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Frontiers of Agriculture in China

ISSN 1673-7334

ISSN 1673-744X(Online)

CN 11-5729/S

Front. Agric. China    2008, Vol. 2 Issue (4) : 372-379    https://doi.org/10.1007/s11703-008-0084-5
Molecular analysis of cultivated naked barley ( L.) from Qinghai-Tibet Plateau in China using SSR markers
PAN Zhifen1, LONG Hai1, YU Maoqun1, DENG Guangbing2, ZHAI Xuguang2, TANG Yawei3, QIANG Xiaolin3
1.Chengdu Institute of Biology, Chinese Academy of Sciences; 2.Chengdu Institute of Biology, Chinese Academy of Sciences;Graduate School of the Chinese Academy of Sciences; 3.Tibet Academy of Agricultural and Animal Husbandry Sciences;
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Abstract Naked barley is widely planted in Qinghai-Tibet Plateau in China and is essential for the daily life of Tibetans in those regions. In this study, the genetic diversity of 64 cultivated naked barley accessions from Qinghai-Tibet Plateau in China was analyzed using 30 mapped SSRs linked with the important traits of barley improvement. A total of 132 alleles were identified at 22 polymorphic SSR loci, with the number of each locus ranging from 2 to 15, the polymorphism information content (PIC) values ranging from 0.16 to 0.91, and with an average of 0.65. Of the selected SSRs, 13 SSR markers with high PIC value were highly efficient for the genetic analysis of Chinese barley. The accessions were divided into five main groups by cluster analysis and could be differentiated from each other. The genetic diversity in the Tibet accessions was slightly higher than in the Sichuan accessions. It is found that there were specific genes linked with the collecting sites. These results indicate the cultivated naked barley from Qinghai-Tibet Plateau in China are highly polymorphic and could be considered as an important resource bank for cultivated naked barley breeding in the future.
Issue Date: 05 December 2008
 Cite this article:   
DENG Guangbing,PAN Zhifen,ZHAI Xuguang, et al. Molecular analysis of cultivated naked barley ( L.) from Qinghai-Tibet Plateau in China using SSR markers[J]. Front. Agric. China, 2008, 2(4): 372-379.
 URL:  
https://academic.hep.com.cn/fag/EN/10.1007/s11703-008-0084-5
https://academic.hep.com.cn/fag/EN/Y2008/V2/I4/372
1 Akagi H, Yokozeki Y, Inagaki A (1996). Microsatellite DNA markers for ricechromosomes. Theor Appl Genet, 93: 1071–1077.
doi:10.1007/BF00230127
2 Barandalla L, Ruiz de Galarreta J I, Rios D, Ritter E (2006). Molecular analysis of local potato cultivars from TenerifeIsland using microsatellite markers. Euphytica, 152: 283–291.
doi:10.1007/s10681-006-9215-3
3 Becker J, Heun M (1995). Barleymicrrosatellites: allele variation and mapping. Plant Mol Biol, 27: 835–845.
doi:10.1007/BF00020238
4 Bhatty R S (1986). The potential of hull-less barley, a review. Cereal Chemistry, 63: 97–103
5 Dávila J A, Loarce Y, Ramsay L, Waugh R, Ferrer E (1999). Comparison of RAMPand SSR markers for the study of wild barley genetic diversity. Hereditas, 131: 5–13.
doi:10.1111/j.1601-5223.1999.00005.x
6 Dávila J A, Sánchez de la Hoz M P, Loarce Y, Ferrer E (1998). The use of random amplified microsatellitepolymorphic DNA and coefficients of parentage to determine geneticrelationships in barley. Genome, 41: 477–486.
doi:10.1139/gen-41-4-477
7 Diwan N, Cregan P B, Dean R E, Dahlberg J A, Hopkins M S, Mitchell S E, Kresovich S (1999). Automated sizing of fluorescent-labeled simple sequencerepeat (SSR) markers to assay genetic variation in soybean. Theor Appl Genet, 95: 723–733.
doi:10.1007/s001220050618
8 Djà Y, Heuertz M, Lefàbvre C, Vekemans X (2000). Assessment of genetic diversity within and among germplasmaccessions in cultivated sorghum using microsatellite markers. Theor Appl Genet, 100: 918–925.
doi:10.1007/s001220051371
9 Feng Z Y, Zhang Y Z, Zhang L L, Ling H Q (2003). Genetic diversity and geographical differentiation of Hordeum vulgare ssp. spontaneum in Tibet using microsatellite markers. High Technology Letters, 10: 46–53 (in Chinese)
10 Heun M, Kennedy A E, Anderson J A, Lapitan N L V, Sorrels M E, Tanksley S D (1991). Construction of a restriction fragmentlength polymorphism map for barley (Hordeumvulgare). Genome, 34: 437–477
11 Hou Y Z, Yan Z H, Wei Y M, Zheng Y L (2005). Genetic diversity in barley from west China based on RAPD and ISSRanalysis. Barley Genetics Newsletter, 35: 9–22
12 Ivandic V, Hackett C A, Nevo E, Keith R, Thomas W T B, Forster B P (2002). Analysis of simple sequence repeats (SSRs) in wild barleyfrom the Fertile Crescent: associations with ecology, geography andflowering time. Plant Molecular Biology, 48: 511–527.
