Please wait a minute...
Journal of Integrative Agriculture  2016, Vol. 15 Issue (10): 2299-2308    DOI: 10.1016/S2095-3119(16)61413-2
Plant Protection Advanced Online Publication | Current Issue | Archive | Adv Search |
Genetic diversity of Ustilago hordei in Tibetan areas as revealed by RAPD and SSR
ZHOU Yu1*, CHAO Gui-mei1*, LIU Jia-jia1, ZHU Ming-qi2, WANG Yang2, FENG Bai-li1
1 State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling 712100, P.R.China
2 State Key Laboratory of Crop Stress Biology for Arid Areas/College of Plant Protection, Northwest A&F University, Yangling 712100, P.R.China
Download:  PDF in ScienceDirect  
Export:  BibTeX | EndNote (RIS)      
Abstract      Covered smut, which is caused by Ustilago hordei (Pers.) Lagerh., is one of the most damaging diseases of highland barley (Hordeum vulgare Linn. var. nudum Hook. f) in Tibetan areas of China. To understand the molecular diversity of U. hordei, a total of 27 isolates, which were collected from highland barley plants from Tibet, Sichuan, Qinghai, and Gansu provinces/autonomous region, were analyzed using random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers. Among the 100 RAPD primers used, 24 primers exhibited polymorphism. A total of 111 fragments were amplified, of which 103 were polymorphic with a polymorphic rate of 92.79%. The average observed number of alleles (Na), effective number of alleles (Ne), Nei’s genetic diversity (H), Shannon’s information index (I) and polymorphism information content (PIC) value in the RAPD markers were 1.9279, 1.5016, 0.2974, 0.4503 and 0.6428, respectively. For the SSR markers, 40 of the 111 primer pairs exhibited polymorphism and provided a total of 119 bands, of which 109 were polymorphic and accounted for 91.60% of the total bands. The Na, Ne, H, I and PIC values of the SSR markers were 1.9160, 1.4639, 0.2757, 0.4211 and 0.4340, respectively. The similarity coefficients ranged from 0.4957 to 0.9261 with an average of 0.7028 among all the 27 isolates used. The dendrogram, which was developed based on the RAPD and SSR combined marker dataset showed that the 27 U. hordei isolates were divided into 3 clusters at similarity coefficient of 0.7314. We determined that RAPD and SSR markers can be successfully used to assess the genetic variation among U. hordei isolates. The RAPD markers revealed higher levels of genetic polymorphism than did the SSR markers in this study. There existed a moderate genetic difference among isolates. The molecular variation and differentiation was somewhat associated with geographical origin but not for all of the isolates.
Keywords:  highland barley        Ustilago hordei        RAPD        SSR        genetic diversity  
Received: 18 December 2015   Accepted:

The study was sponsored by the National Millet Crops Research and Development System, China (CARS-07-12.5-A9), the National Key Technology R&D Program of China, (2014BAD07B03) and the National Natural Science Foundation of China (31371529).

Corresponding Authors:  FENG Bai-li, Tel/Fax: +86-29-87082899, E-mail:   
About author:  ZHOU Yu, E-mail:; CHAO Gui-mei, E-mail:;

Cite this article: 

ZHOU Yu, CHAO Gui-mei, LIU Jia-jia, ZHU Ming-qi, WANG Yang, FENG Bai-li. 2016. Genetic diversity of Ustilago hordei in Tibetan areas as revealed by RAPD and SSR. Journal of Integrative Agriculture, 15(10): 2299-2308.

Aamodt O S, Johnston W H. 1935. Reaction of barley varieties to infection with covered smut (Ustilgo hordei Pers. K & S). Canadian Journal of Research, 5, 590–613.

Anderson J A, Churchill G A, Autrique J E, Tanksley S D, Sorrells M E. 1993. Optimizing parental selection for genetic linkage maps. Genome, 1, 181–188.

Bouajila A, Abang M M, Haouas S, Udupa S, Rezgui S, Baum M, Yahyaoui A. 2007. Genetic diversity of Rhynchosporium secalis in Tunisia as revealed by pathotype, AFLP, and microsatellite analyses. Mycopathologia, 163, 281–294.

Braithwaite K S, Bakkeren G, Croft B J, Brumbley S M. 2004. Genetic variation in a worldwide collection of the sugarcane smut fungus Ustilago scitaminea. Proceedings of the Australian Society of Sugar Cane Technologists, 26, 48–56..

Caten C E. 1987. The concept of race in plant pathology. In: Wolfe M S, Caten C E, eds., Populations of the Plant Pathogens: Their Dynamics and Genetic. Blackwell Scientific Publications, Oxford. pp. 21–37.

