利用微卫星标记分析山西糜子的遗传多样性
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摘要
山西是中国糜子主产区之一,有丰富的地方品种和农家种种质资源。利用微卫星标记分析糜子资源的遗传多样性,明确其遗传背景,便于加强糜子各品种之间的基因交流以及优异种质的筛选和利用,同时对种质资源的亲缘关系分析提供科学依据。利用27对SSR引物分析57份山西糜子的遗传差异,采用PowerMarker 3.25计算每对引物的多态性信息含量,采用PopGen1.32计算每对引物和两个生态区的观测等位基因等遗传参数。用MEGA5.0构建Neighbour-Joining聚类图,利用Structure 2.3.4鉴定遗传类群,采用Ntsys2.11进行主成分分析。结果显示27对SSR引物共检测出71个等位变异,平均每个位点扩增出2.6296个等位基因,各引物对的有效等位变异占观测等位变异的76.94%。各引物对的基因多样性指数为0.4140～1.0446,平均为0.7686;PIC为0.0601～0.7158,平均为0.5667。两生态区的观测杂合度等遗传参数相差不大。基于N-J遗传距离将57份材料分为3个类群,类群Ⅰ属于黄土高原春夏糜子区,类群Ⅱ、类群Ⅲ均属均于北方春糜子区和黄土高原春夏糜子区。遗传结构分析将57份糜子材料分为3个类群,绿色类群的基因多样性指数和PIC比蓝色、红色类群高。两种聚类结果基本一致,分布方式均与地理位置相关。主成分分析结果将晋北部材料与晋中、晋南部材料相区别,说明两生态区糜子的遗传背景因地理气候因素有明显差异,与遗传结构群体分析结果一致。研究表明,山西省糜子资源的遗传多样性丰富。
Shanxi province of China acts as one of the main producing areas of common millets and also a center of local varieties and farmer germplasm resources.Exploration of genetic diversity in common millet germplasms will provide a scientific basis for studying the origin and evolution of common millet,which would strengthen gene transfer between varieties of common millet and facilitate the utilization of excellent resources.In this study,we analyzed the genetic differences among 57 common millet accessions from Shanxi province by 27 pairs of SSR polymorphic primers.The statistical analysis were conducted by software PowerMarker 3.25,PopGen 1.32,MEGA 5.0,Structure 2.3.4 and Ntsys 2.11.Within this accessions,71 alleles were detected with an average of 2.6296 alleles at each locus.The number of effective allele account for 76.94% of the observed one.The Shannon index of all primers ranged from 0.4140 to 1.0446,with an average of 0.7686,The range of PIC was 0.0601-0.7158,with an average of 0.5667.The values of genetic diversity indexes such as the observed heterozygosity have no much difference between two ecotopes.Basing on Neighbor-joined genetic distance,57 materials were divided into 3 groups,the group Ⅰ belongs to the Loess Plateau spring & summer-sowing ecotopes,the group Ⅱ belongs to the Loess Plateau spring & summersowing and Northeast spring-sowing,the same as the group Ⅲ.The analysis of genetic structure divided 57 common millet accessions into three groups.In terms of the values of Shannon's information index and PIC,the green group is higher than that of the others.The results of two cluster analysis are consistent and they showed a close correlation between geographical region and the method of clustering.Meanwhile the materials in northern of Shanxi province were distinguished from the middle and the southern of Shanxi province by the means of PCA,The result indicated that the genetic background of two ecotopes has obvious differences due to geographical and climatic factors,which is consistent with the result of genetic structure analysis between populations.Thus,the genetic diversity of common millet resources in Shanxi province was abundant.
Shanxi province of China acts as one of the main producing areas of common millets and also a center of local varieties and farmer germplasm resources.Exploration of genetic diversity in common millet germplasms will provide a scientific basis for studying the origin and evolution of common millet,which would strengthen gene transfer between varieties of common millet and facilitate the utilization of excellent resources.In this study,we analyzed the genetic differences among 57 common millet accessions from Shanxi province by 27 pairs of SSR polymorphic primers.The statistical analysis were conducted by software PowerMarker 3.25,PopGen 1.32,MEGA 5.0,Structure 2.3.4 and Ntsys 2.11.Within this accessions,71 alleles were detected with an average of 2.6296 alleles at each locus.The number of effective allele account for 76.94% of the observed one.The Shannon index of all primers ranged from 0.4140 to 1.0446,with an average of 0.7686,The range of PIC was 0.0601-0.7158,with an average of 0.5667.The values of genetic diversity indexes such as the observed heterozygosity have no much difference between two ecotopes.Basing on Neighbor-joined genetic distance,57 materials were divided into 3 groups,the group Ⅰ belongs to the Loess Plateau spring & summer-sowing ecotopes,the group Ⅱ belongs to the Loess Plateau spring & summersowing and Northeast spring-sowing,the same as the group Ⅲ.The analysis of genetic structure divided 57 common millet accessions into three groups.In terms of the values of Shannon's information index and PIC,the green group is higher than that of the others.The results of two cluster analysis are consistent and they showed a close correlation between geographical region and the method of clustering.Meanwhile the materials in northern of Shanxi province were distinguished from the middle and the southern of Shanxi province by the means of PCA,The result indicated that the genetic background of two ecotopes has obvious differences due to geographical and climatic factors,which is consistent with the result of genetic structure analysis between populations.Thus,the genetic diversity of common millet resources in Shanxi province was abundant.
