Abstract
Molecular diversity of 40 accessions of Tibetan wild barley (TB), 10 Syrian (SY), 72 North American (NA), 36 European (EU), 9 South American (SA) and 8 Australian (AU) varieties were characterized using multiple microsatellite loci. The 42 SSR primers amplified 278 alleles across the 175 barley accessions tested in the present study. The average gene diversity for the whole sample was 0.3387 whereas the mean value for the each population was as follows: TB = 0.3286, SY = 0.2474, EU = 0.299, AU = 0.2867, NA = 0.3138, SA = 0.2536. Clustering analysis based on Nei’s original genetic distance showed that the EU and NA barley populations were grouped together. The TB population was well separated from the other 5 barley populations. Associations between microsatellite markers and 14 quantitative traits were also investigated. Significant associations were found for 18 microsatellite marker loci. The number of marker loci associated with each trait ranged from one (stem diameter, filled grains per plant, grain weight per plant, length of main spike and awn length) to seven (plant height). The percentage of the total variation explained by each marker ranged from 4.59% (HVM2 associated with plant height) to 17.48% (Bmac90 associated with density of main spike). This study provides candidate markers for further QTL mapping of these traits and for marker-assisted selection.
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Achleitner A, Tinker NA, Zechner E, Buerstmayr H (2008) Genetic diversity among oat varieties of worldwide origin and associations of AFLP markers with quantitative traits. Theor Appl Genet 117:1041–1053
Anderson JA, Churchill GA, Autrique JE, Tanksley SD, Sorrells ME (1993) Optimizing parental selection for genetic linkage maps. Genome 36:181–186
Becker J, Heum M (1995) Barley microsatellites: alleles variation and mapping. Plant Mol Biol 27:835–845
Bezant J, Laurie D, Pratchett N, Chojecki J, Kearsey M (1997) Mapping QTL controlling yield and yield components in a spring barley (Hordeum vulgare L.) cross using marker regression. Mol Breed 3:29–38
Breseghello F, Sorrells ME (2006) Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172:1165–1177
Brown AHD, Munday J (1982) Population genetic structure and optimal sampling of land races of barley from Iran. Genetica 58:85–96
Brücher H, Åberg E (1950) Die-primitiv-gersten des hochlands von Tibet, ihre bedeutung fuer die zuechtung und das verstandis des ursprungs und der klassifizierung der gersten. Ann KGL Landwei Hochsch Schwedens 17:247–319
Caldwell KS, Russell J, Langridge P, Powell W (2006) Extreme population-dependent linkage disequilibrium detected in an inbreeding plant species, Hordeum vulgare. Genetics 172:557–567
Cho YG, Ishii T, Temnykh S, Chen X, Lipovich L, McCouch SR, Park WD, Ayres N, Cartihour S (2000) Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theor Appl Genet 100:713–722
Cockram J, White J, Leigh FJ, Lea VJ, Chiapparino E, Laurie DA, Mackay IJ, Powell W, O’Sullivan MO (2008) Association mapping of partitioning loci in barley. BMC Genet 9:16
Dawson IK, Chalmers KJ, Waugh R, Powell W (1993) Detection genetic variation in Hordeum spontaneum populations from Israel using RAPD markers. Mol Ecol 2:51–59
Dizkirici A, Guren HE, Onde S, Temel F, Akar T, Budak H, Kaya Z (2008) Microsatellite (SSR) variation in barley germplasm and its potential use for marker assisted selection in scald resistance breeding. Int J Integr Biol 4:9–15
Feng ZY, Zhang LL, Zheng YZ, Ling HQ (2006) Genetic diversity and geographical differentiation of cultivated six-rowed naked barley landraces from Qinghai-Tibet plateau of China detected by SSR analysis. Genet Mol Biol 29:330–338
Fischbeck G (2003) Diversification through breeding. In: von Bothmer R, van Hintum T, Knüpffer H, Sato K (eds) Diversity in barley. Elsevier Science, Amsterdam, pp 29–50
Franckowiak JD, Lundqvist U (1997) BGS 6, six-rowed spike 1, vrs1. Barley Genet Newsl 26:49–50
