Advertisement

Theoretical and Applied Genetics

, Volume 122, Issue 5, pp 989–1004 | Cite as

Genetic structure and relationships within and between cultivated and wild sorghum (Sorghum bicolor (L.) Moench) in Kenya as revealed by microsatellite markers

  • E. MutegiEmail author
  • F. Sagnard
  • K. Semagn
  • M. Deu
  • M. Muraya
  • B. Kanyenji
  • S. de Villiers
  • D. Kiambi
  • L. Herselman
  • M. Labuschagne
Original Paper

Abstract

Understanding the extent and partitioning of diversity within and among crop landraces and their wild/weedy relatives constitutes the first step in conserving and unlocking their genetic potential. This study aimed to characterize the genetic structure and relationships within and between cultivated and wild sorghum at country scale in Kenya, and to elucidate some of the underlying evolutionary mechanisms. We analyzed at total of 439 individuals comprising 329 cultivated and 110 wild sorghums using 24 microsatellite markers. We observed a total of 295 alleles across all loci and individuals, with 257 different alleles being detected in the cultivated sorghum gene pool and 238 alleles in the wild sorghum gene pool. We found that the wild sorghum gene pool harbored significantly more genetic diversity than its domesticated counterpart, a reflection that domestication of sorghum was accompanied by a genetic bottleneck. Overall, our study found close genetic proximity between cultivated sorghum and its wild progenitor, with the extent of crop-wild divergence varying among cultivation regions. The observed genetic proximity may have arisen primarily due to historical and/or contemporary gene flow between the two congeners, with differences in farmers’ practices explaining inter-regional gene flow differences. This suggests that deployment of transgenic sorghum in Kenya may lead to escape of transgenes into wild-weedy sorghum relatives. In both cultivated and wild sorghum, genetic diversity was found to be structured more along geographical level than agro-climatic level. This indicated that gene flow and genetic drift contributed to shaping the contemporary genetic structure in the two congeners. Spatial autocorrelation analysis revealed a strong spatial genetic structure in both cultivated and wild sorghums at the country scale, which could be explained by medium- to long-distance seed movement.

Keywords

Sorghum Allelic Richness Cetyl Trimethyl Ammonium Bromide Rift Valley Spatial Genetic Structure 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

This study formed part of the project, “Environmental risk assessment for the introduction of genetically modified sorghum in Mali and Kenya” funded by the United States Agency for International Development (USAID) Biotechnology and Biodiversity Interface (BBI) Program. We are deeply indebted to the late Dr. Fabrice Sagnard (Principle Investigator), who offered exemplary leadership and immense scientific contribution to the entire project. We acknowledge Caroline Mwongera, Charles Marangu and Bernard Rono who participated in collections as well as farmers from various sorghum growing areas of Kenya and the National Genebank of Kenya for providing the seed samples used in this study.

Supplementary material

122_2010_1504_MOESM1_ESM.doc (42 kb)
Supplementary material 1 (DOC 41 kb)

