215285_T;Chr13_29550344_A;Chr13_44483438_A;Chr14_46525690_G;Chr14_9234257_T;Chr18_56182068_G;
获得的与脂肪含量相关的25个优势等位基因如下:
Chr01_1533882_A;Chr02_5225452_T;Chr02_6300927_T;Chr03_25891807_T;Chr03_36421392_A;Chr03_36426626_T;Chr03_36451021_G;Chr03_36504983_C;Chr03_36789422_G;Chr03_37706557_T;Chr04_8569889_A;Chr06_19781007_T;Chr06_4351486_A;Chr07_1952143_T;Chr09_41676859_A;Chr09_4283906_C;Chr11_2630521_G;Chr13_19460489_C;Chr13_30388748_G;Chr14_48354923_T;Chr14_4978437_A;Chr18_51200487_A;Chr18_55727744_T;Chr18_8671202_A;Chr19_34843169_T;
获得的与主茎节数相关的25个优势等位基因如下:
Chr01_50602779_C;Chr05_39604331_C;Chr05_39788521_C;Chr05_40075652_T;Chr06_13105258_A;Chr06_1756279_A;Chr06_2636926_C;Chr08_22078860_G;Chr10_2927284_T;Chr11_9896347_G;Chr14_45860975_T;Chr14_46525690_G;Chr14_46614414_G;Chr14_47779860_T;Chr15_282154_T;Chr15_49558739_C;Chr15_50357591_G;Chr15_50377398_C;Chr15_50532317_A;Chr16_32911332_G;Chr17_39257059_C;Chr18_6825701_A;Chr18_9165638_C;Chr19_34475899_A;Chr19_34574726_C;
获得的与百粒重相关的25个优势等位基因如下:
Chr01_51315364_A;Chr01_53509482_G;Chr03_1404553_A;Chr03_333082_G;Chr03_37027494_A;Chr05_42019019_T;Chr05_5558466_C;Chr05_5575650_A;Chr07_42689775_T;Chr07_42700692_T;Chr07_42732051_G;Chr07_42782332_T;Chr07_42836543_A;Chr12_35265460_G;Chr12_35289582_G;Chr12_35578344_A;Chr12_8916858_T;Chr15_15854711_T;Chr17_38307270_A;Chr17_38350306_T;Chr18_453852_C;Chr18_48056177_C;Chr18_48125071_A;Chr18_48153620_T;Chr18_54703004_C;
获得的与单株粒重相关的25个优势等位基因如下:
Chr01_4026903_G;Chr04_45658472_G;Chr04_51554352_C;Chr04_51579450_G;Chr06_13432800_C;Chr06_13481784_T;Chr06_4134589_A;Chr06_48428377_C;Chr09_45975341_C;Chr09_46478149_T;Chr09_46836433_A;Chr11_32376132_G;Chr12_36704530_C;Chr13_16484275_C;Chr13_41775097_A;Chr13_42050209_A;Chr13_42383660_A;Chr13_42410927_G;Chr15_3989240_G;Chr16_6026215_A;Chr17_12475327_G;Chr18_1331239_T;Chr18_50326879_G;Chr18_50526685_G;Chr18_5957508_T;
获得的与单株粒数相关的25个优势等位基因如下:
Chr01_4026903_G;Chr01_4050717_A;Chr04_46878018_G;Chr06_10505562_A;Chr06_50163774_G;Chr07_5575080_C;Chr07_5825087_T;Chr08_1028572_A;Chr09_35879535_G;Chr09_46200899_C;Chr09_46308505_A;Chr12_36595459_C;Chr12_36765947_G;Chr13_21768219_G;Chr13_41775097_A;Chr13_42028098_C;Chr13_42150995_T;Chr13_42216053_T;Chr13_42383660_A;Chr13_42410927_G;Chr15_282154_T;Chr15_3989240_G;Chr18_48017092_T;Chr18_50326879_G;Chr18_5957508_T;
获得的与分枝数相关的25个优势等位基因如下:
Chr01_50653236_G;Chr05_32075424_T;Chr05_33844667_G;Chr05_34000026_A;Chr05_36371924_T;Chr09_458254_G;Chr09_475009_G;Chr09_500375_T;Chr12_3951770_A;Chr13_18615062_C;Chr13_45066236_T;Chr15_10109864_T;Chr15_10128698_T;Chr15_10605120_G;Chr15_8981420_T;Chr15_9077137_C;Chr15_9108212_A;Chr15_9138650_C;Chr15_9176525_A;Chr15_9325304_T;Chr15_9632956_A;Chr15_9950434_A;Chr20_39493065_T;Chr20_39531946_A;Chr20_39680045_G;
获得的与底荚高度相关的25个优势等位基因如下:
Chr02_38935935_A;Chr02_44953925_C;Chr02_45012265_T;Chr02_45106877_A;Chr02_45225277_T;Chr02_45460408_G;Chr04_1886636_G;Chr04_51554352_A;Chr05_5613716_C;Chr07_15480093_T;Chr08_7805605_A;Chr08_9185800_G;Chr10_45082937_A;Chr10_45127748_C;Chr10_45175769_A;Chr10_49343783_T;Chr11_2104739_T;Chr11_2167163_T;Chr11_32506058_T;Chr11_33857564_A;Chr13_45794372_T;Chr14_2226559_T;Chr15_6834700_T;Chr19_36797568_A;Chr20_8076579_A;
5)223个优势等位基因的获取
