Hostname: page-component-cd9895bd7-7cvxr Total loading time: 0 Render date: 2024-12-28T17:15:24.142Z Has data issue: false hasContentIssue false
  • English
  • Français

Impact of farmers' practices and seed systems on the genetic structure of common sorghum varieties in Kenya and Sudan

Published online by Cambridge University Press:  05 February 2010

Ismail Y. Rabbi ,
Hartwig H. Geiger ,
Bettina I. G. Haussmann ,
Dan Kiambi ,
Rolf Folkertsma  and
Heiko K. Parzies
Ismail Y. Rabbi*
Affiliation:
Institute of Plant Breeding, Seed Science, and Population Genetics, University of Hohenheim, 70593Stuttgart, Germany
Hartwig H. Geiger
Affiliation:
Institute of Plant Breeding, Seed Science, and Population Genetics, University of Hohenheim, 70593Stuttgart, Germany
Bettina I. G. Haussmann
Affiliation:
Institute of Plant Breeding, Seed Science, and Population Genetics, University of Hohenheim, 70593Stuttgart, Germany ICRISAT Box 320, Bamako, Mali
Dan Kiambi
Affiliation:
Eastern and Southern Africa International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), PO Box 39063-00623, Nairobi, Kenya
Rolf Folkertsma
Affiliation:
Eastern and Southern Africa International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), PO Box 39063-00623, Nairobi, Kenya
Heiko K. Parzies
Affiliation:
Institute of Plant Breeding, Seed Science, and Population Genetics, University of Hohenheim, 70593Stuttgart, Germany
*
*Corresponding author. E-mail: [email protected]
Get access Rights & Permissions [Opens in a new window]

Abstract

To understand the effect of different farming systems on the dynamics of diversity of sorghum (Sorghum bicolor (L.) Moench) crop, genetic structure of widely used landraces and modern varieties collected from two contrasting agroecosystems, in eastern Sudan and western Kenya, were analysed with 16 polymorphic microsatellite markers. A total of 1104 accessions, grouped into 46 samples from individual farmers, were genotyped. Cluster analysis of the samples from the two countries displayed contrasting patterns. Most strikingly, differently named landraces from western Kenya formed widely overlapping clusters, indicating weak genetic differentiation, while those from eastern Sudan formed clearly distinguishable groups. Similarly, samples of the modern variety from Sudan displayed high homogeneity, whereas the most common modern variety from western Kenya was very heterogeneous. The high degree of fragmentation of farmlands of western Kenya, coupled with planting of different sorghum varieties in the same fields, increases the likelihood of inter-variety gene flow. This may explain the low genetic differentiation between the differently named landraces and heterogeneity of the modern variety from western Kenya. This study highlights the important role of farmers in shaping the genetic variation of their crops and provides population parameter estimates allowing forecasting of the fate of ‘modern’ germplasm (conventional or genetically modified) when introduced into subsistence farming systems.

Keywords

farmers' practicesgenetic structuremicrosatellitesseed systemssorghum varieties
Type
Research Article
Information
Plant Genetic Resources , Volume 8 , Issue 2 , August 2010 , pp. 116 - 126
Copyright
Copyright © NIAB 2010

