鸭茅品种的SCoT遗传变异分析

doi:10.11686/cyxb20140128

摘要/Abstract

摘要： 本研究应用SCoT标记对32个鸭茅品种(包括国内栽培驯化品种和国外引进品种)进行研究,为揭示鸭茅栽培驯化品种与引进品种间的遗传变异差异和鸭茅新品种选育提供理论依据。研究结果表明,1)从80个SCoT引物中筛选出22个条带清晰且稳定的引物,共扩增出308条谱带,其中,多态性谱带245条,多态性比率(PPB)为79.55%,平均每个引物扩增多态性条带数为11.14条;2)栽培驯化品种平均遗传距离为0.1242,引进品种平均遗传距离为0.1952,且引进品种在多态性条带(NPB),多态性比率(PPB),基因多样性指数(H),Shannon指数(I)等水平都高于栽培驯化品种,表明栽培驯化品种的遗传多样性水平低于引进品种;3)AMOVA显示存在于栽培驯化品种和引进品种两类群之间和之内的遗传变异分别为16.32%和83.68%,更多的遗传变异存在于类群内;4)UPGMA聚类分析和主成分分析(PCA)结果表明,供试32个鸭茅品种主要聚为6大类,国内栽培驯化品种聚为类群I,国外引进品种分别聚为其他几个类群。

Abstract: Start codon targeted polymorphism (SCoT) was used to analysis 32 cocksfoot (Dactylis glomerata) varieties (including cultivated and introduced varieties),to reveal the differences of genetic diversity in cultivated and introduced varieties and to provide a theoretical basis for breeding new varieties of cocksfoot. 1) Twenty-two primers were selected from 80 SCoT primers,and a total of 308 bands were amplified,of which 245 (79.55%) were polymorphic: the average was 11.14 per primer. 2) The average genetic distance of cultivated varieties was 0.1242 while that of introduced varieties was 0.1952. The introduced varieties had higher genetic distances than the cultivated ones at the level of polymorphism bands (NPB) and percentage of polymorphic bands (PPB). The gene diversity index (H) and Shannon index (I),indicated that the genetic diversity of cultivated varieties was lower than that of introduced varieties. 3) AMOVA analysis showed that the genetic variance within and between cultivated and introduced varieties was 83.68% and 16.32%,respectively and the main genetic variance was in the internal group. 4) The results of UPGMA clustering and PCoA analysis showed that the 32 cocksfoot varieties could be divided into six groups,the cultivated varieties were in group I while the introduced varieties were in the other five groups.

中图分类号:

S543⁺.303

蒋林峰，张新全，黄琳凯，马啸，严德飞，胡强，付玉凤. 鸭茅品种的SCoT遗传变异分析[J]. 草业学报, 2014, 23(1): 229-238.

JIANG Lin-feng,ZHANG Xin-quan,HUANG Lin-kai,MA Xiao,YAN De-fei,HU Qiang,FU Yu-feng. Analysis of genetic diversity in a cocksfoot (Dactylis glomerata) variety using SCoT markers[J]. Acta Prataculturae Sinica, 2014, 23(1): 229-238.

