甘薯核心种质构建方法研究
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摘要
国家种质广州甘薯圃是国内唯一室外营养体保存的国家种质资源圃。本研究以其中的1200份甘薯资源为材料,22个农艺性状为基础,采用因子分析和变量聚类2种方式对农艺性状进行降维处理,两步聚类、快速聚类和分层聚类3种聚类方法结合5个地理来源对资源分组,组内随机取样与必选资源相结合的方式构建核心种质,依照上述方案共构建出含15个甘薯核心种质的样本库。通过变异系数、标准差符合率和极差符合率评价15个构建方案的数量性状的代表性,多样性指数和表形频率方差评价质量性状的代表性。结果表明,以变量聚类进行降维、两步聚类结合地理来源分组、组内随机取样为甘薯构建核心种质的最佳方案,采用该方法构建的核心种质样本很好地保留了总资源的遗传多样性。
The National Germplasm Guangzhou Sweet Potato Nursery Genebank is the only national germplasm nursery with outdoor vegetative conservation in China. Based on 1200 sweetpotato germplasms, we did dimensionality reduction on 22 phenotypic traits by factor analysis and R-cluster. Three kinds of Q-cluster methods including Two Step Cluster, K-Means Cluster and Hierarchieal Cluster were combined with five geographical resources to group germplasms. The core collections were constructed by combing randomly sampled and required germplasms. According to the above scheme, sample database with 15 sweetpotato core collections were constructed. The representativeness of quantitative traits in the 15 construction schemes was evaluated by the coefficient of variation, standard deviation conformity and extreme difference conformity. The representativeness of quality traits was evaluated with Shannon-Weaver index and variance of phenotypic frequency(χ2) test. The results indicated that using R-clustering for dimensionality reduction, Two Step Cluster combined with geographical resources for grouping, and random sampling within the group was the best approach to construct the sweetpotato core collection. By using this strategy, the genetic diversity and variation in the constructed core collection are well presented in the total resources.
The National Germplasm Guangzhou Sweet Potato Nursery Genebank is the only national germplasm nursery with outdoor vegetative conservation in China. Based on 1200 sweetpotato germplasms, we did dimensionality reduction on 22 phenotypic traits by factor analysis and R-cluster. Three kinds of Q-cluster methods including Two Step Cluster, K-Means Cluster and Hierarchieal Cluster were combined with five geographical resources to group germplasms. The core collections were constructed by combing randomly sampled and required germplasms. According to the above scheme, sample database with 15 sweetpotato core collections were constructed. The representativeness of quantitative traits in the 15 construction schemes was evaluated by the coefficient of variation, standard deviation conformity and extreme difference conformity. The representativeness of quality traits was evaluated with Shannon-Weaver index and variance of phenotypic frequency(χ2) test. The results indicated that using R-clustering for dimensionality reduction, Two Step Cluster combined with geographical resources for grouping, and random sampling within the group was the best approach to construct the sweetpotato core collection. By using this strategy, the genetic diversity and variation in the constructed core collection are well presented in the total resources.
引文
[1]蒋玉峰,马代夫.国家甘薯产业技术体系建设推动甘薯产业和学科发展[J].江苏师范大学学报:自然科学版,2016,34(3):23-27.
[2]王洪云,孙健,钮福祥,等.甘薯的功能成分及其药用价值[J].中国食物与营养,2013,19(12):59-62.
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[8]张洪亮,李自超,曹永生,等.表型水平上检验水稻核心种质的参数比较[J].作物学报,2003,29(2):252-257.
[9] Hao C Y, Zhang X Y, Wang L F, et al. Genetic diversity and corecollection evaluations in common wheat germplasm from thenorthwestern spring wheat region in china[J]. Mol Breed,2006,17:69-77.
[10]姚启伦,方平,杨克诚,等.基于SSR标记构建西南玉米地方品种核心种质的方法[J].湖南农业大学学报:自然科学版,2009,35(3):225-228.
[11] Van Hintum, Th J L. Comparison of market systems andconstruction of a core collection in a pedigree of European springbarley[J]. Theoretical&Applied Genetics,1994,89:991-997.
[12]邱丽娟,曹永生,常汝镇,等.中国大豆(Glycine max)核心种质构建Ⅰ.取样方法研究[J].中国农业科学,2003,36(12):1442-1449.
[13] Wang L X, Guan Y, Guan R X, et al. Establishment of Chinesesoybean(Glycine max)core collections with agronomic traits andSSR markers[J]. Euphytica,2006,151:215-223.
[14]刘艳阳,梅鸿献,杜振伟,等.基于表型和SSR分子标记构建芝麻核心种质[J].中国农业科学,2017,13(50),2433-2441.
[15]刘新龙,蔡青,马丽,等.甘蔗杂交品种初级核心种质取样策略[J].作物学报,2009,35(7):1209-1216.
