Skip to main content

Advertisement

SpringerLink
Log in

Genetic structure and diversity of wild sorghum populations (Sorghum spp.) from different eco-geographical regions of Kenya

  • Original Paper
  • Published:
Theoretical and Applied Genetics Aims and scope Submit manuscript

Abstract

Wild sorghums are extremely diverse phenotypically, genetically and geographically. However, there is an apparent lack of knowledge on the genetic structure and diversity of wild sorghum populations within and between various eco-geographical regions. This is a major obstacle to both their effective conservation and potential use in breeding programs. The objective of this study was to assess the genetic diversity and structure of wild sorghum populations across a range of eco-geographical conditions in Kenya. Sixty-two wild sorghum populations collected from the 4 main sorghum growing regions in Kenya were genotyped using 18 simple sequence repeat markers. The study showed that wild sorghum is highly variable with the Coast region displaying the highest diversity. Analysis of molecular variance showed a significant variance component within and among wild sorghum populations within regions. The genetic structure of wild sorghum populations indicated that gene flow is not restricted to populations within the same geographic region. A weak regional differentiation was found among populations, reflecting human intervention in shaping wild sorghum genetic structure through seed-mediated gene flow. The sympatric occurrence of wild and cultivated sorghums coupled with extensive seed-mediated gene flow, suggests a potential crop-to-wild gene flow and vice versa across the regions. Wild sorghum displayed a mixed mating system. The wide range of estimated outcrossing rates indicate that some environmental conditions may exist where self-fertilisation is favoured while others cross-pollination is more advantageous.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • Anas, Yoshida T (2004) Sorghum diversity evaluated by simple sequence repeat (SSR) markers and phenotypic performance. Plant Prod Sci 7:301–308

    Article  Google Scholar 

  • Anttila CK, Daehler CC, Rank NE, Strong DR (1998) Greater male fitness of a rare invader (Spartina alterniflora, Poaceae) threatens a common native (Spartina foliosa) with hybridization. Am J Bot 85:1597–1601

    Article  PubMed  CAS  Google Scholar 

  • Ayana A, Bekele E (1998) Geographical patterns of morphological variation in sorghum (Sorghum bicolor (L.) Moench) germplasm from Ethiopia and Eritrea: qualitative characters. Hereditas 129:195–205

    Article  Google Scholar 

  • Ayana A, Bryngelsson T, Bekele E (2000) Genetic variation of Ethiopian and Eritrean Sorghum (Sorghum bicolor (L.) Moench) germplasm assessed by random amplified polymorphic DNA (RAPD). Genet Resour Crop Evol 47:471–482

    Article  Google Scholar 

  • Barnaud A, Deu M, Garine E (2007) Local genetic diversity of sorghum in a village in northern Cameroon: structure and dynamics of landraces. Theor Appl Genet 114:237–248

    Article  PubMed  Google Scholar 

  • Barnaud A, Triguero G, McKey D, Joly HI (2008) High outcrossing rates in fields with mixed sorghum landraces: how are landraces maintained? Heredity 101:445–452

    Article  PubMed  CAS  Google Scholar 

  • Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F (2004) GENETIX 4.05, logiciel sous Windows TM pour la génétique des populations. Laboratoire Génome, Populations, Interactions, CNRS UMR 5000, Université de Montpellier II, Montpellier, France

  • Bohonak AJ (2002) IBD (isolation by distance): a program for analyses of isolation by distance. J Hered 93:153–154

    Article  PubMed  CAS  Google Scholar 

  • Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331

    PubMed  CAS  Google Scholar 

  • Brown SM, Hopkins MS, Mitchell SE, Senior ML, Wang TY, Duncan RR, Gonzales-Candelas F, Kresovich S (1996) Multiple methods for identification of polymorphic simple sequence repeats (SSRs) in sorghum (Sorghum bicolor (L.) Moench). Theor Appl Genet 93:190–198

    Article  CAS  Google Scholar 

  • 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 111:23–30

    Article  PubMed  CAS  Google Scholar 

  • 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 33:19–46

    Article  PubMed  Google Scholar 

  • De Wet JMJ (1978) Systematics and evolution of Sorghum Sect. Sorghum (Gramineae). Am J Bot 65:477–484

    Article  Google Scholar 

  • De Wet JMJ, Harlan JR (1971) The origin and domestication of Sorghum bicolor. Econ Bot 25:128–135

    Article  Google Scholar 

  • Dillon SL, Shapter FM, Henry RJ, Cordeiro G, Izquierdo L, Lee LS (2007) Domestication to crop improvement: genetic resources for Sorghum and Saccharum (Andropogoneae). Ann Bot 100:975–989