Du Y D, Xing M, Yang Z Y, Liu Y F, Chen X. 2011. Genetic diversity caused by environmental stress in natural populations of Niupidujuan as revealed by RAPD technique. Plant Ecology, 27, 641–645.

Ellegren H. 2004. Microsatellites: Simple sequences with complex evolution. Nature Reviews Genetics, 5, 435–445.

Faris J A .1924a. Physiological specialization of Ustilago hordei. Phytopathology, 14, 537–557.

Faris J A. 1924b. Factors influencing infection of Hordeum sativum by Ustilago hordei. American Journal of Botany, 3, 189–214.

Fernández M E, Figueiras A M, Benito C. 2002. The use of ISSR and RAPD markers for detecting DNA polymorphism, genotype identification and genetic diversity among barley cultivars with known origin. Theoretical and Applied Genetics, 104, 845–851.

Fischer G W, Holton C S. 1957. Biology and control of the smut fungi. Mycologia, 49, 563.

Gaudet D A, Kiesling R L. 1991. Variation in aggressiveness among and within races of Ustilago hordei on barley. Phytopathology, 11, 1385–1390.

Grewal T S, Rossnagel B G, Scoles G J. 2006. Inheritance of resistance to covered smut [Ustilago hordei (Pers.) Lagerh.] in barley. Canadian Journal of Plantence, 3, 829–837.

Hamelin R C, Beaulieu J, Plourde A. 1995. Genetic diversity in populations of Cronartium ribicola in plantations and natural stands of Pinus strobus. Theoretical and Applied Genetics, 91, 1214–1221.

Hellmann R, Christ B J. 1991. Isozyme variation of physiologic races of Ustilago hordei. Phytopathology, 81, 1536–1540.

He Z D, Chen J, Gao Z G, Zhuang J H, Gao Y F. 2007. Study on genetic diversity of Sporisorium reilianum. Journal of Maize Science, 4, 133–136. (in Chinese)

Hu X P, Dong Y L, Gou J J, Yang J R. 2008. Genetic diversity of Venturia inaequalis populations based on SSR analysis. Acta Phytopathologica Sinica, 3, 329–332. (in Chinese)

Hu Z H, Zhao L H, Kong B H, Chen H R, Fan J H, Liu F, Li X P, Cai H, Yang G H, Qin X Y, Fang D H. 2012. Comparison and analysis of molecular methods ISSR and RAPD used for assessment of genetic diversity in Alternaria alternate. Southwest China Journal of Agricultural Sciences, 3, 917–921. (in Chinese)

Jiang Y, Xu X D, Liu Z H, Dong H Y, Zhao S H. 2007. Genetic diversity of Sporisorium reilianum of maize. Journal of Shenyang Agricultural University, 4, 522–526. (in Chinese)

Karaoglu H, Lee C M Y, Meyer W. 2005. Survey of simple sequence repeats in completed fungal genomes. Molecular Biology and Evolution, 3, 639–650.

Karwasra S S, Mukherjee A K, Swain S C, Mohapatra T, Sharma R P. 2002. Evaluation of RAPD, ISSR and AFLP markers for characterization of the loose smut fungus Ustilago tritici. Journal of Plant Biochemistry & Biotechnology, 2, 99–103.

Lamine M, Mliki A. 2015. Elucidating genetic diversity among sour orange rootstocks: a comparative study of the efficiency of RAPD and SSR markers. Applied Biochemistry and Biotechnology, 175, 2996–3013.

Laurie J D, Ali S, Linning, R, Mannbaupt G, Wong P, Güldener U, Münsteerkötter M, Moore R, Knhmann R, Bakkeren G, Schirawski J. 2012. Genome comparison of barley and maize smut fungi reveals targeted loss of RNA silencing components and species-specific presence of transposable elements. The Plant Cell, 24, 1733–1745.

Lou H X. 2000. The development and policy of naked barley in Tibet plateau. Chaidamu Development and Research, 2, 8–31.

Ma J T, Wang D X, Gong X J, Gao J. 2008. Analysis on genetic diversity of Sporisorium reilianum from 6 provinces and regions in China. Journal of Maize Science, 6, 139–143. (in Chinese)

Mantel N. 1967. The detection of disease clustering and a generalized regression approach. Cancer Research, 2, 209–220.

Mathre D E. 1997. Compendium of Barley Diseases. 2nd ed. Montana State University, Bozeman, Montana.