doi:10.1023/A:1014875800036
13 Karakousis A, Barr A R, Chalmers K J, Ablett G A, Holton T A, Henry R J, Lim P, Langridge P (2003b). Potential of SSR markers for plantbreeding and variety identification in Australian barley germplasm. Australian Journal of Agricultural Research, 54: 1197–1210.
doi:10.1071/AR02178
14 Karakousis A, Gustafson J P, Barr A R, Chalmers K J, Langridge P (2003a). A consensusmap of barley integrating SSR, RFLP, and AFLP markers. Australian Journal of Agricultural Research, 54: 1173–1185.
doi:10.1071/AR02177
15 Kleinhofs A, Kilian A, Saghai-Maroof M, Biyashev R, Hayes P M, Chen F, Lapitan N, Fenwick A, Blake T, Kanazin V, Ananiev E, Dahleen L, Kudrna D, Bollinger J, Knapp S, Liu B, Sorrells M, Heun M, Franckowiak J, Hoffman D, Skadsen R, Steffenson B (1993). A molecular,isozyme, and morphological map of the barley (Hordeum vulgare) genome. TheorAppl Genet, 86: 705–712.
doi:10.1007/BF00222660
16 Liu Z W, Biyashev R M, Saghai Maroof M A (1996). Dvelopment of simplesequence repeat DNA markers and their integration into a barley linkagemap. Theor Appl Genet, 93: 869–876.
doi:10.1007/BF00224088
17 Ma D Q, Li Y Q (1997). Collectionand traits identification of germplasm resources of wild relativesbarley in China. Barley Science, 50: 1–4 (inChinese)
18 Ma D Q, Yang J H, Lhosanggengdoi. , Tong D R (2000). The quality evaluation of wild barley germplasm resources in Tibet. Southwest China Journal of Agricultural Science, 13: 31–37 (in Chinese)
19 Nei M (1973). Analyses of gene diversity in subdivided populations. Proc Nalt Acad Sci USA, 70: 3321–3323.
doi:10.1073/pnas.70.12.3321
20 Newman R K, Ore K C, Abbott J, Newman C W (1998). Fiber enrichment of baked products with a barley milling fraction. Cereal Foods World, 43: 23–25
21 Nimazhaxi. (1998). Hulless barley and food safety in the region of plateau. Tibetan Agriculture and Technology, 20: 20–25
22 Oscarsson M, Andersson R, Salomonsson A C, Aman P (1996). Chemical composition of barley samples focusing on dietary fibrecomponents. Journal of Cereal Science, 24: 161–170.
doi:10.1006/jcrs.1996.0049
23 Pan Z F, Deng G B, Zhai X G, Wu F, Yu M Q (2007). Genetic diversityof Acid-PAGE monomeric prolamins in cultivated hulless barley (Hordeum vulgare L.) from Qinghai-Tibet Plateauin China. Genet Resour Crop Evol, 54: 1691–1699.
doi:10.1007/s10722-006-9177-2
24 Pan Z F, Tang Y W, Wu F, Han Z X, Deng G B, Yu M Q (2006). Genetic diversity of β-hordein in hulless barley(Hordeum vulgare L.) from the Qinghai-TibetPlateau in China. Chin J Appl Environ Biol, 12: 601–604 (in Chinese)
25 Pejic I, Ajmone-Marsan P, Morgante M, Kozumplick V, Castiglioni P, Taramino G, Motto M (1998). Comparative analysis of genetic similarity among maize inbred linesdetected by RFLPs, RAPDs, SSRs, and AFLPs. Theor Appl Genet, 97: 1248–1255.
doi:10.1007/s001220051017
26 Petersen L, Østergard H, Giese H (1994). Genetic diversity among wild andcultivated barley as revealed by RFLP. Theor Appl Genet, 89: 676–681.
doi:10.1007/BF00223704
27 Pillen K, Blinder A, Kreuzkam B, Ramsasy L, Waugh R, Föster J, Léon J (2000). Mapping new EMBL-derived barley microsatellites andtheir use in differentiating German barley cultivars. Theor Appl Genet, 101: 652–660.
doi:10.1007/s001220051527
28 Powell W, Machray G C, Provan J (1996b). Polymorphism revealed by simplesequence repeats. Trends Plant Science, 1: 215–222
29 Powell W, Morgante M, Andre C, Hanafey M, Vogel J, Tingey S, Rafalski A (1996a). The comparison of RFLP, RAPD, AFLP and SSR markers forgermplasm analysis. Molecular Breeding, 2: 225–238.
