江淮地区夏大豆新品系SSR和PAV分子标记多样性分析
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摘要
大豆新品系已成为杂交育种中最主要亲本类型,本研究对系谱明确、适合江淮地区种植的296份大豆新品系进行SSR和PAV标记分析,以揭示其遗传关系,促进其育种利用。结果 93个SSR标记共检测到417个等位变异,平均每个位点等位变异数为4.48,变幅为2~15,PIC值为0.46;227对PAV标记每个位点平均等位变异数为2.10,变幅2~4,PIC值为0.22;基于SSR标记所计算的多样性指标数值均高于PAV标记所得。根据核心亲本划分的4个亚群间分子标记遗传多样性值相近,但都存在一些特有和特缺等位变异。基于SSR和PAV标记遗传距离的聚类分析分别可将供试材料分为12和10类,其中4个大类均可与4个核心亲本亚群对应,还发现一些系谱相同/相近的品系被聚在不同类群。两类分子标记都可用于揭示供试材料的遗传背景,利用所有320个标记可将296份新品系分为8类。
New breeding line of soybean has been the most important parent types in hybrid breeding program. In the present study, SSR and PAV marker analysis was conducted to reveal the genetic diversity of 296 new lines of soybean with clear pedigree which was suitable for further plantation in Changjiang and Huaihe region and promote its breeding and utilization. Total 417 allele variations were identified by 93 SSR markers, and the average allele number(AN) per locus was 4.48, ranged from 2~15. The polymorphism information content(PIC) was0.46. The average allele number per locus of 227 PAV markers was 2.10, ranged from 2~4, and the PIC was 0.22.The diversity index values determined based on SSR markers were all higher than those by PAV markers. Genetic diversity values of molecular marker of four subpopulations divided from different core parents were similar, butthey all had several specifically existent and specifically deficient alleles. These test materials could be clustered into 12 and 10 groups based on genetic distances of SSR and PAV markers respectively. Among them, four major groups could correspond to the four subpopulations of the core parents. Some lines of same or similar pedigree were clustered in different groups. Both SSR and PAV markers could be utilized to reveal the genetic background of test materials. All 296 new lines could be clustered into 8 groups based on all 320 markers.
New breeding line of soybean has been the most important parent types in hybrid breeding program. In the present study, SSR and PAV marker analysis was conducted to reveal the genetic diversity of 296 new lines of soybean with clear pedigree which was suitable for further plantation in Changjiang and Huaihe region and promote its breeding and utilization. Total 417 allele variations were identified by 93 SSR markers, and the average allele number(AN) per locus was 4.48, ranged from 2~15. The polymorphism information content(PIC) was0.46. The average allele number per locus of 227 PAV markers was 2.10, ranged from 2~4, and the PIC was 0.22.The diversity index values determined based on SSR markers were all higher than those by PAV markers. Genetic diversity values of molecular marker of four subpopulations divided from different core parents were similar, butthey all had several specifically existent and specifically deficient alleles. These test materials could be clustered into 12 and 10 groups based on genetic distances of SSR and PAV markers respectively. Among them, four major groups could correspond to the four subpopulations of the core parents. Some lines of same or similar pedigree were clustered in different groups. Both SSR and PAV markers could be utilized to reveal the genetic background of test materials. All 296 new lines could be clustered into 8 groups based on all 320 markers.