McCluskey K, Mills D. 1990. Identification and characterization of chromosome length polymorphisms among strains representing fourteen races of Ustilago hordei. Molecular Plant-Microbe Interacttions, 6, 366–373.

Meyer S E, Nelson D L, Clement S, Waters J, Stevens M, Fairbanks D. 2005. Genetic variation in Ustilago bullata: Molecular genetic markers and virulence on Bromus tectorum host lines. International Journal of Plant Sciences, 166, 105–115.

Popovic Z, Menzies J G. 2006. Intensive and extensive sampling techniques used to measure genetic diversity of Ustilago tritici, using virulence and DNA polymorphism. Canadian Journal of Plant Pathology, 28, 197–207.

Semeniuk W. 1940. Physiologic races of Ustilago hordei (Pers.) K. and S. in Alberta. Canadian Journal of Research, 18, 76–78.

Shang H M, Song W B. 2005. Separation and relationship of ten marine scuticociliates (Protozoa, Ciliophora) using RAPD fingerprinting method. Acta Oceanologica Sinica, 23, 78–85.

Shen Y, Frouin J, He Y Q, He Y Q, Kaye C, Xiao F H, Notteghem J L, Liu E M, Tharreau D. 2004. The perfect stage and SSR analysis of Magnaporthe grisea in the Yanxi blast nursery, Hunan Province. Chinese Journal of Rice Science, 3, 262–268. (in Chinese)

Singh N, Somai B M, Pillay D. 2005. Molecular profiling demonstrates limited diversity amongst geographically separate strains of Ustilago scitaminea. FEMS Microbiology Letters, 247, 7–15.

Sonah H, Deshmukh R K, Sharma A, Singh V P, Gupta D K, Gacche R N, Rana J C, Singh N K, Sharma T R. 2011. Genome-wide distribution and organization of microsatellites in plants: An insight into marker development in Brachypodium. PLoS One, 6, e21298.

Tapke V F.1937. Physiologic races of Ustilago hordei. Journal of Agricultural Research, 9, 683–692.

Tapke V F.1945. New physiologic races of Ustilago hordei. Phytopathology, 35, 570–576.

Weising K, Nybom H, Wolff K, Meyer W. 1995. DNA Fingerprinting in Plants and Fungi. CRC Press, Boca Raton, Florida.

Xu L, Que Y, Chen R. 2004. Genetic diversity of Ustilago scitaminea in mainland China. Sugar Tech, 6, 267–271.

Xu X D, Dong H Y, Jiang Y, Bai J K. 2003. Analysis of genetic relationships among Sporisorium reilianum isolates by RAPD. Mycosystema, 1, 56–61. (in Chinese)

Yu T F. 1940. Breeding hulled barley for resistance to covered smut (Ustilago hordei (Pers.) K. and S.) in Kiangsu Province. Nanking Journal, 9, 281–292. (in Chinese)

Yu T F, Fang C T. 1945. A preliminary report on further studies of physiologic specialization in Ustilago hordei. Phytopathology, 35, 517–520.

Zhao Z J, Cao J F, Yang M Y, Sun D W, Li X P, Yang W L. 2008. Genetic diversity of Phytophthora infestans of potato in Yunnan based on two microsatellite (SSR) markers. Scientia Agricultura Sinica, 11, 3610–3617. (in Chinese)