将获得的250个优势等位基因去重后获得223个SNP标记位点,即本发明与大豆农艺性状相关的SNP位点组合。
实施例2:
以所获得的所述223个SNP标记位点为基础,设计检测所述223个SNP标记位点的探针,并制备检测所述223个SNP标记位点的液相基因芯片。
实施例3:
以综合育种值的指标为例,对实施例1获得的与10个性状相关的共计250个优势等位基因进行验证,所述验证的操作方法如下:
1)、选取已经经过表型性状确认的优异大豆种质资源FNGS0756与优异大豆种质资源FNGS0757作为实现材料;采用优异大豆种质资源FNGS0756与优异大豆种质资源FNGS0757构建杂交群体708个个体,用实施例1所述方法测定株高、百粒重、底荚高度、单株粒数、单株荚数、单株粒重、主茎节数、分枝数、脂肪含量、蛋白含量这10个农艺性状指标;
2)测定优异大豆种质资源FNGS0756与优异大豆种质资源FNGS0757构建杂交群体708个个体中与各农艺性状关联的223个SNP标记位点的基因型;
3)分析优异大豆种质资源FNGS0756与优异大豆种质资源FNGS0757构建杂交群体708个个体中所述与10个农艺性状相关的共计250个优势等位基因聚合情况,结果见图2,结果显示:个体聚合的所述与10个农艺性状相关的共计250个优势等位基因越多,其综合育种值越高,因此,可以采用实施例1所获得相应表型性状的优势等位基因来对大豆植株的综合育种值进行评估,与10个农艺性状相关的共计250个优势等位基因聚合越多,则所述目标植株在所综合育种值上的表现越佳。
实施例4
以筛选综合育种值高的品种为例,介绍实施例1获得的223个SNP标记位点在分子辅助育种中的应用的方法,包括如下步骤:
1、待测目标植株的获得:采用优异大豆种质资源FNGS0756(综合育种值为135)与优异大豆种质资源FNGS0757(综合育种值为152)构建杂交群体708个(群体综合育种值的均值为95.19);
2、提取样本的基因组DNA,并构建样品文库;
1)、样品DNA提取
采用CTAB法对样本DNA进行提取。
2)、样品DNA质检
将测试样品DNA,用Qubit Fluorometric Quantitation(Thermo Fisher)对DNA浓度进行测定,用1%琼脂糖凝胶电泳检测DNA的完整性。检测合格的样品放入4℃冰箱,保存、备用。
3)、样品DNA片段化
取12μL质检合格的DNA放置于0.2μL PCR管中,将管置于超声波破碎仪中对DNA进行随机物理破碎,片段破碎至200~400bp。
4)、样品末端修复
向管中加入4μL GenoBaits End Repair Buffer(GenoBaits,即石家庄博瑞迪生物科技有限公司)和2.7μL GenoBaits End Repair Enzyme,补水至20μL,放入ABI 9700PCR仪中37℃温育20分钟,完成破碎片段的末端修复和加A过程。
5)、样品测序接头连接
从PCR仪中取出小管加入2μL GenoBaits Ultra DNA ligase、8μL GenoBaitsUltra DNA Ligase Buffer和2μL GenoBaits Adapter,补水至40μL,然后放置于ABI9700PCR仪上22℃反应30分钟,完成测序接头的连接。
6)、样品DNA纯化
向连接产物中加入48μL的Beackman AMPure XP Beads(Beackman公司)对连接产物进行纯化,纯化后采用磁珠进行片段筛选,保留插入片段在200~300bp的连接产物。
7)、样品文库扩增
向上一步的PCR管中加入5μL带有Barcode序列的测序接头、1μL P5接头、10μLGenoBaits PCR Master Mix,并用纯水补至20μL;用ABI 9700PCR仪进行扩增,扩增程序为:95℃预变性5min,95℃变性30s,60℃退火30s,72℃延伸30s;重复2-4步,共8个循环;72℃延伸5min。不同的Barcode用于区分不同的样品。
8)、样品文库纯化
向第二轮PCR产物中加入24μL Beckmen AMPure XP Beads(Beackman公司),用移液器上下吸打均匀后,将0.2μL的PCR管置于磁力架上至溶液澄清,弃去上清并用75%乙醇洗涤磁珠一次,用pH值为8.0的Tris-HCl将文库DNA洗脱下来。
3、利用实施例2制备的液相基因芯片测定目标植株在223个优势等位基因的基因型;
1)、DNA杂交
取500ng已完成构建的基因组DNA测序文库,加入5μL GenoBaits Block I和2μLGenoBaits Block II,置于Eppendorf Concentrator plus(Eppendorf公司)真空浓缩仪上,在≤70℃的温度下蒸干至干粉。向干粉管中加入8.5μL GenoBaits 2x Hyb Buffer、2.7μL GenoBaits Hyb Buffer Enhancer、2.8μL Nuclease-Free Water,用移液器吸打混匀后放置于ABI 9700PCR仪上95℃温育10分钟,然后取出PCR管加入3μL已经合成的探针(所述探针的浓度为60ng/μl),旋涡震荡混匀后放置于ABI 9700PCR仪上65℃温育2小时,完成探针杂交反应。
2)、DNA捕获
向上一步杂交完成的反应体系中加入100μL GenoBaits DNA Probe Beads,上下吸打10次,放入ABI 9700PCR仪上65℃温育45分钟,使磁珠与探针结合。用100μL GenoBaitsWash Buffer I、150μL GenoBaits Wash BufferII分别对结合探针后的磁珠进行65℃热洗,然后再用100μL GenoBaits Wash Buffer I、150μL GenoBaits Wash Buffer II和150μL GenoBaits Wash Buffer III分别对磁珠进行常温洗涤。洗涤完成的磁珠用20μLNuclease-Free Water进行重悬。
取13μL重悬后的DNA(带磁珠)加入到新的0.2mL PCR管中,然后加入15μLGenoBaits PCR Master Mix、2μL GenoBaits Primer Mix配置post-PCR体系,用ABI9700PCR仪进行文库扩增,扩增程序为:95℃预变性5min,95℃变性30s,60℃退火30s,72℃延伸30s;重复2-4步,共15个循环;72℃延伸5min。
向post-PCR产物中加入45μL Beckmen AMPure XP Beads(Beackman公司)并用移液器上下吸打均匀,然后将0.2mL PCR管置于磁力架上至溶液澄清,弃去上清并用75%乙醇洗涤磁珠两次,用pH为8.0的Tris-HCl将文库DNA洗脱下来。完成探针的杂交捕获工作。
3)、DNA杂交捕获文库质检
用Qubit Fluorometric Quantitation(Thermo Fisher)对文库的DNA浓度进行测定,然后用琼脂糖凝胶电泳检测文库DNA的片段大小是否在300~400bp之间。
4)、DNA杂交捕获文库测序
将构建好的DNA文库用华大MGISEQ2000测序仪进行测序。
5)、基因型数据分析