[16]栾明宝,陈建华,许英,等.苎麻核心种质构建方法[J].作物学报,2010,36(12):2099-2106.
[17]郭亚宁,兴旺,周建朝,等.甜菜核心种质构建研究[J].中国农学通报,2017,33(24):41-46.
[18]李慧峰,陈天渊,黄咏梅,等.基于形态性状的甘薯核心种质取样策略研究[J].植物遗传资源学报,2013,14(1):91-96.
[19]张允刚,房伯平.甘薯种质资源描述规范和数据标准[M].北京:中国农业出版社,2006:10-36.
[20]徐宁,程须珍,王素华,等.以地理来源分组和利用表型数据构建中国小豆核心种质[J].作物学报,2008,34(8):1366-1373.
[21]陆漱韵,刘庆昌,李惟基.甘薯育种学[M].北京:中国农业出版社,1984:335-352.
[22]张洪亮,李自超,曹永生,等.表型水平上检验水稻核心种质的参数比较[J].作物学报,2003,29(2):252-257.
[23]董玉琛,曹永生,张学勇,等.中国普通小麦初选核心种质的产生[J].植物遗传资源学报,2003,4(1):1-8.
[2]王洪云,孙健,钮福祥,等.甘薯的功能成分及其药用价值[J].中国食物与营养,2013,19(12):59-62.
[3] FAO(2014)FAOSTAT[DB]. http://faostat3.fao.org.
[4]邓少春,田易萍,李友勇,等.茶树资源核心种质研究进展[J].中国农学通报,2015,31(16):121-126.
[5] Frankle O H. Genetic perspectives of germplasm conservation[A].//In:Arber W, Illmensee K, Peacock W J, et al. GeneticManipulation:Impact on Man and Society[M]. Cambridge:Cambridge University Press,1984:161-170.
[6] Frankel O H, Brown A H D. Plant Genetic Resources today:ACritical Appraisal[A].//In:Holden J H W, Williams J T. CropGenetics Resources:Conservation and Evaluation[M]. London:George Allen and Unwin,1984:249-257.
[7] Brown A H D, Frankel O H, Marshall R D. The Use of PlantGenetic Risources[M]. Cambridge, England:Cambridge UniversityPress,1989:136-156.
[8]张洪亮,李自超,曹永生,等.表型水平上检验水稻核心种质的参数比较[J].作物学报,2003,29(2):252-257.
[9] Hao C Y, Zhang X Y, Wang L F, et al. Genetic diversity and corecollection evaluations in common wheat germplasm from thenorthwestern spring wheat region in china[J]. Mol Breed,2006,17:69-77.
[10]姚启伦,方平,杨克诚,等.基于SSR标记构建西南玉米地方品种核心种质的方法[J].湖南农业大学学报:自然科学版,2009,35(3):225-228.
[11] Van Hintum, Th J L. Comparison of market systems andconstruction of a core collection in a pedigree of European springbarley[J]. Theoretical&Applied Genetics,1994,89:991-997.
[12]邱丽娟,曹永生,常汝镇,等.中国大豆(Glycine max)核心种质构建Ⅰ.取样方法研究[J].中国农业科学,2003,36(12):1442-1449.
[13] Wang L X, Guan Y, Guan R X, et al. Establishment of Chinesesoybean(Glycine max)core collections with agronomic traits andSSR markers[J]. Euphytica,2006,151:215-223.
[14]刘艳阳,梅鸿献,杜振伟,等.基于表型和SSR分子标记构建芝麻核心种质[J].中国农业科学,2017,13(50),2433-2441.
[15]刘新龙,蔡青,马丽,等.甘蔗杂交品种初级核心种质取样策略[J].作物学报,2009,35(7):1209-1216.
[16]栾明宝,陈建华,许英,等.苎麻核心种质构建方法[J].作物学报,2010,36(12):2099-2106.
[17]郭亚宁,兴旺,周建朝,等.甜菜核心种质构建研究[J].中国农学通报,2017,33(24):41-46.
[18]李慧峰,陈天渊,黄咏梅,等.基于形态性状的甘薯核心种质取样策略研究[J].植物遗传资源学报,2013,14(1):91-96.
[19]张允刚,房伯平.甘薯种质资源描述规范和数据标准[M].北京:中国农业出版社,2006:10-36.
[20]徐宁,程须珍,王素华,等.以地理来源分组和利用表型数据构建中国小豆核心种质[J].作物学报,2008,34(8):1366-1373.
[21]陆漱韵,刘庆昌,李惟基.甘薯育种学[M].北京:中国农业出版社,1984:335-352.
[22]张洪亮,李自超,曹永生,等.表型水平上检验水稻核心种质的参数比较[J].作物学报,2003,29(2):252-257.
[23]董玉琛,曹永生,张学勇,等.中国普通小麦初选核心种质的产生[J].植物遗传资源学报,2003,4(1):1-8.