参考文献

Reference：
[1]Li J Q, Wang L H, Zhan Q W, et al. Genetic diversity of 20 ryegrass accessions by SRAP markers[J]. Acta Prataculturae Sinica, 2013, 22(2): 158-164.
[2]Han G H, Xiang S Q, Wang W X, et al. Establishment and application of SCoT molecular marker system for citrus[J]. Acta Horticulturae Sinica, 2011, 38(7): 1243-1250.
[3]Collard B C Y, Mackill D J. Start codon targeted (SCoT) polymorphism: A simple, novel DNA marker technique for generating gene targeted markers in plants[J]. Plant Molecular Biology Reporter, 2009, 27: 86-93.
[4]He Q Y, Wang W B, Yang H Y, et al. Optimization of SCoT reaction system and genetic diversity of different fall dormancy alfalfa[J]. Acta Prataculturae Sinica, 2012, 21(2): 133-140.
[5]Luo C, He X H, Chen H, et al. Analysis of diversity and relationships among mango cultivars using start codon targeted (SCoT) markers[J]. Biochemical Systematics and Ecology, 2010, 38: 1176-1184.
[6]Zeng H Y, Wei L, Liu P, et al. Genetic diversity of energy grass Arundo donax revealed by ISSR markers[J]. Acta Prataculturae Sinica, 2013, 22(3): 266-273.
[7]Zeng L, Yuan Q H, Wang F, et al. Genetic diversity analysis of Agropyron germplasm resources by ISSR[J]. Acta Prataculturae Sinica, 2013, 22(1): 260-267. 
[8]Xiong F Q, Jiang J, Zhong R C, et al. Application of SCoT molecular marker in genus arachis[J]. Acta Agronomica Sinica, 2010, 36(12): 2055-2061.
[9]Guo D L, Zhang J Y, Liu C H. Genetic diversity in some grape varieties revealed by SCoT analyses[J]. Molecular Biology Reports, 2012, 39: 5307-5313.
[10]Luo C, He X H, Chen H, et al. Genetic relationship and diversity of Mangifera indicaL.: revealed through SCoT analysis[J]. Genetic Resources and Crop Evolution, 2012, 59: 1505-1515.
[11]Xiong F Q, Zhong R C, Han Z Q, et al. Start codon targeted polymorphism for evaluation of functional genetic variation and relationships in cultivated peanut（Arachis hypogaea L.) genotypes[J]. Molecular Biology Reports, 2011, 38: 3487-3494.
[12]Gorji A M, Poczai P, Polgar Z, et al. Efficiency of arbitrarily amplified dominant markers (SCOT, ISSR and RAPD) for diagnostic fingerprinting in tetraploid potato[J]. American Journal of Potato Research, 2011, 88: 226-237.
[13]Lindner R, Garcia A. Geographic distribution and genetic resources of Dactylis in Galicia (northwest Spain)[J]. Genetic Resources and Crop Evolution, 1997, 44: 499-507.
[14]Bushman B S, Larson S R, Tuna M, et al. Orchardgrass(Dactylis glomerata L.) EST and SSR marker development, annotation, and transferability[J]. Theoretical and Applied Genetics, 2011,123: 119-129.
[15]Lumaret R. Cytology, genetics, and evolution in the genus Dactylis[J]. Critical Reviews in Plant Sciences, 1988, 7: 55-89.
[16]Sanada Y, Tamura K, Yamada T. Relationship between water soluble carbohydrates in fall and spring and vigor of spring regrowth in orchardgrass[J]. Crop Science, 2010, 50: 380-390.
[17]Jafari A, Naseri H. Genetic variation and correlation among yield and quality traits in cocksfoot (Dactylis glomerataL.)[J]. Journal of Agricultural Science, 2007, 145: 599-610.