引文
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[5]Lu H Y,Zhang J P,Liu K B,Wu N Q,Li Y M,Zhou K S,Ye M L,Zhang T Y,Zhang T Y,Zhang H J,Yang X Y,Shen L C,Xu D K,Li Q.Earliest domestication of common millet(Panicum miliaceum L.)in East Asia extended to 10000 years ago.Proceedings of the National Academy of Sciences,2009,106(18):7367-7372
[6]Diao X M.Production and genetic improvement of minor cereals in China.The Crop Journal,2017,5(2):103-114
[7]李莉,王俊峰,颜廷进,李娜娜,丁汉凤,樊守金.基于SSR标记的山东省小麦DNA指纹图谱的构建.植物遗传资源学报,2013,14(3):537-541Li L,Wang J F,Yan T J,Li N N,Ding H F,Fan S J.Establishiment of DNA fingerprinting for wheat in Shandong province by SSRmarkers.Journal of Plant Genetic Resources,2013,14(3):537-541
[8]郑永胜,张晗,王东建,孙加梅,王雪梅,段丽丽,李华,王玮,李汝玉.基于荧光检测技术的小麦品种SSR鉴定体系的建立.中国农业科学,2014,47(19):3725-3735Zheng Y S,Zhang H,Wang D J,Sun J M,Wang X M,Duan L L,Li H,Wang W,Li R Y.Development of a wheat variety identification system based on fluorescently labeled SSRmarkers.Scientia Agricultura Sinica,2014,47(19):3725-3735
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[10]张科,魏海锋,卓大龙,张晓敬,张帆,周永力,黎志康.黑龙江省近年审定水稻品种基于SSR标记的遗传多样性分析.植物遗传资源学报,2016,17(3):447-454Zhang K,Wei H F,Zhuo D L,Zhang X J,Zhang F,Zhou YL,Li Z K.Genetic diversity analysis of registered rice(Oryza sativa L.)varieties in Heilongjiang province based on SSRmarkers.Journal of Plant Genetic Resources,2016,17(3):447-454
[11]马静,安永平,王兴盛,孙建昌.宁夏水稻品种微卫星标记数据库的建立.植物遗传资源学报,2016,17(2):226-232Ma J,An Y P,Wang X S,Sun J C.Establishment of Ningxia rice microsatellite marker database.Journal of Plant Genetic Resources,2016,17(2):226-232
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[13]王慧,卢有林,孙大鹏,杨华,罗利军,吴爱忠,施标,郑洪建.糯玉米种质品质性状鉴定和SSR标记遗传多样性分析.植物遗传资源学报,2013,14(5):800-808Wang H,Lu Y L,Sun D P,Yang H,Luo L J,Wu A Z,Shi B,Zheng H J.Evaluation of quality traits and genetic diversity analysis for Waxy maize germplasms by SSR markers.Journal of Plant Genetic Resources,2013,14(5):800-808
[14]盖树鹏,盖伟玲,黄进勇.SSR与SRAP标记在玉米品种鉴定中的比较研究.植物遗传资源学报,2011,12(3):468-472Gai S P,Gai W L,Huang J Y.Comparison of SSR and SRAPmarker for varieties identification in Maize(Zea mays L.).Journal of Plant Genetic Resources,2011,12(3):468-472
[15]Hu X Y,Wang J F,Lu P,Zhang H S.Assessment of genetic diversity in broomcorn millet(Panicum miliaceum L.)using SSR markers.Journal of Genetics and Genomics,2009,36(8):491-500
[16]连帅,陆平,乔治军,张琦,张茜,刘敏轩,王瑞云.利用SSR分子标记研究国内外黍稷地方品种和野生资源的遗传多样性.中国农业科学,2016,49(17):3264-3275Lian S,Lu P,Qiao Z J,Zhang Q,Zhang Q,Liu M X,Wang RY.Genetic diversity in broomcorn millet(Panicum miliaceum L.)from China and abroad by using SSR markers.Scientia Agricultura Sinica,2016,49(17):3264-3275
[17]董俊丽,王海岗,陈凌,王君杰,曹晓宁,王纶,乔治军.糜子骨干种质遗传多样性和遗传结构分析.中国农业科学,2015,48(16):3121-3131Dong J L,Wang H G,Chen L,Wang J J,Cao X N,Wang L,Qiao Z J.Analysis of genetic diversity and structure of proso millet core germplasm.Scientia Agricultura Sinica,2015,48(16):3121-3131
[18]Edwards K,Johnstone C,Thompson C.A simple and rapid method for the preparation of plant genomic DNA for PCRanalysis.Nucleic Acids Research,1991,19:1349