References

  1. Aldrich PR, Doebley J (1992) Restriction fragment variation in the nuclear and chloroplast genomes of cultivated and wild Sorghum bicolor. Theor Appl Genet 85:293–302Google Scholar
  2. Aldrich PR, Doebley J, Schertz KF, Stec A (1992) Patterns of allozyme variation in cultivated and wild Sorghum bicolor. Theor Appl Genet 85:451–460Google Scholar
  3. Auer C (2008) Ecological risk assessment and regulation for genetically-modified ornamental plants. Crit Rev Plant Sci 27:255–271CrossRefGoogle Scholar
  4. Ayana A, Bekele E, Bryngelsson T (2000a) Genetic variation in wild sorghum (Sorghum bicolor ssp verticilliflorum (L.) Moench) germplasm from Ethiopia assessed by random amplified polymorphic DNA (RAPD). Hereditas 132:249–254CrossRefPubMedGoogle Scholar
  5. Ayana A, Bryngelsson T, Bekele E (2000b) Genetic variation of Ethiopian and Eritrean sorghum (Sorghum bicolor (L.) Moench) germplasm assessed by random amplified polymorphic DNA (RAPD). Genet Resour Crop Evol 47:471–482CrossRefGoogle Scholar
  6. Ayana A, Byngelsson T, Bekele E (2001) Geographic and altitudinal allozyme variation in sorghum (Sorghum bicolor (L.) Moench) landraces from Ethiopia and Eritrea. Hereditas 135:1–12CrossRefPubMedGoogle Scholar
  7. Barnaud A, Deu M, Garine E, Mckey D, Joly HI (2007) Local genetic diversity of sorghum in a village in northern Cameroon: structure and dynamics of landraces. Theor Appl Genet 114:237–248CrossRefPubMedGoogle Scholar
  8. Barrett BA, Kidwell KK (1998) AFLP-based genetic diversity assessment among wheat cultivars from the Pacific Northwest. Crop Sci 38:1261–1271CrossRefGoogle Scholar
  9. Barro-Kondombo C, Sagnard F, Chantereau J, Deu M, vom Brocke K, Durand P, Gozé E, Zongo JD (2010) Genetic structure among sorghum landraces as revealed by morphological variation and microsatellite markers in three agroclimatic regions of Burkina Faso. Theor Appl Genet 120:1511–1523CrossRefPubMedGoogle Scholar
  10. Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F (2004) GENETIX 405, logiciel sous Windows TM pour la génétique des populations. Laboratoire Génome, Populations, Interactions, CNRS UMR 5000, Université de Montpellier II, MontpellierGoogle Scholar
  11. Bhatia CR, Mitra R (2003) Consequences of gene flow from genetically engineered crops. Curr Sci India 84:138–141Google Scholar
  12. Casa AM, Mitchell SE, Hamblin MT, Sun H, Bowers JE, Paterson AH, Aquadro CF, Kresovich S (2005) Diversity and selection in Sorghum: simultaneous analyses using simple sequence repeats. Theor Appl Genet 111:23–30CrossRefPubMedGoogle Scholar
  13. Chandler S, Dunwell JM (2008) Gene flow, risk assessment and the environmental release of transgenic plants. Crit Rev Plant Sci 27:25–49CrossRefGoogle Scholar
  14. Clayton WD, Renvoize RD (1982) Poaceae. Flora of Tropical East Africa, Part 3 AA Balkema, RotterdamGoogle Scholar
  15. Cleveland DA, Soleri D (2005) Rethinking the risk management process for genetically engineered crop varieties in small-scale, traditionally based agriculture. Ecol Soc 10:1–33Google Scholar
  16. Conner AJ, Glare TR, Nap JP (2003) The release of genetically modified crops into the environment. Part II. Overview of ecological risk assessment. Plant J 33:19–46CrossRefPubMedGoogle Scholar
  17. Cui YX, Xu GW, Magill CW, Schertz KF, Hart GE (1995) RFLP-based assay of Sorghum bicolor (L) Moench. genetic diversity. Theor Appl Genet 90:787–796CrossRefGoogle Scholar
  18. Deu M, Hamon P, Chantereau J, Dufour P, D’Hont A, Lanaud C (1995) Mitochondrial DNA diversity in wild and cultivated sorghum. Genome 38:635–645CrossRefPubMedGoogle Scholar
  19. Deu M, Sagnard F, Chantereau J, Calatayud C, Hérault D, Mariac C, Pham JL, Vigouroux Y, Kapran I, Traoré PS, Mamadou A, Gérard B, Ndjeunga J, Bezançon G (2008) Niger-wide assessment of in situ sorghum genetic diversity with microsatellite markers. Theor Appl Genet 116:903–913CrossRefPubMedGoogle Scholar
