Theoretical and Applied Genetics

, Volume 113, Issue 4, pp 715–729 | Cite as

Genetic relatedness and population differentiation of Himalayan hulless barley (Hordeum vulgare L.) landraces inferred with SSRs

  • Madhav Pandey
  • Carola Wagner
  • Wolfgang Friedt
  • Frank Ordon
Original Paper

Abstract

A set of 107 hulless barley (Hordeum vulgare L. subsp. vulgare) landraces originally collected from the highlands of Nepal along the Annapurna and Manaslu Himalaya range were studied for genetic relatedness and population differentiation using simple sequence repeats (SSRs). The 44 genome covering barley SSRs applied in this study revealed a high level of genetic diversity among the landraces (diversity index, DI = 0.536) tested. The genetic similarity (GS) based UPGMA clustering and Bayesian Model-based (MB) structure analysis revealed a complex genetic structure of the landraces. Eight genetically distinct populations were identified, of which seven were further studied for diversity and differentiation. The genetic diversity estimated for all and each population separately revealed a hot spot of genetic diversity at Pisang (DI = 0.559). The populations are fairly differentiated (θ = 0.433, RST = 0.445) accounting for > 40% of the genetic variation among the populations. The pairwise population differentiation test confirmed that many of the geographic populations significantly differ from each other but that the differentiation is independent of the geographic distance (r = 0.224, P > 0.05). The high level of genetic diversity and complex population structure detected in Himalayan hulless barley landraces and the relevance of the findings are discussed.

