基于表型和SSR分子标记构建芝麻核心种质

doi:10.3864/j.issn.0578-1752.2017.13.003

摘要/Abstract

摘要： 【目的】便于管理、研究和利用芝麻种质资源，为芝麻育种提供优异基因资源。【方法】利用新收集和种质库保存的5 020份芝麻种质资源为基础，首先基于标准化的表型数据按地理来源分组后采用组内比例法聚类抽样构建初级核心种质，然后基于SSR分子标记应用位点优先取样策略逐步聚类，使用t检验检测每次聚类形成的核心种质与初级核心种质的Nei’s基因多样度（He）和Shannon-Wiener指数（I），直到核心种质的遗传多样性与初级核心种质开始有显著差异时，终止多次聚类取样，选择上一个与初级核心资源没有显著差异的核心种质作为最佳核心种质。利用Nei’s 多样性指数、Shannon-Wiener多样性指数、多态条带百分率（PB，%）、多态条带保留率（PBR，%）、变异系数符合率（VR）、极差符合率（CR）、方差差异百分率（VD，%）、均值差异百分率（MD，%）等参数进行核心种质代表性检验和评价。【结果】构建了含有816份资源的初级核心种质和含有501份资源的核心种质，分别占全部种质资源的16.25%和9.98%；核心种质包括国内资源442份，国外资源59份；Nei's基因多样度（0.2789）和Shannon-Wiener指数（0.4243）在P＜0.05概率条件下与初级核心资源（He=0.2791，I=0.4302）无显著性差异，多态条带百分率（PB，%）、多态条带保留率（PBR，%）、变异系数符合率（VR）、极差符合率（CR）分别为91.25%、95.23%、99.14%、86.85%。方差差异百分率（VD，%）和均值差异百分率（MD，%）均为0。t测验结果表明，核心种质的遗传多样性指数与原始种质差异不显著。位点优先取样策略构建的核心种质比对照随机取样策略丢失的多态性位点数少，且同一遗传距离下位点优先取样策略构建的核心种质具有更高的遗传多样性，更能构建一个具有代表性的核心种质，Shannon-Wiener多样性指数比Nei’s多样性指数检测效率高。【结论】基于地理来源分组，组内按表型数据聚类按比例法抽样构建芝麻初级核心种质，再结合SSR分子标记数据，采用SM相似系数进行UPGMA逐步聚类是构建芝麻核心种质较适宜的方法，所构建的核心种质较好地代表了基础种质的遗传多样性。

关键词: 芝麻, 种质资源, 核心种质, 代表性检验

Abstract: 【Objective】The objective of this study was to manage, research and utilization of sesame (Sesamum indicum L.) germplasm resources more effectively, and to provide excellent genetic resources for sesame breeding.【Method】In this study, 5 020 accessions of sesame germplasm resources were systematically identified. Firstly, the primary core collections were constructed by using proportion strategy and UPGMA clustering sampling method within subgroups according to geographical origins. Then using an allele preferred sampling strategy and stepwise UPGMA clustering sampling approach according to SSR molecular data, these accessions were further screened to form core collections. The Nei’s gene diversity (He) and the Shannon-Wiener index (I) of the core collection and the primary one were measured by t-test. The cluster sampling was terminated until the genetic diversity of the core collection begun to have a significant difference with the primary one. Then the core collections without a significant difference with the primary core collection were chosen as the best core collections. The representativeness of the core collections was assessed by the Nei’s diversity index, Shannon-Wiener diversity index, percentage of polymorphic bands, polymorphic band retention, variable rate of coefficient of variation, coincidence rate of range, variance difference percentage and mean difference percentage.【Result】The primary core collections containing 816 accessions and core collections with 501 accessions were constructed, accounting for 16.25% and 9.98% of the total germplasm resources, respectively. The core collections consist of 442 Chinese landraces and 59 foreign germplasm resources. The core collection with 0.2989 in Nei’s diversity index and 0.4243 in Shannon-Wiener diversity index, and did not have a significant difference in molecular diversity with primary core collections (He=0.2791, I=0.4302) at P＜0.05. The percentage of polymorphic loci and reserved rate of number of polymorphic loci, variable rate of coefficient of variation and coincidence rate of range were 91.25%, 95.23%, 99.14%, 86.85%, respectively. Variance difference percentage and phenotypic indexes of mean difference percentage was 0. Results of t-test showed that no significant difference was found in genetic diversity indexes between the core collections and original collections. Compared with the random sampling strategy, allele preferred sampling strategy could construct more representative core collections with higher values of genetic diversity indexes and fewer loss of allele. The Shannon-Wiener index performed higher identifying efficiency than Nei’s diversity index. 【Conclusion】The primary core collections were constructed by using proportion strategy and clustering sampling method within subgroups according to geographical origin, and then using an allele preferred sampling strategy and stepwise UPGMA clustering sampling approach according to SSR molecular data to form core collections, which is a suitable method for constructing sesame core collections. The core collections of sesame are well representative of the original collections in the phenotypic and molecular genetic diversity.