[18]Peng Y, Zhang X Q. Progress in studies on genetic diversity of dactylis glomerata L.[J]. Journal of Plant Genetic Biology, 2003, 4(2): 179-183.
[19]Stebbins G L, Zohary D. Cytogenetics and Evolutionary Studies in the Genus Dactylis L. Morphology, Distribution and Interrelationships of the Diploid Subspecies[M]. California: University of California Press, 1959, 31: 1-40.
[20]Zhong S. The agronomic characters of the hybrid progeny of wild Dactylis glomerata[J]. Acta Prataculturae Sinica, 2007, 16(1): 69-74.
[21]Zhang X Q, Du Y, Zheng D C. Study on PMC meiosis. pollen fertility and seed setting in diploid and tetraploid of Dactylis glomerata[J]. Chinese Journal of Grassland, 1996, (6): 38-40.
[22]Shi S R, Zhang X Q, Bai S J. Esterase and peroxidase in diploid and tetraploid common Orchardgrasses[J]. Pratacultural Science, 1998, (6): 11-1
[23]Xie W G, Zhang X Q, Ma X, et al. Genetic variation of Dactylis glomerata germplasm from Southwest China detected by SSR markers[J]. Acta Prataculturae Sinica, 2009, 18(4): 138-146.
[24]Peng Y, Zhang X Q, Deng Y L, et al. Evaluation of genetic diversity in wild orchardgrass (Dactylis glomerata L.) based on AFLP markers[J]. Hereditas, 2008, 145: 174-181.
[25]Wang G, Zhang X Q, Liu W, et al. Comparison of genetic diversity in cultivated and wild orchardgrass(Dactylis glomerata) detected by SSR markers[J]. Acta Prataculturae Sinica, 2010, 19(6): 187-196.
[26]Doyle J J, Doyle J L, Brown A H D. Analysis of a polyploid complex in glycine with chloroplast and nuclear DNA[J]. Australian Systematic Botany, 1990, 3: 125-136.
[27]Yeh F C, Yang R C, Boyle T. POPGENE VERSION 1.31. Microsoft Windows-based Freeware for Population Genetic Analysis. Quick User Guide[M]. University of Alberta: Center for International Forestry Research, 1999.
[28]Nei M. Analysis of gene diversity in subdivided populations[J]. Proceedings of the National Academy of Sciences of the United States of America, 1973, 70: 3321-3323.
[29]Excoffier L, Smouse P E, Quattro J M. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data[J]. Genetics, 1992, 131(2): 479-491.
[30]Zhang F M, Ge S. Data analysis in population genetics.I.analysis of RAPD data with AMO-VA[J]. Biodiversity Science, 2002, 10: 438-444.
[31]Pavlicek A, Hrda S, Flegr J. FreeTree-free ware program for construction of phylogenetic trees on the basis of distance data and bootstrap/jackknife analysis of the tree robustness. Application in the RAPD analysis of the genus Frenkelia[J]. Folia Biologica, 1999, 45(3): 97.
[32]Nei M, Li W H. Mathematical model for studying the genetic variation in terms of restriction endonucleases[J]. Proceedings of the National Academy of Sciences of the United States of America, 1979, 76: 5269-5273.
[33]Huson D H, Scornavacca C. Dendroscope 3: An interactive viewer for rooted phylogenetic trees and networks[J]. Systematic Biology, 2012, 61: 1061-1067.
[34]Rohlf F J. NTSYS-pc: Numerical Taxonomy and Multivariate Analysis System, version 2.1.User Guide[M]. New York: Exeter Software, 2000.
[35]Luo C, He X H, Chen H, et al. Genetic diversity of mango cultivars estimated using SCoT and ISSR markers[J]. Biochemical Systematics and Ecology, 2011, 39: 676-684.