Zhou Y L, Pan Y J, Xie X W, Zhu L H, Xu J L, Wang S, Li Z K. 2008. Genetic diversity of rice false smut fungus, Ustilaginoidea virens and its pronounced differentiation of populations in North China. Journal of Phytopathology, 156, 559–564.
[1] ZHANG Ying, CAO Yu-fen, HUO Hong-liang, XU Jia-yu, TIAN Lu-ming, DONG Xing-guang, QI Dan, LIU Chao. An assessment of the genetic diversity of pear (Pyrus L.) germplasm resources based on the fruit phenotypic traits[J]. >Journal of Integrative Agriculture, 2022, 21(8): 2275-2290.
[2] GUO Yi, GONG Ying, HE Yong-meng, YANG Bai-gao, ZHANG Wei-yi, CHEN Bo-er, HUANG Yong-fu, ZHAO Yong-ju, ZHANG Dan-ping, MA Yue-hui, CHU Ming-xing, E Guang-xin. Investigation of Mitochondrial DNA genetic diversity and phylogeny of goats worldwide[J]. >Journal of Integrative Agriculture, 2022, 21(6): 1830-1837.
[3] XU Xin, YE Jun-hua, YANG Ying-ying, LI Ruo-si, LI Zhen, WANG Shan, SUN Yan-fei, ZHANG Meng-chen, XU Qun, FENG Yue, WEI Xing-hua, YANG Yao-long. Genetic diversity analysis and GWAS reveal the adaptive loci of milling and appearance quality of japonica (oryza sativa L.) in Northeast China[J]. >Journal of Integrative Agriculture, 2022, 21(6): 1539-1550.
[4] LIU Na, CHENG Fang-yun, GUO Xin, ZHONG Yuan. Development and application of microsatellite markers within transcription factors in flare tree peony (Paeonia rockii) based on next-generation and single-molecule long-read RNA-seq[J]. >Journal of Integrative Agriculture, 2021, 20(7): 1832-1848.
[5] NIE Xing-hua, WANG Ze-hua, LIU Ning-wei, SONG Li, YAN Bo-qian, XING Yu, ZHANG Qing, FANG Ke-feng, ZHAO Yong-lian, CHEN Xin, WANG Guang-peng, QIN Ling, CAO Qing-qin. Fingerprinting 146 Chinese chestnut (Castanea mollissima Blume) accessions and selecting a core collection using SSR markers[J]. >Journal of Integrative Agriculture, 2021, 20(5): 1277-1286.
[6] May Oo kHINE, brozenká MICHAELA, LIU Yan, Jiban kumar kUNDU, WANG Xi-feng. Molecular diversity of barley yellow dwarf virus-PAV from China and the Czech Republic[J]. >Journal of Integrative Agriculture, 2020, 19(11): 2736-2745.
[7] WANG Li-ning, GAO Wei, WANG Qiong-ying, QU Ji-bin, ZHANG Jin-xia, HUANG Chen-yang. Identification of commercial cultivars of Agaricus bisporus in China using genome-wide microsatellite markers[J]. >Journal of Integrative Agriculture, 2019, 18(3): 580-589.
[8] WU Huai-heng, WAN Peng, HUANG Min-song, LEI Chao-liang. Microsatellites reveal strong genetic structure in the common cutworm, Spodoptera litura[J]. >Journal of Integrative Agriculture, 2019, 18(3): 636-643.
[9] WANG Chen, CHEN Yao-sheng, HAN Jian-lin, MO De-lin, LI Xiu-jin, LIU Xiao-hong. Mitochondrial DNA diversity and origin of indigenous pigs in South China and their contribution to western modern pig breeds[J]. >Journal of Integrative Agriculture, 2019, 18(10): 2338-2350.
[10] ZHU Hong, ZHOU Yuan-yuan, ZHAI Hong, HE Shao-zhen, ZHAO Ning, LIU Qing-chang. Transcriptome profiling reveals insights into the molecular mechanism of drought tolerance in sweetpotato[J]. >Journal of Integrative Agriculture, 2019, 18(1): 9-24.
[11] YANG Hai-long, DONG Le, WANG Hui, LIU Chang-lin, LIU Fang, XIE Chuan-xiao. A simple way to visualize detailed phylogenetic tree of huge genomewide SNP data constructed by SNPhylo[J]. >Journal of Integrative Agriculture, 2018, 17(09): 1972-1978.
[12] Engin Yol, Seymus Furat, Hari D Upadhyaya, Bulent Uzun. Characterization of groundnut (Arachis hypogaea L.) collection using quantitative and qualitative traits in the Mediterranean Basin[J]. >Journal of Integrative Agriculture, 2018, 17(01): 63-75.
[13] LI Ming-na, LONG Rui-cai, FENG Zi-rong, LIU Feng-qi, SUN Yan, ZHANG Kun, KANG Jun-mei, WANG Zhen, CAO Shi-hao. Transcriptome analysis of salt-responsive genes and SSR marker exploration in Carex rigescens using RNA-seq[J]. >Journal of Integrative Agriculture, 2018, 17(01): 184-196.
[14] WANG Bao-hua, Daniel J. Ebbole, WANG Zong-hua. The arms race between Magnaporthe oryzae and rice: Diversity and interaction of Avr and R genes[J]. >Journal of Integrative Agriculture, 2017, 16(12): 2746-2760.
[15] Kiflom Weldu Okubazghi, LI Xiao-na, CAI Xiao-yan, WANG Xing-xing, CHEN Hao-dong, ZHOU Zhong-li, WANG Chun-ying, WANG Yu-hong, LIU Fang, WANG Kun-bo. Genome-wide assessment of genetic diversity and fiber quality traits characterization in Gossypium hirsutum races[J]. >Journal of Integrative Agriculture, 2017, 16(11): 2402-2412.
No Suggested Reading articles found!