Key words: sesame, germplasm resources, core collection, representative test

刘艳阳，梅鸿献，杜振伟，武轲，郑永战，崔向华，郑磊. 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, 50(13): 2433-2441.

LIU YanYang, MEI HongXian, DU ZhenWei, WU Ke, ZHENG YongZhan, CUI XiangHua, ZHENG Lei. Construction of Core Collection of Sesame Based on Phenotype and Molecular Markers[J]. Scientia Agricultura Sinica, 2017, 50(13): 2433-2441.

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参考文献

[1] 郭大龙, 刘崇怀, 张君玉, 张国海. 葡萄核心种质的构建. 中国农业科学, 2012, 45(6): 1135-1143.

Guo D L, Liu C H, Zhang J Y, Zhang G H. Construction of grape core collections. Scientia Agricultura Sinica, 2012, 45(6): 1135-1143. (in Chinese)

[2] Frankel O H. Genetic perspectives of germplasm conservation. Cambridge: Cambridge University Press, 1984: 161-170.

[3] 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.

[4] 邱丽娟, 曹永生, 常汝镇, 周新安, 王国勋, 孙建英, 谢华, 张博, 李向华, 许占有, 刘立宏. 中国大豆核心种质构建及其取样方法研究. 中国农业科学, 2003, 36(12): 1442-1449.
Qiu L J, Cao Y S, Chang R Z, Zhou X A, Wang G X, Sun J Y, Xie H, Zhang B, Li X H, Xu Z Y, Liu L H. Establishment of Chinese soybean (G. max L.) core collection and sampling strategy. Scientia Agricultura Sinica, 2003, 36(12): 1442-1449. (in Chinese)

[5] 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.

[6] Bisht I S, Mahajan R K, Loknathan T R, Agrawal R C. Diversity in Indian sesame collection and stratification of germplasm accessions in different diversity groups. Genetic Resourcesand Crop Evolution, 1998, 45: 325-335.

[7] Zhang X R, Zhao Y Z, Cheng Y, Feng X Y, Guo Q Y, Zhou M D, Hodgkin T. Establishment of sesame germplasm core collection in China. Genetic Resourcesand Crop Evolution, 2000(47): 273-279.

[8] Wang L H, Zhang Y X, Li P W, Wang X F, Zhang W, Wei W L, Zhang X R. HPLC analysis of seed sesamin and sesamolin variation in a sesame germplasm collection in China. Journal of the American Oil Chemists' Society, 2012, 89(6): 1011-1020.

[9] 车卓, 张艳欣, 孙建, 张秀荣, 尚勋武, 王化俊. 应用SRAP标记分析黑芝麻核心种质遗传多样性. 作物学报, 2009, 35(10): 1936-1941.

Che Z, Zhang Y X, Sun J, Zhang X R, Shang X W, Wang H J. Genetic diversity analysis of black sesame (Sesamum indicum DC) core collection of china using SRAP markers. Acta Agronomica Sinica, 2009, 35(10): 1936-1941. (in Chinese)

[10] 车卓, 张艳欣, 孙建, 张秀荣, 尚勋武, 王化俊. 芝麻核心收集品中育成品种(系)的遗传多样性分析. 植物遗传资源学报, 2009, 10(3): 373-377.

Che Z, Zhang Y X, Sun J, Zhang X R, Shang X W, Wang H J. Analysis of genetic diversity for cultivars released of sesame core collection. Journal of Plant Genetic Resources, 2009, 10(3): 373-377. (in Chinese)

[11] 危文亮, 张艳欣, 吕海霞, 王林海, 黎冬华, 张秀荣. 芝麻资源群体结构及含油量关联分析. 中国农业科学, 2012, 45(10): 1895-1903.

Wei W L, Zhang Y X, Lü H X, Wang L H, Li D H, Zhang X R. Population structure and association analysis of oil content in a diverse set of Chinese sesame (Sesamum indicum L.) germplasm. Scientia Agricultura Sinica, 2012, 45(10): 1895-1903. (in Chinese)

[12] 丁霞, 王林海, 张艳欣, 黎冬华, 高媛, 危文亮, 王蕾, 张秀荣. 芝麻核心种质株高构成相关性状的遗传变异及关联定位. 中国油料作物学报, 2013, 35(3): 262-270.