References

  1. Abu Assar AH, Uptmoor R, Abdelmula AA, Salih M, Ordon F, Friedt W (2005) Genetic variation in sorghum germplasm from Sudan, ICRISAT, and USA assessed by simple sequence repeats (SSRs). Crop Sci 45:1636–1644CrossRefGoogle Scholar
  2. Assefa A, Labuschagne MT (2004) Phenotypic variation in barley (Hordeum vulgare L.) landraces from north Shewa in Ethiopia. Biodivers Conserv 13:1441–1451CrossRefGoogle Scholar
  3. Atanassov P, Borries C, Zaharieva M, Monneveux P (2001) Hordein polymorphism and variation of agromorphological traits in a collection of naked barley. Genet Resour Crop Evol 48:353–360CrossRefGoogle Scholar
  4. Badr A, Müller K, Schäfer-Pregl R, El Rabey H, Effgen S, Ibrahim HH, Pozzi C, Rohde W, Salamini F (2000) On the origin and domestication history of barley (Hordeum vulgare). Mol Biol Evol 17:499–510PubMedGoogle Scholar
  5. Balloux F, Moulin NL (2002) The estimation of population differentiation with microsatellite markers. Mol Ecol 11:155–165PubMedCrossRefGoogle Scholar
  6. Baniya BK, Dongol DMS, Riley KW (1997) Characterization of Nepalese barley germplasm. Rachis 16:16–19Google Scholar
  7. Bhatty RS (1999) The potential of hull-less barley. Cereal Chem 76:589–599CrossRefGoogle Scholar
  8. Dice LR (1945) Measures of the amount of ecologic association between species. Ecology 26:297–302CrossRefGoogle Scholar
  9. Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–15Google Scholar
  10. Goodman SJ (1997) R ST calc: a collection of computer programs for calculating estimates of genetic differentiation from microsatellite data and determining their significance. Mol Ecol 6:881–885CrossRefGoogle Scholar
  11. Goudet J (2002) FSTAT version 2.9.3.2. A program to estimate and test gene diversities and fixation indices. Institute of Ecology, Lausanne, Switzerland, http://www.unil.ch/izea/softwares/fstat.html
  12. Goudet J, Raymond M, Meeüs T, Rousset F (1996) Testing differentiation in diploid populations. Genetics 144:1933–1940PubMedGoogle Scholar
  13. Hamza S, Hamida WB, Rebai A, Harrabi M (2004) SSR-based genetic diversity assessment among Tunisian winter barley and relationship with morphological traits. Euphytica 135:107–118CrossRefGoogle Scholar
  14. Jain S, Jain RK, McCouch SR (2004) Genetic analysis of Indian aromatic and quality rice (Oryza sativa L.) germplasm using panels of fluorescently-labelled microsatellite markers. Theor Appl Genet 109:965–977PubMedCrossRefGoogle Scholar
  15. Khlestkina EK, Huang XQ, Quenum FJB, Chebotar S, Röder MS, Börner A (2004) Genetic diversity in cultivated plants—loss or stability? Theor Appl Genet 108:1466–1472PubMedCrossRefGoogle Scholar
  16. Kikuchi S, Taketa S, Ichii M, Kawasaki S (2003) Efficient fine mapping of the naked caryopsis gene (nud) by HEGS (High Efficiency Genome Scanning)/AFLP in barley. Theor Appl Genet 108:73–78PubMedCrossRefGoogle Scholar
  17. Konishi T, Matsuura S (1991) Geographic differentiation in isozyme genotypes of Himalayan barley (Hordeum vulgare). Genome 34:704–709Google Scholar
  18. 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 168:435–446PubMedCrossRefGoogle Scholar
  19. Li X, Xu C, Zhang Q (2004) Ribosomal DNA spacer-length polymorphisms in three samples of wild and cultivated barleys and their relevance to the origin of cultivated barley. Plant Breed 123:30–34CrossRefGoogle Scholar
  20. Linhart YB, Grant MC (1996) Evolutionary significance of local genetic differentiation in plants. Annu Rev Ecol Syst 27:237–277CrossRefGoogle Scholar
  21. Liu F, Bothmer R, Salomon B (1999) Genetic diversity among East Asian accessions of the barley core collection as revealed by six isozyme loci. Theor Appl Genet 98:1226–1233CrossRefGoogle Scholar
  22. Liu K, Goodman M, Muse S, Smith JS, Buckler ED, Doebley J (2003) Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites. Genetics 165:2117–2128PubMedGoogle Scholar
  23. Lu H, Redus MA, Coburn JR, Rutger JN, McCouch SR, Tai TH (2005) Population structure and breeding patterns of 145 U.S. rice cultivars based on SSR Marker analysis. Crop Sci 45:66–76CrossRefGoogle Scholar
  24. Macaulay M, Ramsay L, Powell W, Waugh R (2001) A representative, highly informative ‘genotyping set’ of barley SSRs. Theor Appl Genet 102:801–809CrossRefGoogle Scholar
  25. Mantel M (1967) The detection of disease clustering and generalized regression approach. Cancer Res 27:209–220PubMedGoogle Scholar
  26. Murphy PJ, Witcombe JR, (1986) Covered and naked barleys from the Himalaya, 1. Evidence of multivariate differences between the two types. Theor Appl Genet 71:730–735CrossRefGoogle Scholar
  27. Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–590PubMedGoogle Scholar
  28. 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 30:190–193PubMedCrossRefGoogle Scholar
  29. Ordon F, Ahlemeyer J, Werner K, Köhler W, Friedt W (2005) Molecular assessment of genetic diversity in winter barley and its use in breeding. Euphytica 146:21–28CrossRefGoogle Scholar
  30. Pandey M, Wagner C, Friedt W, Ordon F (2004) Genetic diversity of hull-less barley (Hordeum vulgare L.) landraces in the highlands of central Nepal as revealed by SSRs. In: Vollmann J, Grausgruber H, Ruckenbauer P (eds) Genetic variation for plant breeding, Proceedings of the 17th EUCARPIA General Congress, 2004, Tulln, BOKU- University of Natural resources and Applied Life Sciences, Vienna, Austria, pp 45–48Google Scholar