[19]Liu K,Muse S V.PowerMarker:Integrated analysis environment for genetic marker data.Bioinformatics,2005,21:2128-2129
[20]Yeh F C,Boyle T J.Population genetic analysis of co-dominant and dominant markers and quantitative traits.Belgian Journal of Botany,1997,129:157
[21]Tamura K,Peterson D,Peterson N,Stecher G,Nei M,Kumar S.MEGA5:Molecular evolutionary genetics analysis using maximum likelihood,evolutionary distance and maximum parsimony methods.Molecular Biology and Evolution,2011,665:2731-2739
[22]Falush D,Stephens M,Pritchard J K.Inference of population structure using multilocus genotype data:linked loci and correlated allele frequencies.Genetics,2003,164:1567-1587
[23]Nei M,Li W H.Mathematical model for studying genetic variation in terms of restriction endonucleases.Proceedings of the National Academy of Sciences.1979,76:5269-5273
[24]Cho Y I,Chung J W,Lee G A,Ma K H,Dixit A,Gwag J G,Park Y J.Development and characterization of twenty-five new polymorphic microsatellite markers in proso millet(Panicum miliaceum L.).Genes&genomics,2010,32(3):267-273
[25]Liu M,Xu Y,He J,Zhang S,Wang Y Y,Lu P.Genetic diversity and population structure of broomcorn millet(Panicum miliaceum L.)cultivars and landraces in China based on microsatellite markers.International Journal of Molecular Sciences,2016,17(3):E370
[26]王瑞云,季煦,陆平,刘敏轩,许月,王纶,王海岗,乔治军.利用荧光SSR分析中国糜子遗传多样性.作物学报,2017,43(4):530-548Wang R Y,Ji X,Lu P,Liu M X,Xu Y,Wang L,Wang HG,Qiao Z J.Analysis of genetic diversity in common millet(Panicum miliaceum)using fluorescent SSR in China.Acta Agronomica Sinica,2017,43(4):530-548
[27]Hunt H V,Campana M G,Lawes M C,Park Y J,Bower M A,Howe C J,Jones M K.Genetic diversity and phylogeography of broomcorn millet(Panicum miliaceum L.)across Eurasia.Molecular Ecology,2011,20(22):4756-4771
[28]Rajput S G,Santra D K.Evaluation of genetic diversity of proso millet(Panicum miliaceum L.)germplasm available in the USAusing SSR markers.Crop Science,2016,56:1-9
[29]Wang R Y,Hunt H V,Qiao Z J,Wang L,Han Y H.Diversity and cultivation of broomcorn millet(Panicum miliaceum L.)in China:A Review.Economic Botany,2016,70(3):332-342
[30]Wang R Y,Wang H G,Liu X Y,Lian S,Chen L,Qiao Z J,McInerney C E,Wang L.Drought-induced transcription of resistant and sensitive common millet varieties.The Journal of Animal&Plant Sciences,2017,27(4):1303-1314
[31]Wang R Y,Wang H G,Liu X Y,Ji X,Chen L,Lu P,Liu MX,Teng B,Qiao Z J.Waxy allelic diversity in common millet(Panicum miliaceum L.)in China.The Crop Journal,2018,6(4):321-329
[32]王瑞云,刘笑瑜,王海岗,陆平,刘敏轩,陈凌,乔治军.用高基元微卫星标记分析中国糜子遗传多样性.中国农业科学,2017,50(20):3848-3859Wang R Y,Liu X Y,Wang H G,Lu P,Liu M X,Chen L,Qiao Z J.Evaluation of genetic diversity of common millet(Panicum miliaceum)germplasm available in China using high motif nucleotide repeat SSR markers.Scientia Agricultura Sinica,2017,50(20):3848-3859
[33]王瑞云.糜子遗传多样性及进化研究进展.北京:中国农业出版社,2017:116-125Wang R Y.Genetic diversity and evolution advancement in common millet(Panicum miliaceum L.)Beijing:China Agriculture Press,2017:116-125