引文
Bilyeu K.,Ratnaparkhe M.B.,and Kole C.,eds.,2010,Genetics,genomics,and breeding ofsoybean,CRC Press,USA,pp.71-188
Cao T.J.,Xie J.Z.,Wu Q.H.,Chen Y.X.,Wang Z.Z.,Zhao H.,Wang X.C.,Zhan K.H.,Xu R.Q.,Wang J.R.,Luo M.C.,and Liu ZY.,2015,Genetic diversity of registered wheat varieties in Henan province based on pedigree and single-nucleotide polymorphism,Zuowu Xuebao(Acta Agronomica Sinica)41(2):197-206(曹廷杰,谢菁忠,吴秋红,陈永兴,王振忠赵虹,王西成,詹克慧,徐如强,王际睿,罗明成,刘志勇2015,河南省近年审定小麦品种基于系谱和SNP标记的遗传多样性分析,作物学报,41(2):197-206)
Chakraborty R.,and Jin L.,1993,Determination of relatedness between individuals using DNA fingerprinting,Hum.Biol.,65(6):875-895
Cheng W.,Xu Y.,Wang Z.L.,Kong J.J.,Gao X.W.,Gai J.Y.,and Zhao T.J.,Evaluation of resistance to the S1 strain of Pseudomonas syringae pv.glycinea in a soybean breeding line population from Yangtze and Huaihe River Valleys,Dadou Kexue(Soybean Science),35(1):100-105(程伟,许媛,王自力,孔杰杰,高学文,盖钧镒,赵团结,2016,江淮大豆育种种质对细菌性斑点病S1菌株的抗性鉴定,大豆科学,35(1):100-105)
Das S.,Upadhyaya H.D.,Srivastava R.,Bajaj D.,Gowda C.L.L.,Sharma S.,Singh S.,Tyagi A.K.,and Parida S.K.,2015,Genome-wide insertion-deletion(In Del)marker discovery and genotyping for genomics-assisted breeding applications in chickpea,DNA Res.,22(5):377-386
Fang Y.,Yang G.,Sun W.C.,Wang L.P.,Zhang S.J.,Yang J.S.,Liu L.B.,Liu Z.G.,Zeng X.C.,and Wu J.Y.,2015,Genetic diversity of winter-type and spring-type turnip rape(Brassia rapa L.)in north China by In Del and SSR markers,Zhongguo Youliao Zuowu Xuebao(Chinese Journal of Oil Crop Sciences),37(1):21-26(方彦,杨刚,孙万仓,王丽萍,张树娟,杨建胜,刘林波,刘自刚,曾秀存,武军艳,2015,北方地区白菜型冬油菜与春油菜的SSR和In Del遗传多样性分析中国油料作物学报,37(1):21-26)
Feng F.J.,Luo L.J.,Li Y.,Zhou L.G.,Xu X.X.,Wu J.H.,Chen HW.,Chen L.,and Mei H.W.,2005,Comparitive analysis of polymorphism of In Del and SSR markers in rice,Fenz Zhiwu Yuzhong(Molocular Plant Breeding),3(5):725-730(冯芳君,罗利军,李荧,周立国,徐小艳,吴金红,陈宏伟陈亮,梅捍卫,2005,水稻In Del和SSR标记多态性的比较分析,分子植物育种,3(5):725-730)
Gai J.Y.,Xiong D.J.,and Zhao T.J.,eds.,2015,The pedigrees and germplasm bases of soybean cultivars released in China Chinese Agriculture Press,Beijing,China,pp.1923-2005(盖钧镒,熊冬金,赵团结,编著,2015,中国大豆育成品种系谱与种质基础,中国农业出版社,中国,北京,pp.1923-2005)
Guan R.X.,Qu Y.,Guo Y.,Yu L.L.,Liu Y.,Jiang J.H.,Chen JG.,Ren Y.L.,Liu G.Y.,Tian L.,Jin L.G.,Liu Z.X.,Hong HL.,Chang R.Z.,Gilliham M.,and Qiu L.J.,2014,Salinity tolerance in soybean is modulated by natural variation in Gm SALT3,Plant J.,80(6):937-950
Guo S.,Zhang S.P.,Qiu M.Y.,Liu Y.P.,and Wu B.,2014Phylogenetic relationship analysis of Cherry tomato germplasm using In Del and SSR markers,Redai Zuowu Xuebao(Chinese Journal of Tropical Crops),35(8):1464-1468(郭爽,张素平,丘漫宇,刘玉平,吴蓓,2014,樱桃番茄种质资源亲缘关系的In Del和SSR标记分析,热带作物学报,35(8)1464-1468)