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Abu Assar, AH, Uptmoor, R, Abdelmula, AA, Salih, M, Ordon, F and Friedt, W (2005) Genetic variation in sorghum germplasm from Sudan ICRISAT and USA assessed by simple sequence repeats (SSRs). Crop Science 45: 1636–1644.CrossRefGoogle Scholar
Aldrich, PR and Doebley, J (1992) Restriction fragment variation in the nuclear and chloroplast genomes of cultivated and wild Sorghum bicolor. Theor. Appl. Genet. 85: 293–302.CrossRefGoogle ScholarPubMed
Almekinders, CJM, Louwaars, NP and de Bruin, GH (1994) Local seed systems and their importance for an modern seed supply in developing countries. Euphytica 78: 207–216.CrossRefGoogle Scholar
Alvarez, N, Garine, E, Khasah, C, Dounias, E, Hossaert-McKey, M and McKey, D (2005) Farmers' practices, metapopulation dynamics, and conservation of agricultural biodiversity on-farm: a case study of sorghum among the Duupa in sub-Sahelian Cameroon. Biological Conservation 121: 533–543.CrossRefGoogle Scholar
Ayana, A, Bryngelsson, T and Bekele, E (2000) Genetic variation of Ethiopian and Eritrean sorghum (Sorghum bicolor (L.) Moench) germplasm assessed by random amplified polymorphic DNA (RAPD). Genetic Resources and Crop Evolution 47: 471–482.CrossRefGoogle Scholar
Ayoub, AT (1999) Land degradation, rainfall variability and food production in the Sahelian zone of the Sudan. Land Degradation and Development 10: 489–500.3.0.CO;2-U>CrossRefGoogle Scholar
Barnaud, A, Deu, M, Garine, E, McKey, D and Joly, HI (2007) Local genetic diversity of sorghum in a village in northern Cameroon: structure and dynamics of landraces. Theoretical and Applied Genetics 114: 237–248.CrossRefGoogle Scholar
Barnaud, A, Trigueros, G, McKey, D and Joly, HI (2008) High outcrossing rates in fields with mixed sorghum landraces: how are landraces maintained? Heredity 101: 445–452.CrossRefGoogle ScholarPubMed
Barnaud, A, Deu, M, Garine, E, Chantereau, J, Bolteu, J, Koïda, EO, McKey, D and Joly, HI (2009) A weed–crop complex in sorghum: the dynamics of genetic diversity in a traditional farming system. American Journal of Botany 96: 1869–1879.CrossRefGoogle Scholar
Bellon, MR and Brush, SB (1994) Keepers of maize in Chiapas, Mexico. Economic Botany 48: 196–209.CrossRefGoogle Scholar
Bhattramakki, D, Dong, J, Chhabra, AK and Hart, GE (2000) An integrated SSR and RFLP linkage map of Sorghum bicolor (L.) Moench. Genome 43: 988–1002.CrossRefGoogle ScholarPubMed
Bohonak, AJ (2002) IBD (isolation by distance): a program for analyses of isolation by distance. Journal of Heredity 93: 153–154.CrossRefGoogle ScholarPubMed
Borrell, AK, Tao, Y and McIntyre, CL (1999) Physiological basis, QTL and MAS of the stay-green drought resistance trait in grain sorghum. Available at http://www.cimmyt.org/ABC/map/research_tools_results/WSMolecular/WorkshopMolecular/WorkshopMolecularcontents.htm (accessed 7 February 2008).Google Scholar
Botstein, D, White, RL, Skolnick, M and Davis, RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics 32: 314–331.Google ScholarPubMed
Brown, SM, Hopkins, MS, Mitchell, SE, Senior, ML, Wang, TY, Duncan, RR, Gonzalez Candelas, F and Kresovich, S (1996) Multiple methods for the identification of polymorphic simple sequence repeats (SSRs) in sorghum (Sorghum bicolor (L.) Moench). Theoretical and Applied Genetics 93: 190–198.CrossRefGoogle ScholarPubMed
Deu, M, Sagnard, F, Chantereau, J, Calatayud, C, Hérault, D, Mariac, C, Pham, J-L, Vigouroux, Y, Kapran, I, Traore, PS, Mamadou, A, Gerard, B, Ndjeunga, J and Bezançon, G (2008) Niger-wide assessment of in situ sorghum genetic diversity with microsatellite markers. Theoretical and Applied Genetics 116: 903–913.CrossRefGoogle ScholarPubMed