[2]Hulse J H,Laing E M,Pearson O E.Sorghum and the millets:Their composition and nutritive value.London:Academic Press,1980
[3]Devi P B,Vijayabharathi R,Sathyabama S,Malleshi N G,Priyadarisini V B.Health benefits of finger millet(Eleusine coracana L.)polyphenols and dietary fiber:a review.Journal of Food Science and Technology,2014,51(6):1021-1040
[4]Gupta S,Shrivastava S K,Shrivastava M.Proximate composition of seeds of hybrid varieties of minor millets.International Journal of Research in Engineering and Technology,2014,3(2):687-693
[5]Lu H Y,Zhang J P,Liu K B,Wu N Q,Li Y M,Zhou K S,Ye M L,Zhang T Y,Zhang T Y,Zhang H J,Yang X Y,Shen L C,Xu D K,Li Q.Earliest domestication of common millet(Panicum miliaceum L.)in East Asia extended to 10000 years ago.Proceedings of the National Academy of Sciences,2009,106(18):7367-7372
[6]Diao X M.Production and genetic improvement of minor cereals in China.The Crop Journal,2017,5(2):103-114
[7]李莉,王俊峰,颜廷进,李娜娜,丁汉凤,樊守金.基于SSR标记的山东省小麦DNA指纹图谱的构建.植物遗传资源学报,2013,14(3):537-541Li L,Wang J F,Yan T J,Li N N,Ding H F,Fan S J.Establishiment of DNA fingerprinting for wheat in Shandong province by SSRmarkers.Journal of Plant Genetic Resources,2013,14(3):537-541
[8]郑永胜,张晗,王东建,孙加梅,王雪梅,段丽丽,李华,王玮,李汝玉.基于荧光检测技术的小麦品种SSR鉴定体系的建立.中国农业科学,2014,47(19):3725-3735Zheng Y S,Zhang H,Wang D J,Sun J M,Wang X M,Duan L L,Li H,Wang W,Li R Y.Development of a wheat variety identification system based on fluorescently labeled SSRmarkers.Scientia Agricultura Sinica,2014,47(19):3725-3735
[9]马静,孙建昌,安永平,王兴盛,张振海,韩龙植.基于SSR标记的宁夏水稻遗传多样性分析.植物遗传资源学报,2013,14(5):826-832Ma J,Sun J C,An Y P,Wang X S,Zhang Z H,Han L Z.Analysis of genetic diversity with population of Japonica rice from Ningxia using microsatellite markers.Journal of Plant Genetic Resources,2013,14(5):826-832
[10]张科,魏海锋,卓大龙,张晓敬,张帆,周永力,黎志康.黑龙江省近年审定水稻品种基于SSR标记的遗传多样性分析.植物遗传资源学报,2016,17(3):447-454Zhang K,Wei H F,Zhuo D L,Zhang X J,Zhang F,Zhou YL,Li Z K.Genetic diversity analysis of registered rice(Oryza sativa L.)varieties in Heilongjiang province based on SSRmarkers.Journal of Plant Genetic Resources,2016,17(3):447-454
[11]马静,安永平,王兴盛,孙建昌.宁夏水稻品种微卫星标记数据库的建立.植物遗传资源学报,2016,17(2):226-232Ma J,An Y P,Wang X S,Sun J C.Establishment of Ningxia rice microsatellite marker database.Journal of Plant Genetic Resources,2016,17(2):226-232
[12]张全芳,梁水美,李燕,刘艳艳,范阳阳,郭庆法,鲁守平,步迅.基于荧光SSR标记的玉米自交系遗传结构解析.植物遗传资源学报,2017,18(1):19-31Zhang Q F,Liang S M,Li Y,Liu Y Y,Fan Y Y,Guo Q F,Lu S P,Bu X.Analysis of genetic diversity and genetic structure of maize germplasms using fluorescent SSR markers.Journal of Plant Genetic Resources,2017,18(1):19-31
[13]王慧,卢有林,孙大鹏,杨华,罗利军,吴爱忠,施标,郑洪建.糯玉米种质品质性状鉴定和SSR标记遗传多样性分析.植物遗传资源学报,2013,14(5):800-808Wang H,Lu Y L,Sun D P,Yang H,Luo L J,Wu A Z,Shi B,Zheng H J.Evaluation of quality traits and genetic diversity analysis for Waxy maize germplasms by SSR markers.Journal of Plant Genetic Resources,2013,14(5):800-808
[14]盖树鹏,盖伟玲,黄进勇.SSR与SRAP标记在玉米品种鉴定中的比较研究.植物遗传资源学报,2011,12(3):468-472Gai S P,Gai W L,Huang J Y.Comparison of SSR and SRAPmarker for varieties identification in Maize(Zea mays L.).Journal of Plant Genetic Resources,2011,12(3):468-472