Li L.H.,Guo N.,Niu J.P.,Wang Z.L.,Cui X.X.,Sun J.T.,Zhao T.J.,and Xing H.,2016a,Loci and candidate gene identification for resistance to Phytophthora sojae via association analysis in soybean Glycine max(L.)Merr.,Mol.Genet.Genomics,291(3):1095-1103
Li Y.F.,Hong H.L.,Li Y.H.,Ma Y.S.,Chang R.Z.,and Qiu L.J.2016b,The identification of presence/absence variants associated with the apparent differences of growth period structures between cultivated and wild soybeans,J.Integr.Agr.15(2):262-270
Li Y.H.,Li W.,Zhang C.,Yang L.,Chang R.Z.,Gaut B.S.,and Qiu L.J.,2010,Genetic diversity in domesticated soybean(Glycine max)and its wild progenitor(Glycine soja)for simple sequence repeat and single-nucleotide polymorphism loci,New Phytologist,188(1):242-253
Liu K.J.,and Muse S.V.,2005,Power Marker:an integrated analysis environment for genetic marker analysis,Bioinformatics,21(9):2128-2129
Nei M.,Tajima F.,and Tateno Y.,1983,Accuracy of esti-mated phylogenetic trees from molecular data,J.Mol.Evol.,19(2)153-170
Nelson R.L.,Vodkin L.O.,and Thompson J.A.,1998,Identification of diverse soybean germplasm using RAPD markers,Crop Sci.,38(5):1348-1355
Shen X.,Liu Z.Q.,Mocoeur A.,Xia Y.,and Jing H.C.,2015,PAV markers in Sorghum bicolour:genome pattern,affected genes and pathways,and genetic linkage map construction,Theor.Appl.Genet.,128(4):623-637
Springer N.M.,Ying K.,Fu Y.,Ji T.,Yeh C.T.,Jia Y.,Wu W.,Richmond T.,Kitzman J.,Rosenbaum H.,Iniguez A.L.,Barbazuk W.B.,Jeddeloh J.A.,Nettleton D.,and Schnable P.S.,2009,Maize inbreds exhibit high levels of copy number variation(CNV)and presence/absence variation(PAV)in genome content,PLo S Genet.,5(11):e1000734
Vicente D.,Schuster I.,Lazzari F.,Paranzini J.P.D.,Oliveira M.A.R.D.,and Prete C.E.C.,2016,Mapping and validation of molecular markers of genes Dt1 and Dt2 to determine the type of stem growth in soybean,Acta Sci.Agron.,38(1):61-68
Wang W.B.,Li X.L.,Chen S.X.,Song S.Y.,Gai J.Y.,and Zhao T.J.,2016,Using presence/absence variation markers to identify the QTL/allele system that confers the small seed trait in wild soybean(Glycine soja Sieb.and Zucc.),Euphytica,208(1):101-111
Wang Y.D.,Xu M.G.,Zhang Y.J.,Weng Y.Y.,Li X.Y.,Kong J.J.,Zhao T.J.,and He X.H.,2017,Identification of droughttolerance of soybean germplasm from Yangtze and Huaihe River valleys at seedling stage,Dadou Kexue(Soybean Science),36(5):669-678(王应党,许孟歌,张雅娟,翁烨阳,李晓勇,孔杰杰,赵团结,何小红,2017,江淮大豆育种种质苗期耐旱性鉴定,大豆科学,36(5):669-678)
Wang Y.F.,Lu J.J.,Chen S.Y.,Shu L.P.,Palmer R.G.,Xing G.N.,Li Y.,Yang S.P.,Yu D.Y.,Zhao T.J.,and Gai J.Y.,2014,Exploration of presence/absence variation and corresponding polymorphic markers in soybean genome,J.Integr.Plant Biol.,56(10):1009-1019
Wang Z.L.,Guo C.Y.,Zhang J.S.,Sun F.L.,Li Z.Y.,He X.H.,Kong J.J.,Gai J.Y.,and Zhao T.J.,2015,Identification and genetic relationship of elite soybean breeding lines with high seed protein content in Yangtze-Huai River Valleys,Zhongguo Youliao Zuowu Xuebao(Chinese Journal of Oil Crop Sciences),37(6):780-788(王自力,郭呈宇,张吉顺,孙峰峦,李忠洋,何小红,孔杰杰,盖钧镒,赵团结,2015,江淮地区大豆籽粒高蛋白含量新品系的发掘与遗传关系分析,中国油料作物学报,37(6):780-788)
