Scientia Agricultura Sinica ›› 2012, Vol. 45 ›› Issue (6): 1135-1143.doi: 10.3864/j.issn.0578-1752.2012.06.011

• HORTICULTURE • Previous Articles     Next Articles

Construction of Grape Core Collections

 GUO  Da-Long, LIU  Chong-Huai, ZHANG  Jun-Yu, ZHANG  Guo-Hai   

  1. 1.河南科技大学林学院，河南洛阳 471003
    2.中国农业科学院郑州果树研究所，郑州 450009
  • Received:2011-09-15 Online:2012-03-15 Published:2011-12-15

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Abstract: 【Objective】 Core collections of grape(Vitis vinifera) germplasm were constructed using SSR molecular markers based on the established grape primary core collections.【Method】The methods of M strategy (Core Finder and Power Core), genetic distance sampling (least distance stepwise sampling，LDSS and genetic distance optimization，GDOPT) and Core Hunter were used to construct core collections. The genetic diversity indexes of He, Ho and I and phenotypic indexes of mean difference percentage (MD%), variance difference percentage (VD%), coincidence rate of range (CR%) and variable rate of coefficient of variation (VR%) were used to evaluate the representativeness of core collections. The principal components analysis based on SSR and SRAP markers were also performed to validate the core collections. 【Result】 The core collections from M strategy have retained all the alleles of primary core collection, while those from genetic distance sampling have good representative. Core collections from M strategy, genetic distance sampling and Core Hunter were merged together in order to obtain maximum genetic distance and genetic diversity. At last, 48 materials of grape core collections retained 96.21% alleles of primary core collection and 92.90% genetic diversity of the original whole germplasm with 5.53% of the sampling ratio.【Conclusion】Core collections constructed in this study were proved to have good representative and enough genetic diversity according to the molecular and phenotypic statistic test. The method used in this study has important reference value for core collection construction of other plants.

Key words: grape(Vitis vinifera), core collection, SSR, SRAP, M strategy, genetic distance sampling

[1]Maul E, Topfer R, Eibach R. Vitis international variety catalogue: http://www. vivc.bafz.de, 2008.

[2]Brown A H D. Core collections: a practical approach to genetic resources management. Genome, 1989, 31(2): 818-824.

[3]Frankel O H. Genetic perspectives of germplasm conservation. In: Arber W, Llimensee K, Peacock W, Starlinger P. Genetic Manipulation: Impact on Man and Society. Cambridge, UK: Cambridge University Press, 1984: 161-170.

[4]王永康, 吴国良, 李登科, 冀爱青, 隋串玲, 赵爱玲. 果树核心种质研究进展. 植物遗传资源学报, 2010, 11(3): 380-385.

Wang Y K, Wu G L, Li D K, Ji A Q, Sui C L, Zhao A L. Advances in core collection of fruit germplasm. Journal of Plant Genetic Resources, 2010, 11(3): 380-385. (in Chinese)

[5]Zhang H, Zhang D, Wang M, Sun J, Qi Y, Li J, Wei X, Han L, Qiu Z, Tang S, Li Z. A core collection and mini core collection of Oryza sativa L. in China. Theoretical and Applied Genetics, 2010, 122(1): 49-61.

[6]Balfourier F, Roussel V, Strelchenko P, Exbrayat-Vinson F, Sourdille P, Boutet G, Koenig J, Ravel C, Mitrofanova O, Beckert M, Charmet G. A worldwide bread wheat core collection arrayed in a 384-well plate. Theoretical and Applied Genetics, 2007, 114(7): 1265-1275.

[7]宋喜娥, 李英慧, 常汝镇, 郭平毅, 邱丽娟. 中国栽培大豆(Glycine max(L.) Merr.)微核心种质的群体结构与遗传多样性. 中国农业科学, 2010, 43(11): 2209-2219.

Song X E, Li Y H, Chang R Z, Guo P Y, Qiu L J. Population structure and genetic diversity of mini core collection of cultivated soybean (Glycine max(L.) Merr.) in China. Scientia Agricultura Sinica, 2010, 43(11): 2209-2219. (in Chinese)

[8]张春雨, 陈学森, 张艳敏, 苑兆和, 刘遵春, 王延龄, 林  群. 采用分子标记构建新疆野苹果核心种质的方法. 中国农业科学, 2009, 42(2): 597-604.