Frank RB, Ana GBM (2001) RAPD data do not support a second center of barley domestication in Morocco. Genet Resour Evol 48:13–19
Graner A, Siedler H, Jahoor A, Herrmann RG, Wenzel G (1990) Assessment of the degree and the type of restriction fragment length polymorphism in barley (Hordeum vulgare). Theor Appl Genet 80:826–832
Gupta PK, Rustgi S, Kulwal PL (2005) Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Mol Biol 57:461–485
Harlan JR (1976) Barley. In: Simmonds N (ed) Evolution of crop plants. Academic Press, London, pp 93–98
Hayes PM, Castro A, Marquez-Cedillo L, Corey A, Henson C, Jones B, Kling J, Mather D, Matus I, Rossi C, Sato K (2003) Genetic diversity for quantitatively inherited agronomic and malting quality traits. In: Von Bothmer R, Knupfeer H, van Hintum T, Sato K (eds) Diversity barley. Elsevier Science Publishers, Amsterdam, The Netherlands
Igartua E, Casas AM, Ciudad F, Montoya JL, Romagosa I (1999) RFLP markers associated with major genes controlling heading date evaluated in a barley germplasm pool. Heredity 83:551–559
Ivandic V, Hackett CA, Nevo E, Keith R, Thomas WT, Forster BP (2002) Analysis of simple sequence repeats (SSRs) in wild barley from the Fertile Crescent: associations with ecology, geography and flowering time. Plant Mol Biol 48:511–527
Ivandic V, Thomas WTB, Nevo E, Zhang Z, Forster BP (2003) Association of SSRs with quantitative trait variation including biotic and abiotic stress tolerance in Hordeum spontaneum. Plant Breed 122:300–304
Jana S (1999) Some recent issues on the conservation of crop genetic resources in developing countries. Genome 44:562–569
Jana S, Pietrzak LN (1988) Comparative assessment of genetic diversity in wild and primitive cultivated barley in a center of diversity. Genetics 119:981–990
Karakousis A, Gustafson JP, Chalmers KJ, Barr AR, Langridge P (2003) A consensus map of barley integrating SSR, RFLP, and AFLP markers. Aust J Agric Res 54:1173–1185
Kimura M, Crow JF (1964) The number of alleles that can be maintained in a finite population. Genetics 49:725–738
Kraakman ATW, Niks RE, Van den Berg PMMM, Stam P, van Eeuwijk FA (2004) Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars. Genetics 168:435–446
Kresovich S, Szewe-McFadden AK, Bliek SM, McFerson JR (1995) Abundance and characterization of simple sequence repeats (SSRs) isolated from a size fractionated genomic library of Brassica napus L. (rapeseed). Theor Appl Genet 91:206–211
Laurie DA, Pratchett N, Romero C, Simpson E, Snape JW (1993) Assignment of the denso dwarfing gene to the long arm of chromosome 3(3H) of barley by use of RFLP markers. Plant Breed 111:198–203
Liu ZW, Biyashev RM, Saghai-Maroof MA (1996) Development of simple sequence repeat DNA markers and their integration into a barley linkage map. Theor Appl Genet 93:869–876
Lundqvist U, Franckowiak JD (1997) BGS 178, intermedium spike-c, int-c. Barley Genet Newsl 26:200–201
Malysheva-Otta LV, Ganal MW, Röder MS (2006) Analysis of molecular diversity, population structure and linkage disequilibrium in a worldwide survey of cultivated barley germplasm (Hordeum vulgare L.). BMC Genet 7:6
Marquez-Cedillo LA, Hayes PM, Jones BL, Kleinhofs A, Legge WG, Rossnagel BG, Sato K, Ullrich SE, Wesenberg DM, The North American Barley Genome Mapping Project (2000) QTL analysis of malting quality in barley based on the double haploid progeny of two elite North American varieties representing different germplasm groups. Theor Appl Genet 101:173–184
Matus I, Hayes PM (2002) Genetic diversity in three groups of barley germplasm assessed by simple sequence repeats. Genome 45:1095–1106
Nei M (1972) Genetic distance between populations. Am Nat 106:283–292
Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA 70:3321–3323
Nordborg M, Borevitz JO, Bergelson J, Berry CC, Chory J, Hagenblad J, Kreitman M, Maloof JN, Noyes T, Oefner PJ, Stahl EA, Weigel D (2002) The extent of linkage disequilibrium in Arabidopsis thaliana. Nat Genet 30:190–193