Wang Z.L.,Zhang J.S.,Guo C.Y.,Sun F.L.,Li Z.Y.,Kong J.J.,Gai J.Y.,and Zhao T.J.,2016,Genetic relationship of three Soybean core parents and their derived breeding lines detected by presence/absence variation markers,Dadou Kexue(Soybean Science),35(1):1-10(王自力,张吉顺,郭呈宇孙峰峦,李忠洋,孔杰杰,盖钧镒,赵团结,2016,大豆3个核心亲本及其衍生品系基于PAV分子标记的亲缘关系研究,大豆科学,35(1):1-10)
Wen Z.X.,Ding Y.L.,Zhao T.J.,and Gai J.Y.,2009,Genetic diversity and peculiarity of annual wild soybean(G.soja Sieb et Zucc.)from various eco-regions in China,Theor.Appl.Genet.,119(2):371-381
Zhang D.,Song H.N.,Cheng H.,Hao D.R.,Wang H.,Kan G.Z.Jin H.X.,and Yu D.Y.,2014,The acid phosphatase-encoding gene Gm ACP1 contributes to soybean tolerance to low-phosphorus stress,PLo S Genet.,10(1):e1004061
Zhang J.,Zhao T.J.,and Gai J.Y.,2008,Genetic diversity and genetic structure of Soybean cultivar population released in northeast China,Zuowu Xuebao(Acta Agronomica Sinica),34(9):1529-1536(张军,赵团结,盖钧镒,2008,中国东北大豆育成品种遗传多样性和群体遗传结构分析,作物学报,34(9):1529-1536)
Zhang S.S.,Li Y.H.,Li J.Y.,and Qiu L.J.,2013,Genetic dissection of elite line Zhongpin 03-5373 pedigree and identification of candidate markers related to resistance to soybean cyst nematode,Zuowu Xuebao(Acta Agronomica Sinica),39(10):1746-1753(张姗姗,李英慧,李金英,邱丽娟,2013,优良品系中品03-5373系谱的遗传解析及抗大豆胞囊线虫病相关标记鉴定,作物学报,39(10):1746-1753)
Cao T.J.,Xie J.Z.,Wu Q.H.,Chen Y.X.,Wang Z.Z.,Zhao H.,Wang X.C.,Zhan K.H.,Xu R.Q.,Wang J.R.,Luo M.C.,and Liu ZY.,2015,Genetic diversity of registered wheat varieties in Henan province based on pedigree and single-nucleotide polymorphism,Zuowu Xuebao(Acta Agronomica Sinica)41(2):197-206(曹廷杰,谢菁忠,吴秋红,陈永兴,王振忠赵虹,王西成,詹克慧,徐如强,王际睿,罗明成,刘志勇2015,河南省近年审定小麦品种基于系谱和SNP标记的遗传多样性分析,作物学报,41(2):197-206)
Chakraborty R.,and Jin L.,1993,Determination of relatedness between individuals using DNA fingerprinting,Hum.Biol.,65(6):875-895
Cheng W.,Xu Y.,Wang Z.L.,Kong J.J.,Gao X.W.,Gai J.Y.,and Zhao T.J.,Evaluation of resistance to the S1 strain of Pseudomonas syringae pv.glycinea in a soybean breeding line population from Yangtze and Huaihe River Valleys,Dadou Kexue(Soybean Science),35(1):100-105(程伟,许媛,王自力,孔杰杰,高学文,盖钧镒,赵团结,2016,江淮大豆育种种质对细菌性斑点病S1菌株的抗性鉴定,大豆科学,35(1):100-105)
Das S.,Upadhyaya H.D.,Srivastava R.,Bajaj D.,Gowda C.L.L.,Sharma S.,Singh S.,Tyagi A.K.,and Parida S.K.,2015,Genome-wide insertion-deletion(In Del)marker discovery and genotyping for genomics-assisted breeding applications in chickpea,DNA Res.,22(5):377-386
Fang Y.,Yang G.,Sun W.C.,Wang L.P.,Zhang S.J.,Yang J.S.,Liu L.B.,Liu Z.G.,Zeng X.C.,and Wu J.Y.,2015,Genetic diversity of winter-type and spring-type turnip rape(Brassia rapa L.)in north China by In Del and SSR markers,Zhongguo Youliao Zuowu Xuebao(Chinese Journal of Oil Crop Sciences),37(1):21-26(方彦,杨刚,孙万仓,王丽萍,张树娟,杨建胜,刘林波,刘自刚,曾秀存,武军艳,2015,北方地区白菜型冬油菜与春油菜的SSR和In Del遗传多样性分析中国油料作物学报,37(1):21-26)