    Article  PubMed  Google Scholar 

  • Djè Y, Heuertz M, Lefèbvre C, Vekemans X (2000) Assessment of genetic diversity within and among germplasm accessions in cultivated sorghum using microsatellite markers. Theor Appl Genet 100:918–925

    Article  Google Scholar 

  • Dje´ Y, Heuertz M, Ater M, Lefebvre C, Vekemans X (2004) In situ estimation of outcrossing rate in sorghum landraces using microsatellite markers. Euphytica 138:205–212

    Article  Google Scholar 

  • Doggett H (1988) Sorghum, 2nd edn. Longman, London

    Google Scholar 

  • Duvall MR, Doebley JF (1990) Restriction site variation in the chloroplast genome of Sorghum (Poaceae). Syst Bot 15:472–480

    Article  Google Scholar 

  • Ellstrand NC, Schierenbeck KA (2000) Hybridization as a stimulus for the evolution of invasiveness in plants? Proc Natl Acad Sci USA 97:7043–7050

    Article  PubMed  CAS  Google Scholar 

  • Epperson BK (1993) Recent advances in correlation analysis of spatial patterns of genetic variation. Evol Biol 27:95–155

    Google Scholar 

  • Epperson BK (2004) Multilocus estimation of genetic structure within populations. Theor Popul Biol 65:227–237

    Article  PubMed  Google Scholar 

  • Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620

    Article  PubMed  CAS  Google Scholar 

  • Excoffier L, Laval G, Schneider S (2006) An integrated software package for population genetics data analysis. Arlequin v3.1. http://cmpg.unibe.ch/software

  • Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567–1587

    PubMed  CAS  Google Scholar 

  • Folkertsma RT, Frederick H, Rattunde W (2005) The pattern of genetic diversity of Guinea-race Sorghum bicolor (L.) Moench landraces as revealed with SSR markers. Theor Appl Genet 111:399–409

    Article  PubMed  CAS  Google Scholar 

  • Gao H, Williamson S, Bustamante CD (2007) An MCMC approach for joint inference of population structure and inbreeding rates from multi-locus genotype data. Genetics (online)

  • Goudet J (2002) FSTAT, a program to estimate and test gene diversity and fixation indices. (version 2 9 3 2)

  • Hails RS, Morley K (2005) Genes invading new populations: a risk assessment perspective. Trends Ecol Evol 20:245–252

    Article  PubMed  Google Scholar 

  • Hardy OJ, Vekemans X (2002) SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol Ecol 2:618–620

    Article  Google Scholar 

  • Harlan JR, de Wet JMJ (1972) A simplified classification of cultivated sorghum. Crop Sci 12:172–176

    Article  Google Scholar 

  • Hokanson KE, Ellstrand NC, Ouedragado JT, Olwenya PA, Schaals B, Reybould AF (2010) Biofortified sorghum in Africa: using problem formulation to inform risk assessment. Nat Biotech 28:900–903

    Article  CAS  Google Scholar 

  • IBPGR/ICRISAT (1993) Descriptors for sorghum (Sorghum bicolor (L.) Moench). International Board of Plant Genetic Resources, Rome, Italy. International Crop Research Institute for Semi-Arid Tropics, Patancheru

    Google Scholar 

  • Kalinowski S (2005) HP-RARE 1.0: a computer program for performing rarefaction on measures of allelic richness. Mol Ecol 5:187–189

    Article  CAS  Google Scholar 

  • Kong L, Dong J, Hart GE (2000) Characteristics, linkage-map positions and allelic differentiation of Sorghum bicolor (L.) Moench DNA simple-sequence repeats (SSRs). Theor Appl Genet 101:438–448

    Article  CAS  Google Scholar 

  • Levin DA, Kerster HW (1974) Gene flow in seeds plants. Evol Biol 7:139–220

    Google Scholar 

  • Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics Research Center, North Carolina State University, Raleigh

  • Loiselle BA, Sork VL, Nason J, Graham C (1995) Spatial genetic structure of a tropical understory shrub, Psychotria officinalis (Rubiaceae). Am J Bot 82:1420–1425

    Article  Google Scholar 

  • Lowe A, Harris S, Ashton P (2004) Ecological genetics: design analysis and application. Blackwell Publishing, USA, pp 70–72

    Google Scholar 

  • Mace ES, Buhariwalla HK, Crouch JH (2003) A high throughput DNA extraction protocol for molecular breeding programs. Plant Mol Biol Report 21:459a–459h

    Article  Google Scholar 

  • Manly BFJ (1994) Multivariate statistical methods: a primer. Chapman and Hall, New York