Ding X, Wang L H, Zhang Y X, Li D H, Gao Y, Wei W L, Wang Lei, Zhang X R. Genetic variation and associated mapping for traits related to plant height constitutions in core collections of sesame (Sesamum indicum L.). Chinese Journal of Oil Crop Sciences, 2013, 35(3): 262-270. (in Chinese)

[13] 王蕾, 黎冬华, 齐小琼, 张艳欣, 丁霞, 王林海, 危文亮, 高媛, 张秀荣. 芝麻核心种质芝麻素和芝麻酚林的关联分析. 中国油料作物学报, 2014, 36(1): 32-37.

Wang L, Li D H, Qi X Q, Zhang Y X, Ding X, Wang L H, Wei W L, Gao Y, Zhang X R. Association analysis of sesamin and sesamolin in the core sesame (Sesamum indicum L.) germplasm. Chinese Journal of Oil Crop Sciences, 2014, 36(1): 32-37. (in Chinese)

[14] 张艳欣, 王林海, 黎冬华, 危文亮, 高媛, 张秀荣. 芝麻茎点枯病抗性关联分析及抗病载体材料挖掘. 中国农业科学, 2012, 45(13): 2580-2591.

Zhang Y X, Wang L H, Li D H, Wei W L, Gao Y, Zhang X R. Association mapping of sesame (Sesamum indicum L.) resistance to macrophomina phaseolina and identification of resistant accessions. Scientia Agricultura Sinica, 2012, 45(13): 2580-2591. (in Chinese)

[15] Zhang Y X, Zhang X R, Che Z, Wang L H, Wei W L, Li D H. Genetic diversity assessment of sesame core collection in China by phenotype and molecular markers and extraction of a mini-core collection. BMC Genetics,2012, 13: 102.

[16] Kang C W, Kim S Y, Lee S W, Mathur P N, Hodgkin T, Zhou M D, Lee J R. Selection of a core collection of Korean sesame germplasm by a stepwise clustering method. Breeding Science, 2006, 56: 85-91.

[17] Mahajan R K, Bisht I S, Dhillon B S. Establishment of a core collection of world sesame (Sesamum indicum L.) germplasm accessions. Journal of Breeding and Genetics, 2007, 39(1): 53-64.

[18] Park J H, Suresh S, Cho G T, Choi N G, Baek H J, Lee C W, Chung J W. Assessment of molecular genetic diversity and population structure of sesame (Sesamum indicum L.) core collection accessions using simple sequence repeat markers. Plant Genetic Resources, 2013, 12(1): 112-119.

[19] Park J H, Suresh S, Raveendar S, Baek H J, Kim C K, Lee S, Cho G T, Ma K H, Lee C W, Chung J W. Development and evaluation of core collection using qualitative and quantitative trait descriptor in sesame (Sesamum indicum L.) germplasm. Korean Journal of Crop Science, 2015, 60(1): 75-84.

[20] 张秀荣, 冯祥运. 芝麻种质资源描述规范和数据标准. 北京: 中国农业出版社, 2006: 22-37.

Zhang X R, Feng X Y. Descriptor and data standard for sesame (Sesamum indicum L.). Beijing: China Agriculture Press, 2006: 22-37. (in Chinese)

[21] Zhang H Y, Miao H M, Wei L B, Li C, Zhao R H, Wang C Y. Genetic analysis and QTL mapping of seed coat color in sesame (Sesamum indicum L.). Plos One, 2013, 8(5): e63898.

[22] Dixit A, Jin M H, Chung J W, Yu J W, Chung H K, Ma K H, Park Y J, Cho E G. Development of polymorphic microsatellite markers in sesame (Sesamum indicum L.). Molecular Ecology Notes, 2005, 5: 736-738.

[23] Wang L H, Zhang Y X, Qi X Q, Gao Y, Zhang X R. Development and characterization of 59 polymorphic cDNA-SSR markers for the edible oil crop Sesamum indicum (Pedaliaceae). American Journal of Botany, 2012, 99(10): e394-8.

[24] Pham T D. Analyses of genetic diversity and desirable traits in sesame (Sesamum indicum L., Pedaliaceae): Implication for breeding and conservation[D]. Swedish University of Agricultural Sciences, 2011.

[25] 李自超, 张洪亮, 曹永生, 裘宗恩, 魏兴华, 汤圣祥, 余萍, 王象坤. 中国地方稻种资源初级核心种质取样策略研究. 作物学报, 2003, 29(1): 20-24.

Li Z C, Zhang H L, Cao Y S, Qiu Z E, Wei X H, Tang S X, Yu P, Wang X K. Studies on the sampling strategy for primary core collection of Chinese ingenious rice. Acta Agronomica Sinica, 2003, 29(1): 20-24. (in Chinese)

[26] 刘新龙, 刘洪博, 马丽, 李旭娟, 徐超华, 苏火生, 应雄美, 蔡青, 范源洪. 利用分子标记数据逐步聚类取样构建甘蔗杂交品种核心种质库. 作物学报, 2014, 40(11): 1885-1894.