Zhang C Y, Chen X S, Zhang Y M, Yuan Z H, Liu Z C, Wang Y L, Lin Q. A method for constructing core collection of Malus sieversii using molecular markers. Scientia Agricultura Sinica, 2009, 42(2): 597-604. (in Chinese)

[9]Le Cunff L, Fournier-Level A, Laucou V, Vezzulli S, Lacombe T, Adam-Blondon A F, Boursiquot J M, This P. Construction of nested genetic core collections to optimize the exploitation of natural diversity in Vitis vinifera L. subsp. sativa. BMC Plant Biology, 2008, 8(1): 31-31.

[10]Cipriani G, Spadotto A, Jurman I, Di Gaspero G, Crespan M, Meneghetti S, Frare E, Vignani R, Cresti M, Morgante M, Pezzotti M, Pe E, Policriti A, Testolin R. The SSR-based molecular profile of 1005 grapevine (Vitis vinifera L.) accessions uncovers new synonymy and parentages, and reveals a large admixture amongst varieties of different geographic origin. Theoretical and Applied Genetics, 2010, 121(8): 1569-1585.

[11]刘闯萍, 王  军, 沈育杰, 路文鹏. 山葡萄(Vitis amurensis)资源核心种质的初步构建. 植物遗传资源学报, 2008, 9(3): 372-374.

Liu C P, Wang J, Shen Y J, Lu W P. Preliminary construction of core collection in Vitis amurensis. Journal of Plant Genetic Resources, 2008, 9(3): 372-374. (in Chinese)

[12]Kim K W, Chung H K, Cho G T, Ma K H, Chandrabalan D, Gwag J G, Kim T S, Cho E G, Park Y J. PowerCore: a program applying the advanced M strategy with a heuristic search for establishing core sets. Bioinformatics, 2007, 23(16): 2155-2162.

[13]Thachuk C, Crossa J, Franco J, Dreisigacker S, Warburton M, Davenport G F. Core Hunter: an algorithm for sampling genetic resources based on multiple genetic measures. BMC Bioinformatics, 2009, 10: 243.

[14]Jansen J, van Hintum T. Genetic distance sampling: a novel sampling method for obtaining core collections using genetic distances with an application to cultivated lettuce. Theoretical and Applied Genetics, 2007, 114(3): 421-428.

[15]Wang J C, Hu J, Xu H M, Zhang S. A strategy on constructing core collections by least distance stepwise sampling. Theoretical and Applied Genetics, 2007, 115(1): 1-8.

[16]Odong T, Heerwaarden J, Jansen J, Hintum T, Eeuwijk F. Statistical Techniques for Defining Reference Sets of Accessions and Microsatellite Markers. Crop Science, 2011, 51:2401-2411.

[17] Zhao W, Cho G, Ma K, Chung J, Gwag J, Park Y. Development of an allele-mining set in rice using a heuristic algorithm and SSR genotype data with least redundancy for the post-genomic era. Molecular Breeding, 2010, 26(4): 639-651.

[18]刘鑫铭, 刘崇怀, 樊秀彩, 郭大龙, 张国海, 孙海生. 葡萄种质资源初级核心群的构建. 植物遗传资源学报, 2012，13(1): 72-76.

Liu X M, Liu C H, Fan X C, Guo D L, Zhang G H, Sun H S. Construction of primary core collections of grape genetic resources. Journal of Plant Genetic Resources, 2011, 12, 13(1): 72-76. (in Chinese)

[19]郭大龙, 张君玉, 李  猛, 张国海, 刘崇怀. 葡萄SRAP反应体系优化及引物筛选. 基因组学与应用生物学, 2010, 29(2): 379-384.

Guo D L, Zhang J Y, Li M, Zhang G H, Liu C H. Optimization of SRAP-PCR system in grape and primers screening. Genomics and Applied Biology, 2010, 29(2): 379-384. (in Chinese)

[20]Liu K, Muse S V. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics, 2005, 21(9): 2128-2128.