测序数据经过FastQC(www.bioinformatics.babraham.ac.uk/project)质控后,用BWA(bio-bwa.sourceforge.net)的默认参数将测序数据比对到参考基因组上,用GATK(software.broadinstitute.org/gatk)软件对测序数据进行SNP鉴定,用自编的Perl脚本对探针捕获测序的基因型分型信息进行提取,形成最终的基因型分型文件。
4、将测得的目标植株的223个SNP标记位点的基因型与实施例1中获得的与与10个农艺性状相关的共计250个优势等位基因进行比对,得出目标植株中存在与10个农艺性状关联的优势等位基因数量;
5、利用育种家选择指数对大豆10个性状(株高、百粒重、低荚高度、单株粒数、单株荚数、单株粒重、主茎节数、分枝数、脂肪含量、蛋白含量)确定各性状的权重,获得目标植株的综合育种值,筛选出综合育种值靠前的10个个体,获得综合育种值较优的10个大豆品系,结果见下表,最终筛选出下表所示的10个综合育种值高的大豆品系,其平均综合育种值为111.8,较群体综合育种值的平均值95.19高出16.61,证实了该方法的应用价值。
品系编号 | 与10个农艺性状相关的优势等位基因数目 | 综合育种值 |
FNGS00213 | 110 | 88 |
FNGS00214 | 107 | 165 |
FNGS00215 | 107 | 104 |
FNGS00216 | 106 | 100 |
FNGS00217 | 103 | 119 |
FNGS00218 | 103 | 88 |
FNGS00219 | 103 | 141 |
FNGS00220 | 102 | 91 |
FNGS00221 | 101 | 114 |
FNGS00222 | 101 | 108 |
以上所述实施方式仅为本发明的优选实施例,而并非本发明可行实施的穷举。对于本领域一般技术人员而言,在不背离本发明原理和精神的前提下对其所作出的任何显而易见的改动,都应当被认为包含在本发明的权利要求保护范围之内。
Claims (4)
1.一种与大豆农艺性状相关的SNP位点组合在分子辅助育种或全基因组育种中的应用,其特征在于,所述分子辅助育种或全基因组育种基于大豆农艺性状进行育种,所述大豆农艺性状指株高、百粒重、底荚高度、脂肪含量、蛋白含量、单株粒数、单株荚数、主茎节数、单株粒重和分枝数;
所述与大豆农艺性状相关的SNP位点组合由以下223个SNP位点组成,每个SNP位点包含两个不同碱基变异位点,用于检测该位点的等位基因变化,所述223个SNP位点的物理位置是基于大豆品种Williams82的全基因组序列比对确定的,所述大豆品种Williams82的全基因组序列的版本号为Glycine max Wm82.a2.v1,所述223个SNP位点的变异信息如下:
Chr01_01533882 A/G;Chr01_04026903 G/A;Chr01_04050717 A/T;Chr01_04092615G/A;Chr01_39860894 C/T;Chr01_49903973 A/G;Chr01_50602779 A/C;Chr01_50653236T/G;Chr01_51315364 A/G;Chr01_53509482 G/A;Chr01_54065323 C/T;Chr01_55547694T/A;Chr02_05225452 C/T;Chr02_06300927 C/T;Chr02_38935935 A/G;Chr02_43559616G/A;Chr02_44953925 G/C;Chr02_45012265 C/T;Chr02_45106877 G/A;Chr02_45225277A/T;Chr02_45460408 A/G;Chr03_00155260 C/T;Chr03_00333082 G/C;Chr03_00558044C/G;Chr03_01404553 G/A;Chr03_18107159 G/A;Chr03_25891807 T/G;Chr03_36421392A/G;Chr03_36426626 T/C;Chr03_36451021 G/A;Chr03_36504983 C/A;Chr03_36789422G/C;Chr03_37027494 C/A;Chr03_37706557 T/A;Chr03_38305381 G/A;Chr04_01886636G/A;Chr04_03350250 C/A;Chr04_08569889 T/A;Chr04_16473219 A/G;Chr04_45658472T/G;Chr04_46878018 G/A;Chr04_50850178 G/A;Chr04_51554352 C/A;Chr04_51579450G/A;Chr05_05558466 C/T;Chr05_05575650 A/G;Chr05_05613716 T/C;Chr05_18929941T/C;Chr05_22058564 A/G;Chr05_32075424 C/T;Chr05_33844667 A/G;Chr05_34000026G/A;Chr05_34977447 C/T;Chr05_36371924 C/T;Chr05_39604331 C/T;Chr05_39788521C/T;Chr05_40075652 T/C;Chr05_42019019 G/T;Chr06_01756279 A/C;Chr06_02636926T/C;Chr06_03286909 C/T;Chr06_04134589 A/T;Chr06_04351486 G/A;Chr06_10505562T/A;Chr06_13105258 A/T;Chr06_13432800 C/A;Chr06_13481784 T/G;Chr06_15231313G/T;Chr06_15968336 A/C;Chr06_17382650 T/C;Chr06_17582094 G/A;Chr06_17602402T/C;Chr06_17626369 T/A;Chr06_19781007 C/T;Chr06_27625128 A/G;Chr06_28928355G/T;Chr06_42252843 C/T;Chr06_48428377 C/T;Chr06_50163774 G/A;Chr06_50975144T/G;Chr07_01952143 T/C;Chr07_05575080 C/T;Chr07_05825087 T/C;Chr07_15480093T/C;Chr07_19025998 C/T;Chr07_42689775 C/T;Chr07_42700692 G/T;Chr07_42732051A/G;Chr07_42782332 A/T;Chr07_42836543 T/A;Chr08_00776002 C/T;Chr08_01028572C/A;Chr08_07805605 A/C;Chr08_09185800 C/G;Chr08_22078860 G/A;Chr09_00458254G/A;Chr09_00475009 G/A;Chr09_00500375 T/C;Chr09_04283906 A/C;Chr09_06653411T/A;Chr09_35879535 G/A;Chr09_38843968 T/A;Chr09_40052962 A/T;Chr09_41676859G/A;Chr09_45975341 C/A;Chr09_46200899 C/A;Chr09_46308505 G/A;Chr09_46478149T/A;Chr09_46836433 A/G;Chr10_02750802 G/C;Chr10_02870996 