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Acta Agron Sin ›› 2014, Vol. 40 ›› Issue (11): 1885-1894.doi: 10.3724/SP.J.1006.2014.01885


Construction of Sugarcane Hybrids Core Collection by Using Stepwise Clustering Sampling Approach with Molecular Marker Data

LIU Xin-Long1,LIU Hong-Bo1,MA Li1,LI Xu-Juan1,XU Chao-Hua1,SU Huo-Sheng1,YING Xiong-Mei1,CAI Qing1,2,FAN Yuan-Hong1,*   

  1. 1 Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences / Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China; 2 Yunnan Agricultural Biotechnology Key Laboratory, Kunming 650223, China
  • Received:2014-04-13 Revised:2014-07-06 Online:2014-11-12 Published:2014-07-23
  • Contact: 范源洪, E-mail: fyhysri@vip.sohu.com


Sugarcane hybrids are important breeding parent sources of commercial varieties. To use efficiently and evaluate the sugarcane hybrids conserved in National Nursery of Sugarcane Germplasm Resources (NNSGR), we selected a total of 161 accessions of sugarcane hybrids including 136 accessions from the pre-core collection of sugarcane hybrids constructed previously and 25 accessions introduced recently for constructing a core collection. Using stepwise UPGMA clustering sampling approach with three kinds of genetic similarity coefficient calculated according to SSR molecular data, these accessions were further screened to form a core collection with random sampling strategy as control. We tested the quality of core collections using nine indices, including Nei’s diversity index, Shannon-Wiener diversity index, total band number, polymorphic band number, percentage of polymorphic bands (PPB), variable rate of coefficient of variation (VR), coincidence rate of range (CR), variance difference percentage (VD) and mean difference percentage (MD). The results showed that 161 sugarcane hybrids possessed abundant genetic diversity at 20 SSR loci, which amplified 294 bands with 290 polymorphic bands taking up a mean of 98.64% of total bands. According to three kinds of genetic similarity coefficient (Jaccard, SM, and Dice) and two sampling strategies, ultimately eight core collections were gained. In the quality evaluating of core collections, three indices including Shannon-Wiener diversity index, total band number and polymorphic band number, performed high identifying efficiency, but the rest presented low efficiency. The core collection constructed on the basis of Jaccard or Dice genetic similarity coefficient was higher in quality than others, which consisted of 107 sugarcane hybrids with 0.9785 in Nei’s diversity index and 4.1854 in Shannon-Wiener diversity index, and did not have significant difference in molecular diversity with total resource at P < 0.05, moreover, MD = 0.00% (< 20.00%) and CR = 94.32% ( > 80.00%). All the mentioned above indicated the core collection can represent completely the diversity level of total resource in agronomic traits and molecular markers, and will can provide crucial basis for evaluating and utilizing sugarcane hybrids, and mining elite genes.

Key words: Sugarcane hybrids, Molecular marker, Core collection, Clustering, Diversity index

[1]Henry R J, Kole C. Genetics, Genomics and Breeding of Sugarcane. New Hampshire, USA: Science Publishers, En?eld, 2010. pp 1−9

[2]陈如凯. 现代甘蔗遗传育种理论. 北京: 中国农业出版社, 2011. pp 1−19

Chen R K. Theory and Practice in Modern Sugarcane Breeding. Beijing: China Agriculture Press, 2011. pp 1−19 (in Chinese)

[3]刘新龙, 蔡青, 马丽, 吴才文, 陆鑫, 应雄美, 范源洪. 甘蔗杂交品种初级核心种质取样策略. 作物学报, 2009, 35: 1209−1216

Liu X L, Cai Q, Ma L, Wu C W, Lu X, Ying X M, Fan Y H. Strategy of sampling for pre-core collection of sugarcane hybrid. Acta Agron Sin, 2009, 35: 1209−1216 (in Chinese with English abstract)

[4]Diederichsen A, Kusters P M, Kessler D, Bainas Z, Gugel R K. Assembling a core collection from the flax world collection maintained by plant gene resources of Canada. Genet Resour Crop Evol, 2013, 60: 1479−1485

[5]魏兴华, 汤圣祥, 余汉勇, 江云珠, 裘宗恩. 中国粳稻地方种资源核心样品的构建方法研究. 中国水稻科学, 2000, 14: 237−240

Wei X H, Tang S X, Yu H Y, Jiang Y Z, Qiu Z E. Studies on methods of developing a core collection for China traditional       japonica rice germplasm. Chin J Rice Sci, 2000, 14: 237−240 (in Chinese with English abstract)

[6]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: 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 Agron Sin, 2003, 29: 20−24 (in Chinese with English abstract)

[7]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: 1−8

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 collection in Chinese common wheat germplasm. J Plant Genet Resour, 2003, 4: 1−8 (in Chinese with English abstract)