    Google Scholar 

  • Mann JA, Kimber CT, Miller FR (1983) The origin and early cultivation of sorghums in Africa. Texas Agricultural Experiment Station, Bulletin 1454

  • Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27:209–220

    PubMed  CAS  Google Scholar 

  • Manzelli M, Pileri L, Lacerenza N, Benedettelli S, Vecchio V (2007) Genetic diversity assessment in Somali sorghum (Sorghum bicolor (L.) Moench) accessions using microsatellite markers. Biodivers Conserv 16:1715–1730

    Article  Google Scholar 

  • Menz MA, Klein RR, Unruh NC, Rooney WL, Klein PE, Mullet JE (2004) Genetic diversity of public inbreds of sorghum determined by mapped AFLP and SSR markers. Crop Sci 44:1236–1244

    Article  CAS  Google Scholar 

  • Miller MP (2000) Tools for Population Genetic Analyses version 1.3. A Windows program for the analysis of allozyme and molecular population genetic data. Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ

  • Muraya MM, Hartwig HH, Mutegi E, Kanyenji BM, Sagnard F, de Villiers S, Kiambi D, Heiko K, Parzies HK (2010) Geographical patterns of phenotypic diversity and structure of Kenyan wild sorghum populations (Sorghum spp.) as an aid to germplasm collection and conservation strategy. Plant Genet Resour 8:217–224

    Article  Google Scholar 

  • Muraya MM, Mutegi E, Geiger HH, de Villiers S M, Sagnard F, Kanyenji BM, Kiambi D, Parzies HK (2011) Wild sorghum from different eco-geographic regions of Kenya display a mixed mating system. Theor Appl Genet 122:1631–1639

    Google Scholar 

  • Muteg 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 in Kenya: implications for conservation and crop-to-wild gene flow. Genet Resour Crop Evol 57:243–253

    Article  Google Scholar 

  • Nei M (1987) Molecular evolutionary genetics. Columbia University press, New York

    Google Scholar 

  • Pilson D, Prendeville HR (2004) Ecological effects of transgenic crops and the escape of transgenes into wild populations. Ann Rev Ecol Evol Syst 35:149–174

    Article  Google Scholar 

  • Price HJ, Dillon SL, Hodnett G, Rooney WL, Ross L, Johnston JS (2005) Genome Evolution in the Genus Sorghum (Poaceae). Ann Bot 95:219–227

    Article  PubMed  CAS  Google Scholar 

  • Pritchard JK, Stephens M, Donnely P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    PubMed  CAS  Google Scholar 

  • Pritchard JK, Wen X, Falush D (2007) Documentation for structure software: Version 2.2. http://www.biovip.org/UploadFiles/2009-12/1219737299.pdf

  • Rabbi IY, Parzies HK, Kiambi D, Haussmann BIG, Folkertsma R, Geiger HH (2010) Experimental studies on pollen-mediated gene flow in Sorghum bicolor (L.) Moench using malesterile bait plants. Plant Breed doi:10.1111/j.1439-0523.2010.01775.x

  • Rich PJ, Grenier C, Ejeta G (2004) Striga resistance in the wild relatives of sorghum. Crop Sci 44:2221–2229

    Article  Google Scholar 

  • Rieseberg LH (1991) Homoploid reticulate evolution in Helianthus: evidence from ribosomal genes. Am J Bot 78:1218–1237

    Article  Google Scholar 

  • Rieseberg LH (1997) Hybrid origins of plant species. Annu Rev Ecol Syst 28:359–389

    Article  Google Scholar 

  • Rieseberg LH, Raymond O, Rosenthal DM, Lai Z, Livingstone K, Nakazato T, Durphy JL, Schwarzbach AE, Donovan LA, Lexer C (2003) Major ecological transitions in wild sunflowers facilitated by hybridization. Science 301:1211–1216

    Article  PubMed  CAS  Google Scholar 

  • Rousset F (1997) Genetic differentiation and estimation of gene flow from F statistics under isolation by distance. Genetics 145:1219–1228

    PubMed  CAS  Google Scholar 

  • Schloss SJ, Mitchell SE, White GM, Kukatla R, Bowers JE, Paterson AH, Kresovich S (2002) Characterization of RFLP probe sequences for gene discovery and SSR development in Sorghum bicolor (L.) Moench. Theor Appl Genet 105:912–920

    Article  PubMed  CAS  Google Scholar 

  • Slatkin M (1993) Isolation by distance in equilibrium and non-equilibrium populations. Evolution 47:264–279