G/T;Chr10_02887410A/T;Chr10_02927284 T/A;Chr10_31900041 T/C;Chr10_45082937 A/G;Chr10_45127748T/C;Chr10_45175769 G/A;Chr10_48926597 G/A;Chr10_49256007 A/G;Chr10_49302884T/C;Chr10_49343783 C/T;Chr11_02104739 T/C;Chr11_02167163 T/G;Chr11_02630521T/G;Chr11_04153990 C/T;Chr11_04306322 T/C;Chr11_09896347 G/T;Chr11_32376132G/A;Chr11_32506058 C/T;Chr11_32929777 C/T;Chr11_33857564 G/A;Chr12_03951770G/A;Chr12_08916858 T/C;Chr12_35265460 G/A;Chr12_35289582 G/T;Chr12_35578344A/G;Chr12_36595459 C/A;Chr12_36704530 G/C;Chr12_36736475 G/A;Chr12_36765947T/G;Chr13_16484275 T/C;Chr13_18615062 A/C;Chr13_19460489 T/C;Chr13_21768219C/G;Chr13_29215285 G/T;Chr13_29550344 G/A;Chr13_30388748 A/G;Chr13_41775097G/A;Chr13_42028098 A/C;Chr13_42050209 T/A;Chr13_42150995 C/T;Chr13_42216053C/T;Chr13_42383660 C/A;Chr13_42410927 A/G;Chr13_44483438 A/G;Chr13_45066236G/T;Chr13_45794372 C/T;Chr14_02226559 C/T;Chr14_04785275 A/C;Chr14_04978437A/G;Chr14_09234257 T/C;Chr14_45860975 A/T;Chr14_46525690 A/G;Chr14_46614414A/G;Chr14_47779860 A/T;Chr14_48354923 C/T;Chr15_00207098 A/G;Chr15_00282154T/C;Chr15_00474286 T/C;Chr15_03989240 G/C;Chr15_06834700 G/T;Chr15_08981420C/T;Chr15_09077137 C/G;Chr15_09108212 G/A;Chr15_09138650 T/C;Chr15_09176525G/A;Chr15_09325304 C/T;Chr15_09632956 A/G;Chr15_09950434 A/G;Chr15_10109864T/G;Chr15_10128698 T/G;Chr15_10605120 G/A;Chr15_15854711 A/T;Chr15_49558739A/C;Chr15_50357591 A/G;Chr15_50377398 T/C;Chr15_50532317 A/G;Chr16_04075059A/T;Chr16_06026215 A/C;Chr16_18681277 C/T;Chr16_32911332 G/C;Chr17_08312752G/A;Chr17_12475327 A/G;Chr17_38307270 A/G;Chr17_38350306 T/G;Chr17_39257059C/A;Chr18_00453852 T/C;Chr18_01331239 T/A;Chr18_05957508 T/C;Chr18_06825701A/T;Chr18_08671202 A/G;Chr18_09165638 C/A;Chr18_48017092 T/C;Chr18_48056177T/C;Chr18_48125071 G/A;Chr18_48153620 C/T;Chr18_50326879 G/A;Chr18_50526685G/A;Chr18_50554508 T/C;Chr18_51200487 C/A;Chr18_54703004 C/G;Chr18_55727744C/T;Chr18_55800924 A/G;Chr18_56182068 G/C;Chr19_00005221 C/T;Chr19_34475899A/G;Chr19_34574726 C/T;Chr19_34843169 C/T;Chr19_36797568 G/A;Chr20_08076579A/G;Chr20_39493065 T/A;Chr20_39531946 A/C;Chr20_39680045 G/A;
与蛋白含量相关的25个SNP位点及其优势等位基因如下:
Chr01_49903973_A;Chr01_54065323_T;Chr02_6300927_C;Chr03_18107159_G;Chr04_3350250_A;Chr04_8569889_T;Chr05_18929941_T;Chr05_22058564_G;Chr06_17382650_T;Chr06_17582094_G;Chr06_17602402_T;Chr06_17626369_T;Chr06_27625128_G;Chr06_28928355_T;Chr06_42252843_T;Chr09_40052962_A;Chr09_6653411_A;Chr10_31900041_C;Chr14_48354923_C;Chr14_4978437_G;Chr16_4075059_A;Chr18_55727744_C;Chr18_55800924_G;Chr19_34843169_C;Chr19_5221_C;
与单株荚数相关的25个SNP位点及其优势等位基因如下:
Chr01_39860894_T;Chr01_4026903_G;Chr01_4092615_G;Chr02_43559616_G;Chr03_38305381_A;Chr04_16473219_G;Chr04_45658472_G;Chr06_3286909_T;Chr06_50975144_G;Chr07_19025998_T;Chr08_776002_T;Chr09_38843968_T;Chr11_32929777_C;Chr12_36704530_C;Chr12_36736475_A;Chr14_4785275_A;Chr15_207098_A;Chr15_282154_T;Chr15_474286_T;Chr16_18681277_C;Chr17_8312752_A;Chr18_50326879_G;Chr18_50526685_G;Chr18_50554508_T;Chr18_5957508_T;
与株高相关的25个SNP位点及其优势等位基因如下:
Chr01_55547694_A;Chr03_155260_C;Chr03_558044_C;Chr04_50850178_G;Chr05_34977447_C;Chr05_40075652_T;Chr06_15231313_G;Chr06_15968336_A;Chr10_2750802_G;Chr10_2870996_G;Chr10_2887410_A;Chr10_2927284_T;Chr10_45082937_A;Chr10_45127748_C;Chr10_48926597_A;Chr10_49256007_G;Chr10_49302884_C;Chr11_4153990_C;Chr11_4306322_T;Chr13_29215285_T;Chr13_29550344_A;Chr13_44483438_A;Chr14_46525690_G;Chr14_9234257_T;Chr18_56182068_G;
与脂肪含量相关的25个SNP位点及其优势等位基因如下:
Chr01_1533882_A;Chr02_5225452_T;Chr02_6300927_T;Chr03_25891807_T;Chr03_36421392_A;Chr03_36426626_T;Chr03_36451021_G;Chr03_36504983_C;Chr03_36789422_G;Chr03_37706557_T;Chr04_8569889_A;Chr06_19781007_T;Chr06_4351486_A;Chr07_1952143_T;Chr09_41676859_A;Chr09_4283906_C;Chr11_2630521_G;Chr13_19460489_C;Chr13_30388748_G;Chr14_48354923_T;Chr14_4978437_A;Chr18_51200487_A;Chr18_55727744_T;Chr18_8671202_A;Chr19_34843169_T;
与主茎节数相关的25个SNP位点及其优势等位基因如下:
Chr01_50602779_C;Chr05_39604331_C;Chr05_39788521_C;Chr05_40075652_T;Chr06_13105258_A;Chr06_1756279_A;Chr06_2636926_C;Chr08_22078860_G;Chr10_2927284_T;Chr11_9896347_G;Chr14_45860975_T;Chr14_46525690_G;Chr14_46614414_G;Chr14_47779860_T;Chr15_282154_T;Chr15_49558739_C;Chr15_50357591_G;Chr15_50377398_C;Chr15_50532317_A;Chr16_32911332_G;Chr17_39257059_C;Chr18_6825701_A;Chr18_9165638_C;Chr19_34475899_A;Chr19_34574726_C;
与百粒重相关的25个SNP位点及其优势等位基因如下:
Chr01_51315364_A;Chr01_53509482_G;Chr03_1404553_A;Chr03_333082_G;Chr03_37027494_A;Chr05_42019019_T;Chr05_5558466_C;Chr05_5575650_A;Chr07_42689775_T;Chr07_42700692_T;Chr07_42732051_G;Chr07_42782332_T;Chr07_42836543_A;Chr12_35265460_G;Chr12_35289582_G;Chr12_35578344_A;Chr12_8916858_T;Chr15_15854711_T;Chr17_38307270_A;Chr17_38350306_T;Chr18_453852_C;Chr18_48056177_C;Chr18_48125071_A;Chr18_48153620_T;Chr18_54703004_C;
与单株粒重相关的25个SNP位点及其优势等位基因如下:
Chr01_4026903_G;Chr04_45658472_G;Chr04_51554352_C;Chr04_51579450_G;Chr06_13432800_C;Chr06_13481784_T;Chr06_4134589_A;Chr06_48428377_C;Chr09_45975341_C;Chr09_46478149_T;Chr09_46836433_A;Chr11_32376132_G;Chr12_36704530_C;Chr13_16484275_C;Chr13_41775097_A;Chr13_42050209_A;Chr13_42383660_A;Chr13_42410927_G;Chr15_3989240_G;Chr16_6026215_A;Chr17_12475327_G;Chr18_1331239_T;Chr18_50326879_G;Chr18_50526685_G;Chr18_5957508_T;
与单株粒数相关的25个SNP位点及其优势等位基因如下:
Chr01_4026903_G;Chr01_4050717_A;Chr04_46878018_G;Chr06_10505562_A;Chr06_50163774_G;Chr07_5575080_C;Chr07_5825087_T;Chr08_1028572_A;Chr09_35879535_G;Chr09_46200899_C;Chr09_46308505_A;Chr12_36595459_C;Chr12_36765947_G;Chr13_21768219_G;Chr13_41775097_A;Chr13_42028098_C;Chr13_42150995_T;Chr13_42216053_T;Chr13_42383660_A;Chr13_42410927_G;Chr15_282154_T;Chr15_3989240_G;Chr18_48017092_T;Chr18_50326879_G;Chr18_5957508_T;
与分枝数相关的25个SNP位点及其优势等位基因如下:
Chr01_50653236_G;Chr05_32075424_T;Chr05_33844667_G;Chr05_34000026_A;Chr05_36371924_T;Chr09_458254_G;Chr09_475009_G;Chr09_500375_T;Chr12_3951770_A;Chr13_18615062_C;Chr13_45066236_T;Chr15_10109864_T;Chr15_10128698_T;Chr15_10605120_G;Chr15_8981420_T;Chr15_9077137_C;Chr15_9108212_A;Chr15_9138650_C;Chr15_9176525_A;Chr15_9325304_T;Chr15_9632956_A;Chr15_9950434_A;Chr20_39493065_T;Chr20_39531946_A;Chr20_39680045_G;
与底荚高度相关的25个SNP位点及其优势等位基因如下:
Chr02_38935935_A;Chr02_44953925_C;Chr02_45012265_T;Chr02_45106877_A;Chr02_45225277_T;Chr02_45460408_G;Chr04_1886636_G;Chr04_51554352_A;Chr05_5613716_C;Chr07_15480093_T;Chr08_7805605_A;Chr08_9185800_G;Chr10_45082937_A;Chr10_45127748_C;Chr10_45175769_A;Chr10_49343783_T;Chr11_2104739_T;Chr11_2167163_T;Chr11_32506058_T;Chr11_33857564_A;Chr13_45794372_T;Chr14_2226559_T;Chr15_6834700_T;Chr19_36797568_A;Chr20_8076579_A。