[8]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: 908−915

Hao C Y, Dong Y C, Wang L F, You G X, Zhang H N, Ge H M, Jia J Z, Zhang X Y. Genetic diversity and construction of core collection in Chinese wheat genetic resources. Chin Sci Bull, 2008, 53: 908−915 (in Chinese)

[9]Li Y, Shi Y S, Cao Y S, Wang T Y. Establishment of a core collection for maize germplasm preserved in Chinese national gene bank using geographic distribution and characterization data. Genet Resour Crop Evol, 2004, 51: 845−852

[10]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(Glycine max)核心种质构建: I. 取样方法研究. 中国农业科学, 2003, 36: 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 (Glycine max) core collection: I. Sampling strategy. Sci Agric Sin, 2003, 36: 1442−1449 (in Chinese with English abstract)

[11]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(Glycine soja)核心资源构建. 科学通报, 2005, 50: 989−996

Zhao L M, Dong Y S, Liu B, Hao S, Wang K J, Li X H. Establishment of a core collection for the Chinese annual wild soybean (Glycine soja). Chin Sci Bull, 2005, 50: 989−996 (in Chinese)

[12]Wang L X, Guan Y, Guan R X, Li Y H, Ma Y S, Dong Z M, Liu X, Zhang H Y, Zhang Y Q, Liu Z X, Chang R Z, Xu H M, Li L H, Lin F Y, Luan W J, Yan Z, Ning X C, Zhu L, Cui Y H, Piao R H, Liu Y, Chen P Y, Qiu L J. Establishment of Chinese soybean (Glycine max) core collections with agronomic traits and SSR markers. Euphytica, 2006, 151: 215−223

[13]张秀荣, 郭庆元, 赵应忠, 冯祥运, 周明德. 中国芝麻资源核心收集品研究. 中国农业科学, 1998, 31: 1−4

Zhang X R, Guo Q Y, Zhao Y Z, Feng X Y, Zhou M D. Establishment of sesame germplasm core collection in China. Sci Agric Sin, 1998, 31: 1−4 (in Chinese with English abstract)

[14]Upadhyaya H D, Ortiz R. A mini core subset for capturing and promoting utilization of chickpea genetic resource in crop improvement. Theor Appl Genet, 2001, 102: 1292−1298

[15]Reddy L J, Upadhyaya H D, Gowda C L L, Singh S. Development of core collection in pigeonpea [Cajanus cajan (L.) Millspaugh] using geographic and qualitative morphological descriptors. Genet Resour Crop Evol, 2005, 52: 1049−1056

[16]Zewdie Y, Tong N K, Bosl P. Establishing a core collection of capsicum using a cluster analysis with enlightened selection of accessions. Genet Resour Crop Evol, 2004, 51: 147−151

[17]Xu H M, Mei Y J, Hu J, Zhu J, Gong P. Sampling a core collection of island cotton (Gossypium barbadense L.) based on the genotypic values of fiber traits. Genet Resour Crop Evol, 2006, 53: 515−521

[18]刘长友, 王素华, 王丽侠, 孙蕾, 梅丽, 徐宁, 程须珍. 中国绿豆种质资源初选核心种质构建. 作物学报, 2008, 34: 700−705

Liu C Y, Wang S H, Wang L X, Sun L, Mei L, Xu N, Cheng X Z. Establishment of candidate core collection in Chinese mungbean germplasm. Acta Agron Sin, 2008, 34: 700−705 (in Chinese with English abstract)

[19]栾明宝, 陈建华, 许英, 王晓飞, 孙志民. 苎麻核心种质构建方法. 作物学报, 2010, 36: 2099−2106

Luan M B, Chen J H, Xu Y, Wang X F, Sun Z M. Method of establishing ramie core collection. Acta Agron Sin, 2010, 36: 2099−2106 (in Chinese with English abstract)

[20]Tai P Y P, Miller J D. A core collection for Saccharum spontaneum L. from the world collection of sugarcane. Crop Sci, 2001, 41: 879−885

[21]苏火生, 刘新龙, 毛钧, 应雄美, 陆鑫, 马丽, 蔡青. 割手密初级核心种质取样策略研究. 湖南农业大学学报(自然科学版), 2011, 37: 253−259

Su H S, Liu X L, Mao J, Ying X M, Lu X, Ma L, Cai Q. Sampling strategy of pre-core collection for Saccharum spontaneum. J Hunan Agric Univ (Nat Sci), 2011, 37: 253−259 (in Chinese with English abstract)