[21]Yeh F C, Yang R C, Boyle T. POPGENE Version 1.32, Microsoft Window Base Software for Population Genetic Analysis: A Quick User's Guide. Alberta, Canada: University of Alberta. Center for International Forestry Research, 1999.

[22]Hu J, Zhu J, Xu H M. Methods of constructing core collections by stepwise clustering with three sampling strategies based on the genotypic values of crops. Theoretical and Applied Genetics, 2000, 101(1): 264-268.

[23]刘遵春, 张春雨, 张艳敏, 张小燕, 吴传金, 王海波, 石  俊, 陈学森. 利用数量性状构建新疆野苹果核心种质的方法. 中国农业科学, 2010, 43(2): 358-370.

Liu Z C, Zhang C Y, Zhang Y M, Zhang X Y, Wu C J, Wang H B, Shi J, Chen X S. Study on method of constructing core collection of Malus sieversii based on quantitative traits. Scientia Agricultura Sinica, 2010, 43(2): 358-370. (in Chinese)

[24]郝晨阳, 董玉琛, 王兰芬, 游光霞, 张洪娜, 盖红梅, 贾继增, 张学勇. 我国普通小麦核心种质的构建及遗传多样性分析. 科学通报, 2008, 53(8): 908-915.

Hao C Y, Dong Y C, Wang L F, You G X, Zhang H N, Gai H M, Jia J Z, Zhang X Y. Construction of core collection and analysis of genetic diversity of Chinese wheat. Chinese Science Bulletin, 2008, 53(8): 908-915. (in Chinese)

[25]王建成, 胡  晋, 黄歆贤, 徐盛春. 植物核心种质构建数据和代表性评价参数的研究进展. 种子, 2008, 27(8): 52-55.

Wang J C, Hu J, Huang X X, Xu S C. Progress in constructing data and evaluating parameters of representativeness for plant core collection. Seed, 2008, 27(8): 52-55. (in Chinese)

[26]董玉琛, 曹永生, 张学勇, 刘三才, 王兰芬, 游光霞, 庞斌双, 李立会, 贾继增. 中国普通小麦初选核心种质的产生. 植物遗传资源学报, 2003, 4(1): 1-8.

Dong Y C, Cao Y S, Zhang X Y, Liu S C, Wang L F, You G X, Pang B S, Li L H, Jia J Z. Establishment of candidate core collections in Chinese common wheat germplasm. Journal of Plant Genetic Resources, 2003, 4(1): 1-8.(in Chinese)

[27]王丽侠, 李英慧, 李  伟, 朱  莉, 关  媛, 宁学成, 关荣霞, 刘章雄, 常汝镇, 邱丽娟. 长江春大豆核心种质构建及分析. 生物多样性, 2004, 12(6): 578-585.

Wang L X, Li Y H, Li W, Zhu L, Guan Y, Ning X C, Guan R X, Liu Z X, Chang R Z, Qiu L J. Establishment of a core collection of Changjiang spring sowing soybean. Chinese Biodiversity, 2004, 12(6): 578-585. (in Chinese)

[28]Quero-Garcia J, Noyer J L, Perrier X, Marchand J L, Lebot V. A germplasm stratification of taro (Colocasia esculenta) based on agro-morphological descriptors, validation by AFLP markers. Euphytica, 2004, 137(3): 387-395.

[29]Zhang Y F, Zhang Q L, Yang Y, Luo Z R. Development of Japanese persimmon core collection by genetic distance sampling based on SSR Markers. Biotechnology & Biotechnological Equipment, 2009, 23(4): 1474-1478.

[30]Gouesnard B, Bataillon T M, Decoux G, Rozale C, Schoen D J, David J L. MSTRAT: An algorithm for building germplasm core collections by maximizing allelic or phenotypic richness. Journal of Heredity, 2001, 92(1): 93.

[31]Franco J C, Warburton J, Taba M L. Sampling strategies for conserving maize diversity when forming core subsets using genetic markers. Crop Science, 2006, 46(2): 854-864.
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