Liu X L, Liu H B, Ma L, Li X J, Xu C H, Su H S, Ying X M, Cai Q, Fan Y H. Construction of sugarcane hybrids core collection by using stepwise clustering sampling approach with molecular marker data. Acta Agronomica Sinica, 2014, 40(11): 1885-1894. (in Chinese)

[27] 李自超, 张洪亮, 曾亚文, 杨忠义, 申时全, 孙传清, 王象坤. 云南地方稻种资源核心种质取样方案研究. 中国农业科学, 2000, 33(5): 1-7.

Li Z C, Zhang H L, Zeng Y W, Yang Z Y, Shen S Q, Sun C Q, Wang X K. Study on sampling schemes of core collection of local varieties of rice in Yunnan, China. Scientia Agricultura Sinica, 2000, 33(5): 1-7. (in Chinese)

[28] Brown A H D. Core collection: a practical approach to genetic resources management. Genome, 1989, 31: 818-824.

[29] Ersking W, Muehlbauer F J. Allozyme and morphological variability, out crossing rate and core collection formation in lentil germplasm. Theoretical and Applied Genetics, 1991, 83: 119-125.

[30] Jansen J, 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: 421-428.

[31] 胡兴雨, 王纶, 张宗文, 陆平, 张红生. 中国黍稷核心种质的构建. 中国农业科学, 2008, 41(11): 3489-3502.

Hu X Y, Wang L, Zhang Z W, Lu P, Zhang H S. Establishment of broomcorn millet core collection in China. Scientia Agricultura Sinica, 2008, 41(11): 3489-3502. (in Chinese)

[32] 高志红, 章镇, 韩振海, 房经贵. 中国果梅核心种质的构建与检测. 中国农业科学, 2005, 38(2): 363 -368.

Gao Z H, Zhang Z, Han Z H, Fang J G. Development and evaluation of core collection of Japanese apricot germplasms in China. Scientia Agricultura Sinica, 2005, 38(2): 363-368. (in Chinese)

[33] 齐永文, 樊丽娜, 罗青文, 王勤南, 陈勇生, 黄忠兴, 刘睿, 刘少谋, 邓海华, 李奇伟. 甘蔗细茎野生种核心种质构建. 作物学报, 2013, 39(4): 649-656.

Qi Y W, Fan L N, Luo Q W, Wang Q N, Chen Y S, Huang Z X, Liu R, Liu S M, Deng H H, Li Q W. Establishment of Saccharum spontaneum L. core collections. Acta Agronomica Sinica, 2013, 39(4): 649-656. (in Chinese)

[34] Li Z C, Zhang H L, Zeng Y W, Yang Z Y, Shen S Q, Sun C Q, Wang X K. Studies on sampling schemes for the establishment of core collection of rice landraces in Yunnan, China. Genetic Resources and Crop Evolution, 2002, 49: 67-74.

[35] 毛钧, 刘新龙, 苏火生, 陆鑫, 林秀琴, 蔡青, 范源洪. 基于表型与分子数据的斑茅核心种质构建. 植物遗传资源学报, 2016, 17(4): 607-615.

Mao J, Liu X L, Su H S, Lu X, Lin X Q, Cai Q, Fan Y H. Constructing core collection of Eriaanthus arundianceus based on phenotype and molecular markers. Journal of plant genetic resources, 2016, 17(4): 607-615. (in Chinese)

[36] 徐海明, 邱英雄, 胡晋, 王建成. 不同遗传距离聚类和抽样方法构建作物核心种质的比较. 作物学报, 2004, 30(9): 932-936.

Xu H M, Qiu Y X, Hu J, Wang J C. Methods of constructing core collection of crop germplasm by comparing different genetic distances, cluster methods and sampling strategies. Acta Agronomica Sinica, 2004, 30(9): 932-936. (in Chinese)

[37] 赵丽梅, 董英山, 刘宝, 郝水, 王克晶, 李向华. 中国一年生野生大豆核心资源的构建. 科学通报, 2005, 50(10): 989-996.

Zhao L M, Dong Y S, Liu B, Hao S, Wang K J, Li X H. Construction of core resources of annual wild soybean (Glycine soja) in China. Chinese Science Bulletin, 2005, 50(10): 989-996. (in Chinese)

[38] 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 S, 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)

[39] Ortiz R, Ruiz-Tapia E N, Mujica-Sanchez A. Sampling strategy for a core collection of Peruvian quinoa germplasm. Theoretical and Applied Genetics, 1998, 96: 475-483.

[40] Yonezawa K, Nomura T, Morishima H. Sampling strategies for use in stratified germplasm collections//Hodgkin T, Brown A H D, van Hintum T J L, Morales E A V. Core Collections of Plant Genetic Resources. USA: John Wiley & Son, 1995: 35-53.