2.一种用于检测权利要求1所述的与大豆农艺性状相关的SNP位点组合的探针在分子辅助育种或全基因组育种中的应用,其特征在于,所述分子辅助育种或全基因组育种基于大豆农艺性状进行育种,所述大豆农艺性状指株高、百粒重、底荚高度、脂肪含量、蛋白含量、单株粒数、单株荚数、主茎节数、单株粒重和分枝数;
与蛋白含量相关的25个SNP位点及其优势等位基因如下:
Chr01_49903973_A;Chr01_54065323_T;Chr02_6300927_C;Chr03_18107159_G;Chr04_3350250_A;Chr04_8569889_T;Chr05_18929941_T;Chr05_22058564_G;Chr06_17382650_T;Chr06_17582094_G;Chr06_17602402_T;Chr06_17626369_T;Chr06_27625128_G;Chr06_28928355_T;Chr06_42252843_T;Chr09_40052962_A;Chr09_6653411_A;Chr10_31900041_C;Chr14_48354923_C;Chr14_4978437_G;Chr16_4075059_A;Chr18_55727744_C;Chr18_55800924_G;Chr19_34843169_C;Chr19_5221_C;
与单株荚数相关的25个SNP位点及其优势等位基因如下:
Chr01_39860894_T;Chr01_4026903_G;Chr01_4092615_G;Chr02_43559616_G;Chr03_38305381_A;Chr04_16473219_G;Chr04_45658472_G;Chr06_3286909_T;Chr06_50975144_G;Chr07_19025998_T;Chr08_776002_T;Chr09_38843968_T;Chr11_32929777_C;Chr12_36704530_C;Chr12_36736475_A;Chr14_4785275_A;Chr15_207098_A;Chr15_282154_T;Chr15_474286_T;Chr16_18681277_C;Chr17_8312752_A;Chr18_50326879_G;Chr18_50526685_G;Chr18_50554508_T;Chr18_5957508_T;
与株高相关的25个SNP位点及其优势等位基因如下:
Chr01_55547694_A;Chr03_155260_C;Chr03_558044_C;Chr04_50850178_G;Chr05_34977447_C;Chr05_40075652_T;Chr06_15231313_G;Chr06_15968336_A;Chr10_2750802_G;Chr10_2870996_G;Chr10_2887410_A;Chr10_2927284_T;Chr10_45082937_A;Chr10_45127748_C;Chr10_48926597_A;Chr10_49256007_G;Chr10_49302884_C;Chr11_4153990_C;Chr11_4306322_T;Chr13_29215285_T;Chr13_29550344_A;Chr13_44483438_A;Chr14_46525690_G;Chr14_9234257_T;Chr18_56182068_G;
与脂肪含量相关的25个SNP位点及其优势等位基因如下:
Chr01_1533882_A;Chr02_5225452_T;Chr02_6300927_T;Chr03_25891807_T;Chr03_36421392_A;Chr03_36426626_T;Chr03_36451021_G;Chr03_36504983_C;Chr03_36789422_G;Chr03_37706557_T;Chr04_8569889_A;Chr06_19781007_T;Chr06_4351486_A;Chr07_1952143_T;Chr09_41676859_A;Chr09_4283906_C;Chr11_2630521_G;Chr13_19460489_C;Chr13_30388748_G;Chr14_48354923_T;Chr14_4978437_A;Chr18_51200487_A;Chr18_55727744_T;Chr18_8671202_A;Chr19_34843169_T;
与主茎节数相关的25个SNP位点及其优势等位基因如下:
Chr01_50602779_C;Chr05_39604331_C;Chr05_39788521_C;Chr05_40075652_T;Chr06_13105258_A;Chr06_1756279_A;Chr06_2636926_C;Chr08_22078860_G;Chr10_2927284_T;Chr11_9896347_G;Chr14_45860975_T;Chr14_46525690_G;Chr14_46614414_G;Chr14_47779860_T;Chr15_282154_T;Chr15_49558739_C;Chr15_50357591_G;Chr15_50377398_C;Chr15_50532317_A;Chr16_32911332_G;Chr17_39257059_C;Chr18_6825701_A;Chr18_9165638_C;Chr19_34475899_A;Chr19_34574726_C;
与百粒重相关的25个SNP位点及其优势等位基因如下:
Chr01_51315364_A;Chr01_53509482_G;Chr03_1404553_A;Chr03_333082_G;Chr03_37027494_A;Chr05_42019019_T;Chr05_5558466_C;Chr05_5575650_A;Chr07_42689775_T;Chr07_42700692_T;Chr07_42732051_G;Chr07_42782332_T;Chr07_42836543_A;Chr12_35265460_G;Chr12_35289582_G;Chr12_35578344_A;Chr12_8916858_T;Chr15_15854711_T;Chr17_38307270_A;Chr17_38350306_T;Chr18_453852_C;Chr18_48056177_C;Chr18_48125071_A;Chr18_48153620_T;Chr18_54703004_C;
与单株粒重相关的25个SNP位点及其优势等位基因如下:
Chr01_4026903_G;Chr04_45658472_G;Chr04_51554352_C;Chr04_51579450_G;Chr06_13432800_C;Chr06_13481784_T;Chr06_4134589_A;Chr06_48428377_C;Chr09_45975341_C;Chr09_46478149_T;Chr09_46836433_A;Chr11_32376132_G;Chr12_36704530_C;Chr13_16484275_C;Chr13_41775097_A;Chr13_42050209_A;Chr13_42383660_A;Chr13_42410927_G;Chr15_3989240_G;Chr16_6026215_A;Chr17_12475327_G;Chr18_1331239_T;Chr18_50326879_G;Chr18_50526685_G;Chr18_5957508_T;
与单株粒数相关的25个SNP位点及其优势等位基因如下:
Chr01_4026903_G;Chr01_4050717_A;Chr04_46878018_G;Chr06_10505562_A;Chr06_50163774_G;Chr07_5575080_C;Chr07_5825087_T;Chr08_1028572_A;Chr09_35879535_G;Chr09_46200899_C;Chr09_46308505_A;Chr12_36595459_C;Chr12_36765947_G;Chr13_21768219_G;Chr13_41775097_A;Chr13_42028098_C;Chr13_42150995_T;Chr13_42216053_T;Chr13_42383660_A;Chr13_42410927_G;Chr15_282154_T;Chr15_3989240_G;Chr18_48017092_T;Chr18_50326879_G;Chr18_5957508_T;
与分枝数相关的25个SNP位点及其优势等位基因如下:
Chr01_50653236_G;Chr05_32075424_T;Chr05_33844667_G;Chr05_34000026_A;Chr05_36371924_T;Chr09_458254_G;Chr09_475009_G;Chr09_500375_T;Chr12_3951770_A;Chr13_18615062_C;Chr13_45066236_T;Chr15_10109864_T;Chr15_10128698_T;Chr15_10605120_G;Chr15_8981420_T;Chr15_9077137_C;Chr15_9108212_A;Chr15_9138650_C;Chr15_9176525_A;Chr15_9325304_T;Chr15_9632956_A;Chr15_9950434_A;Chr20_39493065_T;Chr20_39531946_A;Chr20_39680045_G;
与底荚高度相关的25个SNP位点及其优势等位基因如下:
Chr02_38935935_A;Chr02_44953925_C;Chr02_45012265_T;Chr02_45106877_A;Chr02_45225277_T;Chr02_45460408_G;Chr04_1886636_G;Chr04_51554352_A;Chr05_5613716_C;Chr07_15480093_T;Chr08_7805605_A;Chr08_9185800_G;Chr10_45082937_A;Chr10_45127748_C;Chr10_45175769_A;Chr10_49343783_T;Chr11_2104739_T;Chr11_2167163_T;Chr11_32506058_T;Chr11_33857564_A;Chr13_45794372_T;Chr14_2226559_T;Chr15_6834700_T;Chr19_36797568_A;Chr20_8076579_A。
3.一种用于检测权利要求1所述的与大豆农艺性状相关的SNP位点组合的液相基因芯片在分子辅助育种或全基因组育种中的应用,其特征在于,所述分子辅助育种或全基因组育种基于大豆农艺性状进行育种,所述大豆农艺性状指株高、百粒重、底荚高度、脂肪含量、蛋白含量、单株粒数、单株荚数、主茎节数、单株粒重和分枝数;
所述液相基因芯片含有一套如权利要求2所述的探针;
优势等位基因以染色体编号_物理位置_优势基因型的形式表示;
与蛋白含量相关的25个SNP位点及其优势等位基因如下:
Chr01_49903973_A;Chr01_54065323_T;Chr02_6300927_C;Chr03_18107159_G;Chr04_3350250_A;Chr04_8569889_T;Chr05_18929941_T;Chr05_22058564_G;Chr06_17382650_T;Chr06_17582094_G;Chr06_17602402_T;Chr06_17626369_T;Chr06_27625128_G;Chr06_28928355_T;Chr06_42252843_T;Chr09_40052962_A;Chr09_6653411_A;Chr10_31900041_C;Chr14_48354923_C;Chr14_4978437_G;Chr16_4075059_A;Chr18_55727744_C;Chr18_55800924_G;Chr19_34843169_C;Chr19_5221_C;
与单株荚数相关的25个SNP位点及其优势等位基因如下:
Chr01_39860894_T;Chr01_4026903_G;Chr01_4092615_G;Chr02_43559616_G;Chr03_38305381_A;Chr04_16473219_G;Chr04_45658472_G;Chr06_3286909_T;Chr06_50975144_G;Chr07_19025998_T;Chr08_776002_T;Chr09_38843968_T;Chr11_32929777_C;Chr12_36704530_C;Chr12_36736475_A;Chr14_4785275_A;Chr15_207098_A;Chr15_282154_T;Chr15_474286_T;Chr16_18681277_C;Chr17_8312752_A;Chr18_50326879_G;Chr18_50526685_G;Chr18_50554508_T;Chr18_5957508_T;
与株高相关的25个SNP位点及其优势等位基因如下:
Chr01_55547694_A;Chr03_155260_C;Chr03_558044_C;Chr04_50850178_G;Chr05_34977447_C;Chr05_40075652_T;Chr06_15231313_G;Chr06_15968336_A;Chr10_2750802_G;Chr10_2870996_G;Chr10_2887410_A;Chr10_2927284_T;Chr10_45082937_A;Chr10_45127748_C;Chr10_48926597_A;Chr10_49256007_G;Chr10_49302884_C;Chr11_4153990_C;Chr11_4306322_T;Chr13_29215285_T;Chr13_29550344_A;Chr13_44483438_A;Chr14_46525690_G;Chr14_9234257_T;Chr18_56182068_G;
与脂肪含量相关的25个SNP位点及其优势等位基因如下:
Chr01_1533882_A;Chr02_5225452_T;Chr02_6300927_T;Chr03_25891807_T;Chr03_36421392_A;Chr03_36426626_T;Chr03_36451021_G;Chr03_36504983_C;Chr03_36789422_G;Chr03_37706557_T;Chr04_8569889_A;Chr06_19781007_T;Chr06_4351486_A;Chr07_1952143_T;Chr09_41676859_A;Chr09_4283906_C;Chr11_2630521_G;Chr13_19460489_C;Chr13_30388748_G;Chr14_48354923_T;Chr14_4978437_A;Chr18_51200487_A;Chr18_55727744_T;Chr18_8671202_A;Chr19_34843169_T;
与主茎节数相关的25个SNP位点及其优势等位基因如下:
Chr01_50602779_C;Chr05_39604331_C;Chr05_39788521_C;Chr05_40075652_T;Chr06_13105258_A;Chr06_1756279_A;Chr06_2636926_C;Chr08_22078860_G;Chr10_2927284_T;Chr11_9896347_G;Chr14_45860975_T;Chr14_46525690_G;Chr14_46614414_G;Chr14_47779860_T;Chr15_282154_T;Chr15_49558739_C;Chr15_50357591_G;Chr15_50377398_C;Chr15_50532317_A;Chr16_32911332_G;Chr17_39257059_C;Chr18_6825701_A;Chr18_9165638_C;Chr19_34475899_A;Chr19_34574726_C;
与百粒重相关的25个SNP位点及其优势等位基因如下:
Chr01_51315364_A;Chr01_53509482_G;Chr03_1404553_A;Chr03_333082_G;Chr03_37027494_A;Chr05_42019019_T;Chr05_5558466_C;Chr05_5575650_A;Chr07_42689775_T;Chr07_42700692_T;Chr07_42732051_G;Chr07_42782332_T;Chr07_42836543_A;Chr12_35265460_G;Chr12_35289582_G;Chr12_35578344_A;Chr12_8916858_T;Chr15_15854711_T;Chr17_38307270_A;Chr17_38350306_T;Chr18_453852_C;Chr18_48056177_C;Chr18_48125071_A;Chr18_48153620_T;Chr18_54703004_C;
与单株粒重相关的25个SNP位点及其优势等位基因如下:
Chr01_4026903_G;Chr04_45658472_G;Chr04_51554352_C;Chr04_51579450_G;Chr06_13432800_C;Chr06_13481784_T;Chr06_4134589_A;Chr06_48428377_C;Chr09_45975341_C;Chr09_46478149_T;Chr09_46836433_A;Chr11_32376132_G;Chr12_36704530_C;Chr13_16484275_C;Chr13_41775097_A;Chr13_42050209_A;Chr13_42383660_A;Chr13_42410927_G;Chr15_3989240_G;Chr16_6026215_A;Chr17_12475327_G;Chr18_1331239_T;Chr18_50326879_G;Chr18_50526685_G;Chr18_5957508_T;
与单株粒数相关的25个SNP位点及其优势等位基因如下:
Chr01_4026903_G;Chr01_4050717_A;Chr04_46878018_G;Chr06_10505562_A;Chr06_50163774_G;Chr07_5575080_C;Chr07_5825087_T;Chr08_1028572_A;Chr09_35879535_G;Chr09_46200899_C;Chr09_46308505_A;Chr12_36595459_C;Chr12_36765947_G;Chr13_21768219_G;Chr13_41775097_A;Chr13_42028098_C;Chr13_42150995_T;Chr13_42216053_T;Chr13_42383660_A;Chr13_42410927_G;Chr15_282154_T;Chr15_3989240_G;Chr18_48017092_T;Chr18_50326879_G;Chr18_5957508_T;
与分枝数相关的25个SNP位点及其优势等位基因如下:
Chr01_50653236_G;Chr05_32075424_T;Chr05_33844667_G;Chr05_34000026_A;Chr05_36371924_T;Chr09_458254_G;Chr09_475009_G;Chr09_500375_T;Chr12_3951770_A;Chr13_18615062_C;Chr13_45066236_T;Chr15_10109864_T;Chr15_10128698_T;Chr15_10605120_G;Chr15_8981420_T;Chr15_9077137_C;Chr15_9108212_A;Chr15_9138650_C;Chr15_9176525_A;Chr15_9325304_T;Chr15_9632956_A;Chr15_9950434_A;Chr20_39493065_T;Chr20_39531946_A;Chr20_39680045_G;
与底荚高度相关的25个SNP位点及其优势等位基因如下:
Chr02_38935935_A;Chr02_44953925_C;Chr02_45012265_T;Chr02_45106877_A;Chr02_45225277_T;Chr02_45460408_G;Chr04_1886636_G;Chr04_51554352_A;Chr05_5613716_C;Chr07_15480093_T;Chr08_7805605_A;Chr08_9185800_G;Chr10_45082937_A;Chr10_45127748_C;Chr10_45175769_A;Chr10_49343783_T;Chr11_2104739_T;Chr11_2167163_T;Chr11_32506058_T;Chr11_33857564_A;Chr13_45794372_T;Chr14_2226559_T;Chr15_6834700_T;Chr19_36797568_A;Chr20_8076579_A。
4.根据权利要求3所述的一种用于检测与大豆农艺性状相关的SNP位点组合的液相基因芯片在分子辅助育种或全基因组育种中的应用,其特征在于,所述液相基因芯片的溶液体系为无核酸酶的水,所述溶液体系中探针的浓度为60ng/μL。
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