Feng F.J.,Luo L.J.,Li Y.,Zhou L.G.,Xu X.X.,Wu J.H.,Chen HW.,Chen L.,and Mei H.W.,2005,Comparitive analysis of polymorphism of In Del and SSR markers in rice,Fenz Zhiwu Yuzhong(Molocular Plant Breeding),3(5):725-730(冯芳君,罗利军,李荧,周立国,徐小艳,吴金红,陈宏伟陈亮,梅捍卫,2005,水稻In Del和SSR标记多态性的比较分析,分子植物育种,3(5):725-730)
Gai J.Y.,Xiong D.J.,and Zhao T.J.,eds.,2015,The pedigrees and germplasm bases of soybean cultivars released in China Chinese Agriculture Press,Beijing,China,pp.1923-2005(盖钧镒,熊冬金,赵团结,编著,2015,中国大豆育成品种系谱与种质基础,中国农业出版社,中国,北京,pp.1923-2005)
Guan R.X.,Qu Y.,Guo Y.,Yu L.L.,Liu Y.,Jiang J.H.,Chen JG.,Ren Y.L.,Liu G.Y.,Tian L.,Jin L.G.,Liu Z.X.,Hong HL.,Chang R.Z.,Gilliham M.,and Qiu L.J.,2014,Salinity tolerance in soybean is modulated by natural variation in Gm SALT3,Plant J.,80(6):937-950
Guo S.,Zhang S.P.,Qiu M.Y.,Liu Y.P.,and Wu B.,2014Phylogenetic relationship analysis of Cherry tomato germplasm using In Del and SSR markers,Redai Zuowu Xuebao(Chinese Journal of Tropical Crops),35(8):1464-1468(郭爽,张素平,丘漫宇,刘玉平,吴蓓,2014,樱桃番茄种质资源亲缘关系的In Del和SSR标记分析,热带作物学报,35(8)1464-1468)
Li L.H.,Guo N.,Niu J.P.,Wang Z.L.,Cui X.X.,Sun J.T.,Zhao T.J.,and Xing H.,2016a,Loci and candidate gene identification for resistance to Phytophthora sojae via association analysis in soybean Glycine max(L.)Merr.,Mol.Genet.Genomics,291(3):1095-1103
Li Y.F.,Hong H.L.,Li Y.H.,Ma Y.S.,Chang R.Z.,and Qiu L.J.2016b,The identification of presence/absence variants associated with the apparent differences of growth period structures between cultivated and wild soybeans,J.Integr.Agr.15(2):262-270
Li Y.H.,Li W.,Zhang C.,Yang L.,Chang R.Z.,Gaut B.S.,and Qiu L.J.,2010,Genetic diversity in domesticated soybean(Glycine max)and its wild progenitor(Glycine soja)for simple sequence repeat and single-nucleotide polymorphism loci,New Phytologist,188(1):242-253
Liu K.J.,and Muse S.V.,2005,Power Marker:an integrated analysis environment for genetic marker analysis,Bioinformatics,21(9):2128-2129
Nei M.,Tajima F.,and Tateno Y.,1983,Accuracy of esti-mated phylogenetic trees from molecular data,J.Mol.Evol.,19(2)153-170
Nelson R.L.,Vodkin L.O.,and Thompson J.A.,1998,Identification of diverse soybean germplasm using RAPD markers,Crop Sci.,38(5):1348-1355
Shen X.,Liu Z.Q.,Mocoeur A.,Xia Y.,and Jing H.C.,2015,PAV markers in Sorghum bicolour:genome pattern,affected genes and pathways,and genetic linkage map construction,Theor.Appl.Genet.,128(4):623-637
Springer N.M.,Ying K.,Fu Y.,Ji T.,Yeh C.T.,Jia Y.,Wu W.,Richmond T.,Kitzman J.,Rosenbaum H.,Iniguez A.L.,Barbazuk W.B.,Jeddeloh J.A.,Nettleton D.,and Schnable P.S.,2009,Maize inbreds exhibit high levels of copy number variation(CNV)and presence/absence variation(PAV)in genome content,PLo S Genet.,5(11):e1000734