参考文献：
[1]李杰勤, 王丽华, 詹秋文, 等. 20个黑麦草品系的SRAP遗传多样性分析[J]. 草业学报, 2013, 22(2): 158-164.
[2]韩国辉, 向素琼, 汪卫星, 等. 柑橘SCoT分子标记技术体系的建立及其在遗传分析中的应用[J]. 园艺学报, 2011, 38(7): 1243-1250.
[3]Collard B C Y, Mackill D J. Start codon targeted (SCoT) polymorphism: A simple, novel DNA marker technique for generating gene-targeted markers in plants[J]. Plant Molecular Biology Reporter, 2009, 27: 86-93.
[4]何庆元, 王吴斌, 杨红燕, 等. 利用SCoT标记分析不同秋眠型苜蓿的遗传多样性[J]. 草业学报, 2012, 21(2): 133-140.
[5]Luo C, He X H, Chen H,et al. Analysis of diversity and relationships among mango cultivars using start codon targeted (SCoT) markers[J]. Biochemical Systematics and Ecology, 2010, 38: 1176-1184.
[6]曾汉元, 魏麟, 刘鹏, 等. 能源草芦竹遗传多样性的ISSR分析[J]. 草业学报, 2013, 22(3): 266-273.
[7]曾亮, 袁庆华, 王方, 等. 冰草属植物种质资源遗传多样性的ISSR分析[J]. 草业学报, 2013, 22(1): 260-267.
[8]熊发前, 蒋菁, 钟瑞春, 等. 目标起始密码子多态性(SCoT)分子标记技术在花生属中的应用[J]. 作物学报, 2010, 36(12): 2055-2061.
[9]Guo D L, Zhang J Y, Liu C H. Genetic diversity in some grape varieties revealed by SCoT analyses[J]. Molecular Biology Reports, 2012, 39: 5307-5313.
[10]Luo C, He X H, Chen H,et al. Genetic relationship and diversity of Mangifera indicaL.: revealed through SCoT analysis[J]. Genetic Resources and Crop Evolution, 2012, 59: 1505-1515.
[11]Xiong F Q, Zhong R C, Han Z Q,et al. Start codon targeted polymorphism for evaluation of functional genetic variation and relationships in cultivated peanut（Arachis hypogaea L.) genotypes[J]. Molecular Biology Reports, 2011, 38: 3487-3494.
[12]Gorji A M, Poczai P, Polgar Z,et al. Efficiency of arbitrarily amplified dominant markers (SCOT, ISSR and RAPD) for diagnostic fingerprinting in tetraploid potato[J]. American Journal of Potato Research, 2011, 88: 226-237.
[13]Lindner R, Garcia A. Geographic distribution and genetic resources of Dactylis in Galicia (northwest Spain)[J]. Genetic Resources and Crop Evolution, 1997, 44: 499-507.
[14]Bushman B S, Larson S R, Tuna M,et al. Orchardgrass（Dactylis glomerata L.) EST and SSR marker development, annotation, and transferability[J]. Theoretical and Applied Genetics, 2011, 123: 119-129.
[15]Lumaret R. Cytology, genetics, and evolution in the genus Dactylis[J]. Critical Reviews in Plant Sciences, 1988, 7: 55-89.
[16]Sanada Y, Tamura K, Yamada T. Relationship between water-soluble carbohydrates in fall and spring and vigor of spring regrowth in orchardgrass[J]. Crop Science, 2010, 50: 380-390.
[17]Jafari A, Naseri H. Genetic variation and correlation among yield and quality traits in cocksfoot（Dactylis glomerata L.)[J]. Journal of Agricultural Science, 2007, 145: 599-610.
[18]彭燕, 张新全. 鸭茅种质资源多样性研究进展[J]. 植物遗传资源学报, 2003, 4(2): 179-183.
[19]Stebbins G L, Zohary D. Cytogenetics and Evolutionary Studies in the Genus DactylisL. Morphology, Distribution and Interrelationships of the Diploid Subspecies[M]. California: University of California Press, 1959, 31: 1-40.
[20]钟声. 野生鸭茅杂交后代农艺性状的初步研究[J]. 草业学报, 2007, 16(1): 69-74.
[21]张新全, 杜逸, 郑德诚. 鸭茅二倍体和四倍体PMC减数分裂，花粉育性及结实性的研究[J]. 中国草地, 1996, (6): 38-40.
[22]帅素容, 张新全, 白史且. 不同倍性鸭茅同工酶比较研究[J]. 草业科学, 1998, (6): 11-16.
[23]谢文刚, 张新全, 马啸, 等. 中国西南区鸭茅种质遗传变异的SSR分析[J]. 草业学报, 2009, 18(4): 138-146.
[24]Peng Y, Zhang X Q, Deng Y L,et al. Evaluation of genetic diversity in wild orchardgrass（Dactylis glomerata L.) based on AFLP markers[J]. Hereditas, 2008, 145: 174-181.
[25]万刚, 张新全, 刘伟, 等. 鸭茅栽培驯化品种与野生材料遗传多样性比较的SSR分析[J]. 草业学报, 2010, 19(6): 187-196.
[26]Doyle J J, Doyle J L, Brown A H D. Analysis of a polyploid complex in glycine with chloroplast and nuclear DNA[J]. Australian Systematic Botany, 1990, 3: 125-136.
[27]Yeh F C, Yang R C, Boyle T. POPGENE VERSION 1.31. Microsoft Windows-based Freeware for Population Genetic Analysis. Quick User Guide[M]. University of Alberta: Center for International Forestry Research, 1999.
[28]Nei M. Analysis of gene diversity in subdivided populations[J]. Proceedings of the National Academy of Sciences of the United States of America, 1973, 70: 3321-3323.
[29]Excoffier L, Smouse P E, Quattro J M. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data[J]. Genetics, 1992, 131(2): 479-491.
[30]张富民, 葛颂. 群体遗传学研究中的数据处理方法I. RAPD数据的AMOVA分析[J]. 生物多样性, 2002, 10: 438-444.
[31]Pavlicek A, Hrda S, Flegr J. FreeTree-free ware program for construction of phylogenetic trees on the basis of distance data and bootstrap/jackknife analysis of the tree robustness. Application in the RAPD analysis of the genus Frenkelia[J]. Folia Biologica, 1999, 45(3): 97.
[32]Nei M, Li W H. Mathematical model for studying the genetic variation in terms of restriction endonucleases[J]. Proceedings of the National Academy of Sciences of the United States of America, 1979, 76: 5269-5273.
[33]Huson D H, Scornavacca C. Dendroscope 3: An interactive viewer for rooted phylogenetic trees and networks[J]. Systematic Biology, 2012, 61: 1061-1067.
[34]Rohlf F J. NTSYS-pc: Numerical Taxonomy and Multivariate Analysis System, version 2.1.User Guide[M]. New York: Exeter Software, 2000.
[35]Luo C, He X H, Chen H,et al. Genetic diversity of mango cultivars estimated using SCoT and ISSR markers[J]. Biochemical Systematics and Ecology, 2011, 39: 676-684.