Djè, Y, Forcioli, D, Ater, M, Lefèbre, C and Vekemans, X (1999) Assessing population genetic structure of sorghum landraces from North-Western Morocco using allozyme and microsatellite markers. Theoretical and Applied Genetics 99: 157–163.CrossRefGoogle Scholar
Doggett, H (1988) Sorghum. 2nd edn. Essex: Longman.Google Scholar
Ellstrand, NC (2001) When transgenes wander, should we worry? Plant Physiology 125: 1543–1545.CrossRefGoogle ScholarPubMed
Ellstrand, NC (2003) Dangerous liaisons – when cultivated plants mate with their wild relatives. Baltimore, MD/London: Johns Hopkins University Press, p. 244.Google Scholar
Ellstrand, NC, Prentice, HC and Hancock, JF (1999) Gene flow and introgression from domesticated plants into their wild relatives. Annual Review of Ecology and Systematic 30: 539–563.CrossRefGoogle Scholar
Evanno, G, Regnaut, S and Goudet, J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14: 2611–2620.CrossRefGoogle ScholarPubMed
Excoffier, L, Laval, G and Schneider, S (2005) Arlequin ver. 30: an integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 1: 47–50.Google Scholar
FAOSTAT. Available at http://faostat.fao.org/ (accessed 3 October 2009).Google Scholar
Folkertsma, RT, Haussmann, BIG, Parzies, HK, Hoffmann, V and Geiger, HH (2005a) Arresting the scourge of Striga on sorghum in Africa by combining the strengths of marker-assisted backcrossing and farmer-participatory selection. In: Deutscher Tropentag, October 11–13, 2005, Hohenheim. Available at http://www.tropentag.de/2005/abstracts/links/Parzies_NfQBcDqx.pdf (accessed 11 May 2009).Google Scholar
Folkertsma, RT, Rattunde, HFW, Chandra, S, Raju, GS and Hash, CT (2005b) The pattern of genetic diversity of Guinea-race Sorghum bicolor (L.) Moench landraces as revealed with SSR markers. Theoretical and Applied Genetics 111: 399–409.CrossRefGoogle ScholarPubMed
Gepts, P and Papa, R (2003) Possible effects of (trans)gene flow from crops on the genetic diversity from landraces and wild relatives. Env Biosafety Res 2: 89–103.CrossRefGoogle ScholarPubMed
Ghebru, B, Schmidt, RJ and Bennetzen, JL (2002) Genetic diversity of Eritrean sorghum landraces assessed with simple sequence repeat (SSR) markers. Theoretical and Applied Genetics 105: 229–236.CrossRefGoogle ScholarPubMed
Goudet, J (1995) Fstat version 1.2: a computer program to calculate F-statistics. Journal of Heredity 86: 485–486.CrossRefGoogle Scholar
Kaeuffer, R, Réale, D, Coltman, DW and Pontier, D (2007) Detecting population structure using STRUCTURE software: effect of background linkage disequilibrium. Heredity 99: 374–380.CrossRefGoogle ScholarPubMed
Kim, J-S, Klein, PE, Klein, RR, Price, HJ, Mullet, JE and Stelly, DM (2005) Chromosome identification and nomenclature of Sorghum bicolor. Genetics 169: 955–965.CrossRefGoogle ScholarPubMed
Liu, K and Muse, S (2004) POWERMARKER: new genetic data analysis software version 3. Available at http://www.powermarker.net.Google Scholar
Lowe, A, Harris, S and Ashton, P (2004) Ecological genetics: design, analysis and application. 1st edn. Oxford: Blackwell Publishing, p. 60.Google Scholar
Lu, B-R and Yang, C (2009) Gene flow from genetically modified rice to its wild relatives: assessing potential ecological consequences. Biotechnology Advances 27: 1083–1091.CrossRefGoogle ScholarPubMed
Mace, ES, Buhariwalla, HK and Crouch, JHA (2003) A high throughput DNA extraction protocol for molecular breeding programs. Plant Molecular Biology Report 21: 459–460.CrossRefGoogle Scholar
Menz, MA, Klein, RR, Mullet, JE, Obert, JA, Unruh, NC and Klein, PEA (2002) A high-density genetic map of Sorghum bicolor (L.) Moench based on 2926 AFLP (R), RFLP and SSR markers. Plant Molecular Biology 48: 483–499.CrossRefGoogle Scholar