  20. Djè Y, Ater M, Lefèbvre C, Vekemans X (1998) Patterns of morphological and allozyme variation in sorghum landraces of northwestern Morocco. Genet Resour Crop Evol 45:541–548CrossRefGoogle Scholar
  21. Djè Y, Forcioli D, Ater M, Lefèbvre C, Vekemans X (1999) Assessing population genetic structure of sorghum landraces from North-western Morocco using allozyme and microsatellite markers. Theor Appl Genet 99:157–163CrossRefGoogle Scholar
  22. Dogget H (1988) Sorghum. Longman Scientific and Technical, EssexGoogle Scholar
  23. Dogget H, Majisu BN (1968) Disruptive selection in crop development. Heredity 23:1–23CrossRefGoogle Scholar
  24. Dogget H, Prasada Rao KE (1995) Sorghum. In: Smartt J, Simmonds NW (eds) Evolution of crop plants, 2nd edn. Longman Group, Essex, pp 140–159Google Scholar
  25. Duncan RR, Bramel-Cox PJ, Miller FR (1991) Contributions of introduced sorghum germplasm to hybrids development in the USA. In: Shands HL, Wiesner LE (eds) Use of plant introductions in the cultivar development. Crop Science Society of America, Madison, pp 69–101Google Scholar
  26. Ellstrand NC (1992) Gene flow by pollen: Implications for plant conservation genetics. Oikos 63:77–86CrossRefGoogle Scholar
  27. Ellstrand NC, Prentice HC, Hancock JF (1999) Geneflow and introgression from domesticated plants into their wild relatives. Annu Rev Ecol Syst 30:539–563CrossRefGoogle Scholar
  28. Epperson BK (1993) Recent advances in correlation analysis of spatial patterns of genetic variation. Evol Biol 27:95–155Google Scholar
  29. Epperson BK (2004) Multilocus estimation of genetic structure within populations. Theor Popul Biol 65:227–237CrossRefPubMedGoogle Scholar
  30. Evanno S, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620CrossRefPubMedGoogle Scholar
  31. Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479–491PubMedGoogle Scholar
  32. Excoffier L, Laval LG, Schneider S (2005) Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol Bioinform 1:47–50Google Scholar
  33. FAO (2008) FAOSTAT. http://faostat.fao.org
  34. Folkertsma RF, Rattunde HFW, Chandra S, Raju GS, Hash CT (2005) The pattern of genetic diversity of Guinea-race Sorghum bicolor (L.) Moench landraces as revealed with SSR markers. Theor Appl Genet 111:399–409CrossRefPubMedGoogle Scholar
  35. Frankel OH, Hawkes JG (1975) Crop genetic resources for today and tomorrow. Cambridge University Press, CambridgeGoogle Scholar
  36. Frankel OH, Brown AHD, Burdon JJ (1995) The conservation of plant diversity. Cambridge University Press, New YorkGoogle Scholar
  37. Fukunaga K, Hill J, Vigouroux Y, Matsuoka Y, Sanchez G, Liu K, Buckler ES, Doebley J (2005) Genetic diversity and population structure of teosinte. Genetics 169:2241–2254CrossRefPubMedGoogle Scholar
  38. Gepts P (2004) Crop domestication as a long-term selection experiment. In: Jannick J (ed) Plant breeding reviews, Volume 24, Part 2: long-term selection: crops, animals, bacteria. Wiley, New YorkGoogle Scholar
  39. Ghebru B, Schmidt RJ, Bennetzen JL (2002) Genetic diversity of Eritrean sorghum landraces assessed with simple sequence repeat (SSR) markers. Theor Appl Genet 105:229–236CrossRefPubMedGoogle Scholar
  40. Goudet J (2002) FSTAT, a program to estimate and test gene diversity and fixation indices. (version 2932)Google Scholar
  41. Gurney AL, Press MC, Scholes JD (2002) Can wild relatives of sorghum provide new sources of resistance or tolerance against Striga species? Weed Sci 42:317–324Google Scholar
  42. Halfhill MD, Zhu B, Warwick SI, Raymer PI, Millwood RJ, Weissinger AK, Stewart NC Jr (2004) Hybridization and backcrossing between transgenic oilseed rape and two related weed species under field conditions. Environ Biosafety Res 3:73–81CrossRefPubMedGoogle Scholar