Vicente D.,Schuster I.,Lazzari F.,Paranzini J.P.D.,Oliveira M.A.R.D.,and Prete C.E.C.,2016,Mapping and validation of molecular markers of genes Dt1 and Dt2 to determine the type of stem growth in soybean,Acta Sci.Agron.,38(1):61-68
Wang W.B.,Li X.L.,Chen S.X.,Song S.Y.,Gai J.Y.,and Zhao T.J.,2016,Using presence/absence variation markers to identify the QTL/allele system that confers the small seed trait in wild soybean(Glycine soja Sieb.and Zucc.),Euphytica,208(1):101-111
Wang Y.D.,Xu M.G.,Zhang Y.J.,Weng Y.Y.,Li X.Y.,Kong J.J.,Zhao T.J.,and He X.H.,2017,Identification of droughttolerance of soybean germplasm from Yangtze and Huaihe River valleys at seedling stage,Dadou Kexue(Soybean Science),36(5):669-678(王应党,许孟歌,张雅娟,翁烨阳,李晓勇,孔杰杰,赵团结,何小红,2017,江淮大豆育种种质苗期耐旱性鉴定,大豆科学,36(5):669-678)
Wang Y.F.,Lu J.J.,Chen S.Y.,Shu L.P.,Palmer R.G.,Xing G.N.,Li Y.,Yang S.P.,Yu D.Y.,Zhao T.J.,and Gai J.Y.,2014,Exploration of presence/absence variation and corresponding polymorphic markers in soybean genome,J.Integr.Plant Biol.,56(10):1009-1019
Wang Z.L.,Guo C.Y.,Zhang J.S.,Sun F.L.,Li Z.Y.,He X.H.,Kong J.J.,Gai J.Y.,and Zhao T.J.,2015,Identification and genetic relationship of elite soybean breeding lines with high seed protein content in Yangtze-Huai River Valleys,Zhongguo Youliao Zuowu Xuebao(Chinese Journal of Oil Crop Sciences),37(6):780-788(王自力,郭呈宇,张吉顺,孙峰峦,李忠洋,何小红,孔杰杰,盖钧镒,赵团结,2015,江淮地区大豆籽粒高蛋白含量新品系的发掘与遗传关系分析,中国油料作物学报,37(6):780-788)
Wang Z.L.,Zhang J.S.,Guo C.Y.,Sun F.L.,Li Z.Y.,Kong J.J.,Gai J.Y.,and Zhao T.J.,2016,Genetic relationship of three Soybean core parents and their derived breeding lines detected by presence/absence variation markers,Dadou Kexue(Soybean Science),35(1):1-10(王自力,张吉顺,郭呈宇孙峰峦,李忠洋,孔杰杰,盖钧镒,赵团结,2016,大豆3个核心亲本及其衍生品系基于PAV分子标记的亲缘关系研究,大豆科学,35(1):1-10)
Wen Z.X.,Ding Y.L.,Zhao T.J.,and Gai J.Y.,2009,Genetic diversity and peculiarity of annual wild soybean(G.soja Sieb et Zucc.)from various eco-regions in China,Theor.Appl.Genet.,119(2):371-381
Zhang D.,Song H.N.,Cheng H.,Hao D.R.,Wang H.,Kan G.Z.Jin H.X.,and Yu D.Y.,2014,The acid phosphatase-encoding gene Gm ACP1 contributes to soybean tolerance to low-phosphorus stress,PLo S Genet.,10(1):e1004061
Zhang J.,Zhao T.J.,and Gai J.Y.,2008,Genetic diversity and genetic structure of Soybean cultivar population released in northeast China,Zuowu Xuebao(Acta Agronomica Sinica),34(9):1529-1536(张军,赵团结,盖钧镒,2008,中国东北大豆育成品种遗传多样性和群体遗传结构分析,作物学报,34(9):1529-1536)
Zhang S.S.,Li Y.H.,Li J.Y.,and Qiu L.J.,2013,Genetic dissection of elite line Zhongpin 03-5373 pedigree and identification of candidate markers related to resistance to soybean cyst nematode,Zuowu Xuebao(Acta Agronomica Sinica),39(10):1746-1753(张姗姗,李英慧,李金英,邱丽娟,2013,优良品系中品03-5373系谱的遗传解析及抗大豆胞囊线虫病相关标记鉴定,作物学报,39(10):1746-1753)