    Article  Google Scholar 

  • Snowden JD (1936) The cultivated races of Sorghum. Adlard and Son, London

    Google Scholar 

  • 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 180(10):249

    Google Scholar 

  • Soltis DE, Soltis PS (1999) Polyploidy: recurrent formation and genome evolution. Trends Ecol Evol 14:348–352

    Article  PubMed  Google Scholar 

  • Stewart CN, Halfhill MD, Warwick SI (2003) Genetic modification: transgene introgression from genetically modified crops to their wild relatives. Nat Rev Genet 4:806–817

    Article  PubMed  CAS  Google Scholar 

  • Tamura K, Dudley J, Nei M, Kumar S (2006) Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Version 4.0 (Beta release) Center for Evolutionary Functional Genomics Bio design Institute, Arizona State University

  • Taramino G, Tarchini R, Ferrario S, Lee M, Pe` ME (1997) Characterisation and mapping of simple sequence repeats (SSR) in Sorghum bicolor. Theor Appl Genet 95:66–72

    Article  CAS  Google Scholar 

  • R Development Core Team (2008). R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0. http://www.R-project.org

  • Uptmoor R, Wenzel W, Friedt W, Donaldson G, Ayisi K (2003) Comparative analysis on the genetic relatedness of sorghum bicolor accessions from Southern Africa by RADPs, AFLPs and SSRs. Theor Appl Genet 106:1316–1325

    PubMed  CAS  Google Scholar 

  • Weir BS (1996) Genetic data analysis II. Sinauer Associates, Sunderland

    Google Scholar 

Download references

Acknowledgments

This study was funded by the United States Agency for International Development (USAID) Biotechnology and Biodversity Interface Program (BBI; Dr. Fabrice Sagnard), the Institute of plant Breeding and Population Genetics at the University of Hohenheim, Germany, and German Academic Exchange Service (DAAD: A0523923). USAID-BBI funded field experiments and collection trips. Costs of laboratory infrastructure and consumables at the Institute of plant Breeding and Population Genetics at the University of Hohenheim, Germany, were shared by BBI and the University of Hohenheim. We acknowledge the Kenya Agricultural Research Institute and Ben Kanyenji who supervised the collection of genetic materials in full compliance with regulations according to the Convention on Biological Diversity (CBD).

Author information

Authors and Affiliations

  1. Institute of Plant Breeding, Seed science and Population Genetics, University of Hohenheim, Fruwirthstrasse 21, 70599, Stuttgart, Germany

    Moses M. Muraya, Heiko K. Parzies & Hartwig H. Geiger

  2. Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstrasse 3, 06466, Gatersleben, Germany

    Moses M. Muraya

  3. CIRAD, UMR Développement et Amélioration des Plantes, c/o ILRI, PO Box 30709, Nairobi, Kenya

    Fabrice Sagnard

  4. International Crops Research Institute for the Semi-Arid Tropics (ICRISAT-Nairobi), P.O Box 39063-00623, Nairobi, Kenya

    Santie de Villiers, Evans Mutegi, Fabrice Sagnard & Dan Kiambi

  5. Kenya Agricultural Research Institute (KARI), P.O. Box 30148, Nairobi, Kenya

    Evans Mutegi

  6. Kenya Agricultural Research Institute (KARI-Embu), P.O. Box 27-60100, Embu, Kenya

    Ben M. Kanyenji

Authors
  1. Moses M. Muraya
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Santie de Villiers
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Heiko K. Parzies
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Evans Mutegi
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Fabrice Sagnard
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Ben M. Kanyenji
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Dan Kiambi
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Hartwig H. Geiger
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Moses M. Muraya.

Additional information

Communicated by X. Xia.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary Table S1 (DOC 35 kb)

Supplementary Table S2 (DOC 88 kb)

Supplementary Table S3 (DOC 40 kb)

122_2011_1608_MOESM4_ESM.doc

Figure S4: Bar plots of the INSTRUCT analysis. Each of the 62 wild sorghum populations is represented by a vertical bar being partitioned in up to K = 5 coloured segments that designate the population’s estimated membership fraction in the inferred subgroups. Populations are sorted according to regions of origin. Populations were sorted according to regions of origin and were collected from Turkana (1–17), Western (18–29), Coast (30–48) and Eastern (49–62) were collected regions of Kenya, respectively (DOC 369 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Muraya, M.M., de Villiers, S., Parzies, H.K. et al. Genetic structure and diversity of wild sorghum populations (Sorghum spp.) from different eco-geographical regions of Kenya. Theor Appl Genet 123, 571–583 (2011). https://doi.org/10.1007/s00122-011-1608-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-011-1608-6

Keywords

Search

Navigation