Peng JH, Bai Y, Haley SD, Lapitan NLV (2009) Microsatellite-based molecular diversity of bread wheat germplasm and association mapping of wheat resistance to the Russian wheat aphid. Genetica 135:95–122
Petersen L, Østergard H, Giese H (1994) Genetic diversity among wild and cultivated barley as revealed by RFLP. Theor Appl Genet 89:676–681
Pillen K, Binder A, Kreuzkam B, Ramsay L, Waugh R, Förster J, Lèon J (2000) Mapping new EMBL-derived barley microsatellites and their use to differentiate German barley cultivars. Theor Appl Genet 101:652–660
Prichard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959
Ramsay L, Macaulay M, degli Ivanissevich S, MacLean K, Cardle L, Fuller J, Edwards KJ, Tuvesson S, Morgante M, Massari A, Maestri E, Marmiroli N, Sjakste T, Ganal M, Powell W, Waugh R (2000) A simple sequence repeat-based linkage map of barley. Genetics 156:1997–2005
Russell JR, Fuller JD, Young G, Thomas B, Taramino G, Macaulay M, Waugh R, Powell W (1997) Discriminating between barley genotypes using microsatellite markers. Genome 40:442–450
Saghai-Maroof MA, Biyashev RM, Yang GP, Zhang Q, Allard RW (1994) Extraordinarily polymorphic microsatellite DNA in barley: species diversity, chromosomal locations, and population dynamics. Proc Natl Acad Sci USA 91:5466–5470
Shannon CE, Weaver W (1949) The mathematical theory of communication. University of Illinois Press, Urbana, IL
Stein N, Herren G, Keller B (2001) A new DNA extraction method for high-throughput marker analysis in a large-genome species such as Triticum aestivum. Plant Breed 120:354–356
Stracke S, Haseneyer G, Veyrieras JB, Geiger HH, Sauer S, Graner A, Piepho HP (2009) Association mapping reveals gene action and interactions in the determination of flowering time in barley. Theor Appl Genet 118:259–273
Struss D, Plieske J (1998) The use of microsatellite markers for detection of genetic diversity in barley populations. Theor Appl Genet 97:308–315
Turpeinen T, Vanhala T, Nevo E, Nissila E (2003) AFLP genetic polymorphism in wild barley (Hordeum spontaneum) populations in Israel. Theor Appl Genet 106:1333–1339
Varshney RK, Marcel TC, Ramsay L, Russell J, Röder MS, Stein N, Waugh R, Langridge P, Niks RE, Graner A (2007) A high density barley microsatellite consensus map with 775 SSR loci. Theor Appl Genet 114(6):1091–1103
Vavilov NI (1926) Studies on the origin of cultivated plants. Bull Appl Bot Genet Plant Breed USSR 16:1–248
Wang J, Yang J, McNeil DL, Zhou MX (2010) Identification and molecular mapping of a dwarfing gene in barley (Hordeum vulgare L.) and its correlation with other agronomic traits. Euphytica 175:331–342
Williams K, Bogacki P, Scott L, Karakousis A, Wallwork H (2008) Mapping of a gene for leaf scald resistance in barley line ‘B87/14’ and validation of microsatellite and RFLP markers for marker-assisted selection. Plant Breed 120:301–304
Yeh FC, Yang RC (2000) POPGENE version 1.32. University of Albert and Center for International Research. http://www.ualberta.ca/*fyeh/
Zhang J (2003) SSR maker tagging of the dwarfing gene uz in barley (Hordeum velgare L.). Acta Agronom Sin 29:637–640
Zhang QF, Yang GP, Dai XK, Sun JZ (1994) A comparative analysis of genetic polymorphism in wild and cultivated barley from Tibet using isozyme and ribosomal DNA markers. Genome 37:631–638
Zondervan KT, Cardon LR (2004) The complex interplay among factors that influence allelic association. Nat Rev Genet 5:89–100
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This project is supported by the National Natural Science Foundation of China (30630047) and China 863 Project (2006AA10Z1C3).
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Sun, D., Ren, W., Sun, G. et al. Molecular diversity and association mapping of quantitative traits in Tibetan wild and worldwide originated barley (Hordeum vulgare L.) germplasm. Euphytica 178, 31–43 (2011). https://doi.org/10.1007/s10681-010-0260-6
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DOI: https://doi.org/10.1007/s10681-010-0260-6