  43. Hardy OJ, Vekemans X (2002) SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol Ecol 2:618–620CrossRefGoogle Scholar
  44. Harlan JR, De Wet JMJ (1972) A simplified classification of cultivated sorghum. Crop Sci 12:172–177CrossRefGoogle Scholar
  45. Hartl DL, Clark G (1997) Principles of population genetics. Sinauer Associates Inc, SunderlandGoogle Scholar
  46. Haygood R, Ives AR, Andow DA (2003) Consequences of recurrent gene flow from crops to wild relatives. Proc R Soc Lond B 270:1879–1886CrossRefGoogle Scholar
  47. Hulbert SH (1971) The nonconcept of species diversity: a critique and alternative parameters. Ecology 52:577–586CrossRefGoogle Scholar
  48. Idury RM, Cardon LR (1997) A simple method for automated allele binning in microsatellite markers. Genome Res 11:1104–1109Google Scholar
  49. International Ltd VSN (2007) GenStat Discovery Edition 3 VSN International Ltd. Hernel Hempstead, UKGoogle Scholar
  50. Kalinowski S (2005) HP-RARE 10: a computer program for performing rarefaction on measures of allelic richness. Mol Ecol 5:187–189CrossRefGoogle Scholar
  51. Kamala V, Singh SD, Bramel PJ, Rao DM (2002) Sources of resistance to downy mildew in wild and weedy sorghums. Crop Sci 42:1357–1360CrossRefGoogle Scholar
  52. Kamala V, Sharma HC, Manohar Rao D, Varaprasad KS, Bramel PJ (2009) Wild relatives of sorghum as sources of resistance to sorghum shoot fly, Atherigona soccata. Plant Breed 128:137–142CrossRefGoogle Scholar
  53. Ladizinsky G (1999) Plant evolution under domestication. Kluwer Academic Publishers, LondonGoogle Scholar
  54. Levin DA, Kerster HW (1974) Gene flow in seeds plants. Evol Biol 7:139–220Google Scholar
  55. Mace EM, Buhariwalla HK, Crouch JH (2003) A high-throughput DNA extraction protocol for tropical molecular breeding programs. Plant Mol Biol Rep 21:459a–500hCrossRefGoogle Scholar
  56. Mariac C, Luong V, Kapran I, Mamadou A, Sagnard F, Deu M, Chantereau J, Gérard B, Ndjeunga J, Bezançon G, Pham JL, Vigouroux Y (2006) Diversity of wild and cultivated pearl millet accessions (Pennisetum glaucum [L.] R. Br.) in Niger assessed by microsatellite markers. Theor Appl Genet 114:49–58CrossRefPubMedGoogle Scholar
  57. Matsuoka Y, Vigouroux Y, Goodman MM, Sanchez GJ, Buckler E, Doebley J (2002) A single domestication for maize shown by multilocus microsatellite genotyping. Proc Natl Acad Sci USA 99:6080–6084CrossRefPubMedGoogle Scholar
  58. Mohammadi SA, Prasanna BM (2003) Analysis of genetic diversity in crop plants—salient statistical tools and considerations. Crop Sci 43:1235–1248CrossRefGoogle Scholar
  59. Morden CW, Doebley JF, Schertz KF (1990) Allozyme variation among the spontaneous species of Sorghum section Sorghum (Poaceae). Theor Appl Genet 80:296–304CrossRefGoogle Scholar
  60. Mutegi E, Sagnard F, Muraya M, Kanyenji B, Rono B, Mwongera C, Marangu C, Kamau J, Parzies H, de Villiers S, Semagn K, Traoré PS, Labuschagne M (2010) Ecogeographical distribution of wild weedy and cultivated Sorghum bicolor (L.) Moench in Kenya: implications for conservation and crop-to-wild gene flow. Genet Resour Crop Evol 57:243–253CrossRefGoogle Scholar
  61. Neal D (2004) Introduction to population biology. Cambridge University Press, CambridgeGoogle Scholar
  62. Nkongolo KK, Nsapato L (2003) Genetic diversity in Sorghum bicolor (L.) Moench accessions from different ecogeographical regions in Malawi assessed with RAPDs. Genet Resour Crop Evol 50:149–156CrossRefGoogle Scholar
  63. Perrier X, Jacquemoud-Collet JP (2006) DARwin software. http://darwin.cirad.fr/darwin