[15]Hu X Y,Wang J F,Lu P,Zhang H S.Assessment of genetic diversity in broomcorn millet(Panicum miliaceum L.)using SSR markers.Journal of Genetics and Genomics,2009,36(8):491-500
[16]连帅,陆平,乔治军,张琦,张茜,刘敏轩,王瑞云.利用SSR分子标记研究国内外黍稷地方品种和野生资源的遗传多样性.中国农业科学,2016,49(17):3264-3275Lian S,Lu P,Qiao Z J,Zhang Q,Zhang Q,Liu M X,Wang RY.Genetic diversity in broomcorn millet(Panicum miliaceum L.)from China and abroad by using SSR markers.Scientia Agricultura Sinica,2016,49(17):3264-3275
[17]董俊丽,王海岗,陈凌,王君杰,曹晓宁,王纶,乔治军.糜子骨干种质遗传多样性和遗传结构分析.中国农业科学,2015,48(16):3121-3131Dong J L,Wang H G,Chen L,Wang J J,Cao X N,Wang L,Qiao Z J.Analysis of genetic diversity and structure of proso millet core germplasm.Scientia Agricultura Sinica,2015,48(16):3121-3131
[18]Edwards K,Johnstone C,Thompson C.A simple and rapid method for the preparation of plant genomic DNA for PCRanalysis.Nucleic Acids Research,1991,19:1349
[19]Liu K,Muse S V.PowerMarker:Integrated analysis environment for genetic marker data.Bioinformatics,2005,21:2128-2129
[20]Yeh F C,Boyle T J.Population genetic analysis of co-dominant and dominant markers and quantitative traits.Belgian Journal of Botany,1997,129:157
[21]Tamura K,Peterson D,Peterson N,Stecher G,Nei M,Kumar S.MEGA5:Molecular evolutionary genetics analysis using maximum likelihood,evolutionary distance and maximum parsimony methods.Molecular Biology and Evolution,2011,665:2731-2739
[22]Falush D,Stephens M,Pritchard J K.Inference of population structure using multilocus genotype data:linked loci and correlated allele frequencies.Genetics,2003,164:1567-1587
[23]Nei M,Li W H.Mathematical model for studying genetic variation in terms of restriction endonucleases.Proceedings of the National Academy of Sciences.1979,76:5269-5273
[24]Cho Y I,Chung J W,Lee G A,Ma K H,Dixit A,Gwag J G,Park Y J.Development and characterization of twenty-five new polymorphic microsatellite markers in proso millet(Panicum miliaceum L.).Genes&genomics,2010,32(3):267-273
[25]Liu M,Xu Y,He J,Zhang S,Wang Y Y,Lu P.Genetic diversity and population structure of broomcorn millet(Panicum miliaceum L.)cultivars and landraces in China based on microsatellite markers.International Journal of Molecular Sciences,2016,17(3):E370
[26]王瑞云,季煦,陆平,刘敏轩,许月,王纶,王海岗,乔治军.利用荧光SSR分析中国糜子遗传多样性.作物学报,2017,43(4):530-548Wang R Y,Ji X,Lu P,Liu M X,Xu Y,Wang L,Wang HG,Qiao Z J.Analysis of genetic diversity in common millet(Panicum miliaceum)using fluorescent SSR in China.Acta Agronomica Sinica,2017,43(4):530-548
[27]Hunt H V,Campana M G,Lawes M C,Park Y J,Bower M A,Howe C J,Jones M K.Genetic diversity and phylogeography of broomcorn millet(Panicum miliaceum L.)across Eurasia.Molecular Ecology,2011,20(22):4756-4771
[28]Rajput S G,Santra D K.Evaluation of genetic diversity of proso millet(Panicum miliaceum L.)germplasm available in the USAusing SSR markers.Crop Science,2016,56:1-9
[29]Wang R Y,Hunt H V,Qiao Z J,Wang L,Han Y H.Diversity and cultivation of broomcorn millet(Panicum miliaceum L.)in China:A Review.Economic Botany,2016,70(3):332-342
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