[22]齐永文, 樊丽娜, 罗青文, 王勤南, 陈勇生, 黄忠兴, 李奇伟. 甘蔗细茎野生种核心种质构建. 作物学报, 2013, 39: 649−656

Qi Y W, Fan L N, Luo Q W, Wang Q N, Chen Y S, Huang Z X, Li Q W. Establishment of Saccharum spontaneum L. core collections. Acta Agron Sin, 2013, 39: 649−656 (in Chinese with English abstract)

[23]Balakrishnan R, Nair N V, Sreenivasan T V. A method for establishing a core collection of Saccharum officinarum germplasm based on quantitative morphological data. Genet Resour Crop Evol, 2000, 47: 1–9

[24]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. Theor Appl Genet, 2000, 101: 264−268

[25]Wang J C, Hu J. Xu H M, Zhang S. A strategy on constructing core collections by least distance stepwise sampling. Theor Appl Genet, 2007, 115: 1–8

[26]蔡青, 范源洪, Aitken K, Piperidis G, McIntyre C L, Jackson P. 利用AFLP进行“甘蔗属复合体”系统演化和亲缘关系研究. 作物学报, 2005, 31: 551–559

Cai Q, Fan Y H, Aitken K, Piperidis G, McIntyre C L, Jackson P. Assessment of the phylogenetic relationships within the “Saccharum Complex” using AFLP markers. Acta Agron Sin, 2005, 31: 551–559 (in Chinese with English abstract)

[27]Aitken K S, Jackon P A, McIntyre C L. A combination of AFLP and SSR markers provides extensive map coverage and identification of homo(eo)logous linkage groups in a sugarcane cultivar. Theor Appl Genet, 2005, 110: 789–801

[28]刘新龙, 蔡青, 毕艳, 陆鑫, 马丽, 应雄美, 毛钧. 甘蔗AFLP标记和SSR标记的PAGE胶快速银染检测方法. 江苏农业学报, 2009, 25: 433–435

Liu X L, Cai Q, Bi Y, Lu X, Ma L, Ying X M, Mao J. A rapid        silver staining method for PAGE used in sugarcane AFLP and SSR molecular markers. Jiangsu J Agric Sci, 2009, 25: 433–435 (in Chinese with English abstract)

[29]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: 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. Sci Agric Sin, 2009, 42: 597−604 (in Chinese with English abstract)

[30]Pan Y B. Highly polymorphic microsatellite DNA markers for sugarcane germplasm evaluation and variety identity testing. Sugar Tech, 2006, 8: 246–256

[31]刘新龙, 毛钧, 陆鑫, 马丽, Karen S A, Phillip A J, 蔡青, 范源洪. 甘蔗SSR和AFLP分子遗传连锁图谱构建. 作物学报, 2010, 36: 177−183

Liu X L, Mao J, Lu X, Ma L, Karen S A, Phillip A J, Cai Q, Fan Y H. Construction of molecular genetic linkage map of sugarcane based on SSR and AFLP markers. Acta Agron Sin, 2010, 36: 177−183 (in Chinese with English abstract)

[32]Brown A H D. Core collections: a practical approach to genetic resources management. Genome, 1989, 31: 818–824

[33]Upadhyaya H D, Gowda C L L, Pundir R P S, Reddy V G, Singh S. Development of core subset of finger millet germplasm using geographical origin and data on 14 quantitative traits. Genet Resour Crop Evol, 2006, 53: 679−685

[34]Dwivedi S L, Puppala N, Upadhyaya H D, Manivannan N, Singh S. Developing a core collection of peanut specific to valencia market type. Crop Sci, 2008, 48: 624−632

[35]Tanksley S D, McCouch S R. Seed bank and molecular maps: unlocking genetic potential from the wild. Science, 1997, 277: 1063−1066

[36]Zhu J. Methods of predicting genotype value and heterosis for offspring of hybrids. J Biomath, 1993, 8: 32−44

[37]Xu H, Hu J, Qiu Y. Study on constructing core collection based on plant molecular markers and quantitative traits. J Biomath, 2004, 20: 351−355

[38]Van T R, Tchoudinova I, van Soest L J M, van Hintum T J L. Marker-assisted acquisition and core collection formation: a case study in barley using AFLPs and pedigree data. Genet Resour Crop Evol, 2006, 53: 43−52

[39]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. Biotechnol Biotechnol Equip, 2009, 23: 1474−1478

[40]李丽, 何伟明, 马连平, 刘庞源, 徐海明, 徐家柄, 郑晓鹰. 用EST-SSR分子标记技术构建大白菜核心种质及其指纹图谱库. 基因组学与应用生物学, 2009, 28: 76−88

Li L, He W M, Ma L P, Liu P Y, Xu H M, Xu J B, Zheng X Y. Construction Chinese cabbage (Brassica rapa L.) core collection and its EST-SSR fingerprint database by EST-SSR molecular markers. Genom Appl Biol, 2009, 28: 76−88 (in Chinese with English abstract)

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