doi:10.1007/BF00564200
30 Prasad M, Varshney R K, Roy J K, Balyan H S, Gupta P K (2000). The use of microsatellitesfor detecting DNA polymorphism, genotype identification and geneticdiversity in wheat. Theor Appl Genet, 100: 584–592
31 Qiang X L, Liu S H, Luobu Z M (1997). Main characters and features of Tibetanlocal varietal clonies in barley. SouthwestChina Journal of Agricultural Science, 10: 41–48 (in Chinese)
32 Ramsay L, Macaulay M, Mclean K, Fuller J, Edwards K, Tuvesson S, Morgante M, degli Ivanissevich S, Marmiroli N, Maesti E, Massari A, Powell W, Waugh R (2000). A simple sequencerepeat based linkage map of barley. Genetics, 156: 1997–2005
33 Rohlf F J (1998). NTSYS-pc: Numerical Taxonomy and Multivariate AnalysisSystem, Version 2.0, Exeter Software, NewYork, 1998
34 Russell J, Fuller J D, Macaulay M, Hatz B G, Jahoor A, Powell W, Waugh R (1997a). Directcomparison of levels of genetic variation among barley accessionsdetected by RFLPs, AFLPs, SSRs and RAPDs. Theor Appl Genet, 95: 714–722.
doi:10.1007/s001220050617
35 Russell J, Fuller J D, Young G, Thomas B, Taramino G, Macaulay M, Waugh R, Powell W (1997b). Discriminating between barley genotypesusing microsatellite markers. Genome, 40: 442–450.
doi:10.1139/g97-059
36 Saghai-Maroof M A, Biyashev R M, Yang G P, Zhang Q F, Allard R W (1994). Extraordinarily polymorphicmicrosatellite. DNA in barley-species diversity, chromosomal locations,and population dynamics. Proc Natl AcadSci, 91: 5466–5470.
doi:10.1073/pnas.91.12.5466
37 Senior M L, Murphy J P, Goodman M M, Stuber C W (1998). Utility of SSRs for determining genetic similarities and relationshipsin maize using an agarose gel system. CropScience, 38: 1088–1098
38 Smith J S C, Kresovich S, Hopkins M S, Mitchell S E, Dean R E, Woodman W L, Lee M, Porter K (2000). Genetic diversityamong elite sorghum inbred lines assessed with simple sequence repeats. Crop Science, 40: 226–232
39 Struss D, Plieske J (1998). The useof microsatellite markers for detection of genetic diversity in barleypopulations. Theor Appl Genet, 97: 308–315.
doi:10.1007/s001220050900
40 Sun L J, Lu W, Zhang J, Zhang W X (1999). Investigation of barley germplasm in China. Genet Resour Crop Evol, 46: 361–369.
doi:10.1023/A:1008606613602
41 Takahashi R (1955). The origin and evolution of cultivated barley. Adv Genet, 7: 227–266.
doi:10.1016/S0065-2660(08)60097-8
42 Taketa S, Kikuchi S, Awayama T, Yamamoto S, Ichii M, Kawasaki S (2004). Monophyletic origin of naked barleyinferred from molecular analyses of a marker closely linked to thenaked caryopsis gene (nud). Theor ApplGenet, 108: 1236–1242.
doi:10.1007/s00122-003-1560-1
43 Tang H H, Ding Y, Hu Y J (2002). Genetic polymorphism of hordein inwild relatives of barley from China. Journalof Wuhan Botanical Research, 20: 41–48 (in Chinese)
44 Tautz D, Renz M (1984). Simplesequences are ubiquitous repetitive components of eukaryotic genomes. Nucl Acids Res, 12: 4127–4138.
doi:10.1093/nar/12.10.4127
45 Wang G L, Fang H J (1998). PlantGenetic Engineering. Beijing: Scientific Press (in Chinese)
46 Wang Z, Weber J L, Zhong G, Tanksley S D (1994). Survey of plant short tandem DNA repeats. Theol Appl Genet, 88: 1–6
47 Weber J L (1990). The informativeness of human (dC-dA)n. (dG-dT)n polymorphism. Genomics, 7: 524–530.
doi:10.1016/0888-7543(90)90195-Z
48 Yeh F C, Yang R C, Tim B (1999). POPGENE: Microsoft Window-based Freewarefor Population Genetic Analysis. Version 1.31, 1999
49 Yin Y Q, Ma D Q, Ding Y (2003). Analysis of genetic diversity ofhordein in wild close relatives of barley from Tibet. Theor Appl Genet, 107: 837–842.
doi:10.1007/s00122-003-1328-7
50 Zhang Q F, Yang G P, Dai X K, Sun J Z (1994). A comparative analysis of genetic polymorphism in wild and cultivatedbarley from Tibet using isozyme and ribosomal DNA markers. Genome, 37: 631–638.
doi:10.1139/g94-090
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