  31. Patto MCV, Satovic Z, Pego S, Fevereiro P (2004) Assessing the genetic diversity of Portuguese maize germplasm using microsatellite markers. Euphytica 137:63–72CrossRefGoogle Scholar
  32. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedGoogle Scholar
  33. Putkonen JK (2004) Continuous snow and rain data at 500 to 4,400 m altitude near Annapurna, Nepal, 1999–2001. Arctic Antarctic Alpine Res 36:244–248CrossRefGoogle Scholar
  34. Ramsay L, Macaulay M, Ivanissevich SD, 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 156:1997–2005PubMedGoogle Scholar
  35. Remington DL, Thornsberry JM, Matsuoka Y, Wilson LM, Whitt SR, Doebley J, Kresovich S, Goodman MM, Buckler ES (2001) Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc Natl Acad Sci USA 98:11479–11484PubMedCrossRefGoogle Scholar
  36. Rice WR (1989) Analysing tables of statistical tests. Evolution 43:223–225CrossRefGoogle Scholar
  37. Rohlf FJ (2000) NTSYS-pc numerical taxonomy and multivariate analysis system, version 2.1. Exeter Publications, New YorkGoogle Scholar
  38. Rousset F (1997) Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145:1219–1228PubMedGoogle Scholar
  39. Russell JR, Booth A, Fuller JD, Baum M, Ceccarelli S, Grando S, Powell W (2003) Patterns of polymorphism detected in the chloroplast and nuclear genomes of barley landraces sampled from Syria and Jordan. Theor Appl Genet 107:413–421PubMedCrossRefGoogle Scholar
  40. Schoen DJ, Brown AHD (1991) Intraspecific variation in population gene diversity and effective population size correlates with the mating system in plants. Proc Natl Acad Sci USA 88:4494–4497PubMedCrossRefGoogle Scholar
  41. Sharma KP, Dahal KR, Basta BK (1994) Genetic diversity of Nepalese naked barley and possibility of yield improvement. In: Proceedings of the 2nd national conference on science and technology, 1994, Kathmandu. Royal Nepal Acad Sci Tech (RONAST) Kathmandu, pp 231–237Google Scholar
  42. Slatkin M (1995) A measure of population subdivision based on microsatellite allele frequencies. Genetics 139:457–462PubMedGoogle Scholar
  43. Stich B, Melchinger AE, Frisch M, Maurer HP, Heckenberger M, Reif JC (2005) Linkage disequilibrium in European elite maize germplasm investigated with SSRs. Theor Appl Genet 111:723–730PubMedCrossRefGoogle Scholar
  44. Sun L, Wang X (1999) Genetic diversity of Chinese hull-less barley germplasm and its utilization. Plant Genet Res Newsl 120:55–57Google Scholar
  45. Takahashi R (1955) The origin and evolution of cultivated barley. Adv Genet 7:227–266CrossRefGoogle Scholar
  46. Taketa S, Kikuchi S, Awayama T, Yamamoto S, Ichii M, Kawasaki S (2004) Monophyletic origin of naked barley inferred from molecular analyses of a marker closely linked to the naked caryopsis gene (nud). Theor Appl Genet 108:1236–1242PubMedCrossRefGoogle Scholar
  47. Uptmoor R, Wenzel W, Friedt W, Donaldson G, Ayisi K, Ordon F (2003) Comparative analysis on the genetic relatedness of Sorghum bicolor accessions from Southern Africa by RAPDs, AFLPs and SSRs. Theor Appl Genet 106:1316–1325PubMedGoogle Scholar
  48. Valkoun J, Konopka J (2004) Global inventory of barley genetic resources. In: Proceedings of the 9th international barley genetics symposium, 2004, Brno, Czech Republic, pp 31–38Google Scholar
  49. Weber JL (1990) Informativeness of human (dC-dA)n · (dG-dT)n polymorphisms. Genomics 7:524–530PubMedCrossRefGoogle Scholar
  50. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370CrossRefGoogle Scholar
  51. Witcombe JR, Murphy PJ (1986) Covered and naked barleys from the Himalaya, 2. Why do they differ from each other so extensively? Theor Appl Genet 71:736–741CrossRefGoogle Scholar
  52. Wright S (1951) The genetical structure of populations. Annu Eugen 15:323–354Google Scholar
  53. Yeh FC, Yang RC, Boyle T (1999) POPGENE version 1.32. Microsoft window-based freeware for population genetic analysis. University of Alberta, Edmonton, http://www.ualberta.ca/∼fyeh/pr01.htm
  54. Yu SB, Xu WJ, Vijayakumar CHM, Ali J, Fu BY, Xu JL, Jiang YZ, Marghirang R, Domingo J, Aquino C, Virmani SS, Li ZK (2003) Molecular diversity and multilocus organization of the parental lines used in the International Rice Molecular Breeding Program. Theor Appl Genet 108:131–140PubMedCrossRefGoogle Scholar
  55. Zhou H, Xie Z, Ge S (2003) Microsatellite analysis of genetic diversity and population genetic structure of a wild rice (Oryza rufipogon Griff.) in China. Theor Appl Genet 107:332–339PubMedCrossRefGoogle Scholar
  56. Zohary D, Hopf M (2000) Domestication of plants in the old world: the origin and spread of cultivated plants in West Asia, Europe and the Nile Valley. Clarendon, OxfordGoogle Scholar

Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  • Madhav Pandey
    • 1
    • 3
  • Carola Wagner
    • 1
  • Wolfgang Friedt
    • 1
  • Frank Ordon
    • 2
  1. 1.Plant Breeding Department, Research Center for Bio Systems Land Resources and Nutrition (IFZ)Justus-Liebig-University GiessenGiessenGermany
  2. 2.Institute of Epidemiology and Resistance ResourcesFederal Centre for Breeding Research on Cultivated PlantsAscherslebenGermany
  3. 3.Institute of Agriculture and Animal ScienceTribhuvan UniversityRampur, ChitwanNepal

Personalised recommendations