  64. Prasanth V, Chandra S, Jayashree B, Hoisington D (2006) AlleloBin—a program for allele binning of microsatellite markers based on the algorithm of Idury and Cardon (1997). ICRISAT International Crops Research Institute for the Semi, Arid TropicsGoogle Scholar
  65. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedGoogle Scholar
  66. Rao Kameswara N, Reddy LJ, Bramel PJ (2003) Potential of wild species for genetic enhancement of some semi-arid food crops. Genet Resour Crop Evol 50:707–721CrossRefGoogle Scholar
  67. Reed JD, Ramundo BA, Claflin LF, Tuinstra MR (2002) Analysis of resistance to ergot in sorghum and potential alternate hosts. Crop Sci 42:1135–1138CrossRefGoogle Scholar
  68. Rich PJ, Grenier U, Ejeta G (2004) Striga resistance in the wild relatives of sorghum. Crop Sci 44:2221–2229CrossRefGoogle Scholar
  69. Ritland K (1996) Estimators for pairwise relatedness and individual inbreeding coefficients. Genet Res 67:175–185CrossRefGoogle Scholar
  70. Rousset F (2000) Genetic differentiation between individuals. J Evol Biol 13:58–62CrossRefGoogle Scholar
  71. Sagnard F, Barnaud A, Deu M, Barro C, Luce C, Billot C, Rami JF, Bouchet S, Dembelé D, Pomies V, Calatayud C, Rivallan R, Joly H, vom Brocke K, Touré A, Chantereau J, Bezançon G, Vaksmann M (2008) Multi-scale analysis of sorghum genetic diversity: understanding the evolutionary processes for in situ conservation. Cah Agric 17:114–121Google Scholar
  72. Schuelke M (2000) An economic method for the fluorescent labelling of PCR fragments. A poor man’s approach to genotyping for research and high throughput diagnostics. Nat Biotechnol 18:233–234CrossRefPubMedGoogle Scholar
  73. Sharma HC, Franzmann BA (2001) Host plant preference and oviposition responses of the sorghum midge Stenodiplosis sorghicola (Coquillett) (Dipt., Cecidomyiidae) towards wild relatives of Sorghum. J Appl Ent 125:109–114CrossRefGoogle Scholar
  74. Snow AA, Moran-Palma P (1997) Commercialization of transgenic plants: potential ecological risks. Bioscience 47:86–96CrossRefGoogle Scholar
  75. Sokal RR, Oden NL (1978) Spatial autocorrelation in biology 2. Some biological implications and four applications of evolutionary and ecological interest. Biol J Linn Soc 10:249Google Scholar
  76. Sombroek WC, Braun HMH, van der Pour BJA (1982) Explanatory soil map and agro-climatic zone map of Kenya. Report E1:1–56Google Scholar
  77. R Development Core Team (2007) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.r-project.org
  78. Tesso T, Kapran I, Grenier C, Snow A, Sweeney P, Pedersen J, Marx D, Bothma G, Ejeta G (2008) The potential for crop-to-wild gene flow in sorghum in Ethiopia and Niger: a geographic survey. Crop Sci 48:1425–1431CrossRefGoogle Scholar
  79. Thies JE, Devare MH (2007) An ecological assessment of transgenic crops. J Dev Stud 43:97–129CrossRefGoogle Scholar
  80. 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
  81. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • E. Mutegi
    • 1
    • 2
    • 3
    Email author
  • F. Sagnard
    • 2
    • 4
  • K. Semagn
    • 5
  • M. Deu
    • 4
  • M. Muraya
    • 6
  • B. Kanyenji
    • 7
  • S. de Villiers
    • 2
  • D. Kiambi
    • 2
  • L. Herselman
    • 8
  • M. Labuschagne
    • 8
  1. 1.Kenya Agricultural Research Institute (KARI), National GenebankNairobiKenya
  2. 2.International Crops Research Institute for the Semi-Arid Tropics (ICRISAT-Nairobi)NairobiKenya
  3. 3.Department of Evolution, Ecology, and Organismal BiologyOhio State UniversityColumbusUSA
  4. 4.CIRAD, UMR DAPMontpellierFrance
  5. 5.International Maize and Wheat Improvement Center (CIMMYT)NairobiKenya
  6. 6.Leibniz Institute of Plant Genetics and Crop Plant ResearchGaterslebenGermany
  7. 7.KARI-Embu Research StationEmbuKenya
  8. 8.Department of Plant SciencesUniversity of the Free StateBloemfonteinSouth Africa

Personalised recommendations