Morrell, PL, Williams-Coplin, TD, Lattu, AL, Bowers, JE, Chandler, JM and Patterson, AH (2005) Crop-to-weed introgression has impacted allelic composition of johnsongrass populations with and without recent exposure to cultivated sorghum. Molecular Ecology 14: 2143–2154.CrossRefGoogle ScholarPubMed
Ngugi, HK, King, SB, Abayo, GO and Reddy, YVR (2002) Prevalence, incidence, and severity of sorghum diseases in western Kenya. Plant Disease 86: 65–70.CrossRefGoogle ScholarPubMed
Parzies, HK, Spoor, W and Ennos, RA (2004) Inferring seed exchange between farmers from population genetic structure of barley landrace Arabi Aswad from Northern Syria. Genetic Resources and Crop Evolution 51: 471–478.CrossRefGoogle Scholar
Perrier, X, Flori, A and Bonnot, F (2003) Data analysis methods. In: Hamon, P, Seguin, M, Perrier, X and Glaszmann, JC (eds) Genetic Diversity of Cultivated Tropical Plants. Montpellier: Enfield Science Publishers, pp. 43–76.Google Scholar
Pressoir, G and Berthaud, J (2004) Population structure and a strong divergent selection shape phenotypic diversification in maize landraces. Heredity 92: 95–101.CrossRefGoogle Scholar
Pritchard, JK, Stephens, M and Donnelly, P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 45–59.CrossRefGoogle ScholarPubMed
Rabbi, IY, Parzies, HK, Kiambi, D, Haussmann, BIG, Folkertsma, R and Geiger, HH (2010) Experimental studies on pollen-mediated gene flow in Sorghum bicolor (L.) Moench using male-sterile bait plants. Under review in Plant Breeding.CrossRefGoogle Scholar
Schloss, SJ, Mitchell, SE, White, GM, Kukatla, R, Bowers, JE, Paterson, AH and Kresovich, S (2002) Characterization of RFLP probe sequences for gene discovery and SSR development in Sorghum bicolor (L.) Moench. Theoretical and Applied Genetics 105: 912–920.CrossRefGoogle ScholarPubMed
Smith, JSC, Kresovich, S, Hopkins, MS, Mitchell, SE, Dean, RE, Woodman, WL, Lee, M and Porter, K (2000) Genetic diversity among elite sorghum inbred lines assessed with simple sequence repeats. Crop Science 40: 226–232.CrossRefGoogle Scholar
Snow, AA (2003) Genetic engineering: unnatural selection. Nature 424: 619.CrossRefGoogle ScholarPubMed
Taramino, G, Tarchini, R, Ferrario, S, Lee, M and Pe, ME (1997) Characterization and mapping of simple sequence repeats (SSRs) in Sorghum bicolor. Theoretical and Applied Genetics 95: 66–72.CrossRefGoogle Scholar
Teshome, A, Baum, BR, Fahrig, L, Torrance, JK, Arnason, TJ and Lambert, JD (1997) Sorghum [Sorghum bicolor (L.) Moench] landrace variation and classification in North Shewa and South Welo, Ethiopia. Euphytica 97: 255–263.CrossRefGoogle Scholar
Uptmoor, R, Wenzel, W, Friedt, W, Donaldson, G and Ayisi, K (2003) Comparative analysis on the genetic relatedness of Sorghum bicolor accessions from Southern Africa by RAPDs AFLPs and SSRs. Theoretical and Applied Genetics 106: 1316–1325.CrossRefGoogle ScholarPubMed
vom Brocke, K, Christinck, A, Welteien, R, Presterl, T and Geiger, HH (2003) Farmers' seed systems and management practices determine pearl millet genetic diversity patterns in semi-arid regions of India. Crop Science 43: 1680–1689.CrossRefGoogle Scholar
Warwick, SI, Beckie, HJ and Hall, MLM (2009) Gene flow, invasiveness, and ecological impact of genetically modified crops. Annals of New York Academy of Sciences 1168: 72–99.CrossRefGoogle ScholarPubMed
Weir, BS (1996) Genetic Data Analysis II: Methods for Discrete Population Genetic Data. Sunderland, MA: Sinauer Associates.Google Scholar
Zeven, AC (1998) Landraces: a review of definitions and classifications. Euphytica 104: 127–139.CrossRefGoogle Scholar
Supplementary material: File

Rabbi supplementary material

Rabbi supplementary material

Download Rabbi supplementary material(File)
File 551.4 KB