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Genetic variation in lowland sorghum (Sorghum bicolor (L.) Moench) landraces assessed by simple sequence repeats

Published online by Cambridge University Press:  26 June 2014

Beyene Amelework ,
Hussien Shimelis ,
Pangirayi Tongoona ,
Mark Laing  and
Fentahun Mengistu
Beyene Amelework*
Affiliation:
African Center for Crop Improvement, University of KwaZulu-Natal, Private Bag X01, Scottsville 3209, Pietermaritzburg, South Africa
Hussien Shimelis
Affiliation:
African Center for Crop Improvement, University of KwaZulu-Natal, Private Bag X01, Scottsville 3209, Pietermaritzburg, South Africa
Pangirayi Tongoona
Affiliation:
African Center for Crop Improvement, University of KwaZulu-Natal, Private Bag X01, Scottsville 3209, Pietermaritzburg, South Africa
Mark Laing
Affiliation:
African Center for Crop Improvement, University of KwaZulu-Natal, Private Bag X01, Scottsville 3209, Pietermaritzburg, South Africa
Fentahun Mengistu
Affiliation:
Ethiopian Institute of Agricultural Research, P.O. Box 2003, Addis Ababa, Ethiopia
*
*Corresponding authors:Corresponding author. E-mail: amele_g@yahoo.com; assefa@ukzn.ac.za
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Abstract

The regions of north-eastern Ethiopia are known for their high levels of sorghum genetic diversity, and for being drought prone. For centuries, sorghum has been developed and maintained by farmers for its adaptation to the marginal and heterogeneous environment of these regions. The objective of this study was to examine the genetic diversity and population structure of 200 sorghum landraces collected from seven lowland districts, using 30 microsatellite markers sampled from all linkage groups of the sorghum genome. Both distance-based and model-based analytical approaches were used to analyse the data. The data analysis revealed that there was a large variation among all the markers under study. The values of polymorphic information content ranged from 0.26 to 0.88, with a mean value of 0.61, reflecting the high discriminating ability of the markers studied. The mean value of total gene diversity was 0.69, which partitioned 86% among the landraces and 14% within the landraces. Gene diversity among the landraces was largely due to the variation among the genotypes within the geographic origins. Landraces sampled from different collection sites appeared to cluster together, indicating the existence of a high level of gene flow among the sites of collection. This indicates that a relatively small, random collection of landraces would capture the bulk of genetic diversity in the target area. A moderately high level of genetic differentiation and a relatively low level of gene flow were observed between sorghum races and maturity groups. Given that the target area is marginal, drought prone and heterogeneous, the study of genetic diversity among sorghum landraces could serve as an important indicator of valuable alleles for drought tolerance in future sorghum improvement programmes.

Keywords

drought tolerancegenetic diversitymicrosatellite markersSorghum bicolor
Type
Research Article
Information
Plant Genetic Resources , Volume 13 , Issue 2 , August 2015 , pp. 131 - 141
Copyright
Copyright © NIAB 2014 

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References

Aldrich, PR and Doebley, J (1992) Restricted fragment variation in the nuclear and chloroplast genome of cultivated and wild Sorghum bicolor . Theoretical and Applied Genetics 2: 334–340.Google Scholar
Anas, T and Yoshida, T (2004) Genetic diversity among Japanese cultivated sorghum assessed with simple sequence repeat markers. Plant Production Science 7: 217–223.Google 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: 417–482.CrossRefGoogle Scholar
Ayana, A, Bryngelsson, T and Bekele, E (2001) Geographic and altitudinal allozyme variation in sorghum (Sorghum bicolor (L.) Moench) landraces from Ethiopia and Eritrea. Hereditas 135: 1–12.Google Scholar
Billot, C, Rivallan, R, Sall, MN, Fonceka, D, Deu, M, Glaszmann, JC, Noyer, JL, Rami, JF, Risterucci, AM, Wincker, P, Ramu, P and Hash, CT (2012) A reference microsatellite kit to assess for genetic diversity of Sorghum bicolor (Poaceae). American Journal of Botany 99: e245–e250.Google Scholar
Bouchet, S, Pot, D, Deu, M, Rami, JF, Billot, C, Perrier, X, Rivallan, R, Gardes, L, Xia, L, Wenzl, P, Kilian, A and Glaszmann, JC (2012) Genetic structure, linkage disequilibrium and signature of selection in sorghum: lessons from physically anchored DArT markers. PLOS ONE 7: e33470.CrossRefGoogle ScholarPubMed
Case, AM, Mitchell, SE, Hamblin, MT, Sun, H, Bowers, JE, Paterson, AH, Aquadro, CF and Kresovich, S (2005) Diversity and selection in sorghum: simultaneous analysis using simple sequence repeats. Theoretical and Applied Genetics 111: 23–30.Google Scholar
CSA(2012) Report on area and production of crops. Agricultural sample survey on private peasant holdings of 2011/2012 Meher season. Central statistic Authority, Addis Ababa, Ethiopia.Google Scholar
Deu, M, Sagnard, F, Chantereau, J, Calatayud, C, Vigouroux, Y, Pham, JL, Mariac, C, Kapran, I, Mamadoo, A, Gerard, B, Ndjeunga, J and Bezancon, G (2010) Spatio-temporal dynamics of genetic diversity in Sorghum bicolor in Nigeria. Theoretical and Applied Genetics 120: 1301–1313.Google Scholar
Dillon, SL, Lawrence, PK and Henry, RJ (2005) The new use of Sorghum bicolor-derived SSR markers to evaluate genetic diversity in 17 Australian Sorghum species. Plant Genetic Resources 3: 19–28.Google Scholar
Dje, Y, Forciolo, D, Ater, M, Lefèbvre, 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.Google Scholar
Dje, Y, Heuertz, M, Lefèbvre, C and Vekemans, X (2000) Assessment of genetic diversity within and among germplasm accessions in cultivated sorghum using microsatellite markers. Theoretical and Applied Genetics 100: 918–925.Google 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.Google Scholar
Ganapathy, KN, Gomashe, SS, Rakshit, S, Prabhakar, B, Ambekar, SS, Ghorade, RB, Biradar, BD, Saxena, U and Patil, JV (2012) Genetic diversity revealed utility of SSR markers in classifying parental lines and elite genotypes of sorghum (Sorghum bicolor L. Moench). Australian Journal of Crop Science 11: 1486–1493.Google Scholar
Geleta, N, Labuschagne, MT and Viljoen, CD (2006) Genetic diversity analysis in sorghum germplasm as estimated by AFLP, SSR and morpho-agronomical markers. Biodiversity Conservation 15: 3251–3265.CrossRefGoogle Scholar
Goudet, J (2001) FSTAT, a programme to estimate and test gene diversities and fixation index (Version 2.9.3). Available at http://www.unil.ch/popgen/software/fstat.html.Google Scholar
Harlan, JR (1975) Crops and Man. Madison, WI: The American Society of Agronomy, Inc. and the Crop Science Society of America, Inc.Google Scholar
Harlan, JR and de Wet, JMJ (1972) A simplified classification of cultivated sorghum. Crop Science 12: 172–176.Google Scholar
Hartl, DL and Clark, AG (1997) Principle of Population Genetics. 3rd edn. Sunderland, MA: Sinauer Associates, Inc.Google Scholar
Kalinowski, ST (2005) HP-RARE1.0: a computer program for performing rarefaction on measures of allelic richness. Molecular Ecology Notes 5: 187–189.Google Scholar
Kimberley, B, Ritter, C, Lynne, M, Ian, DG, David, RJ and Scott, CC (2007) An assessment of the genetic relationship between sweet and grain sorghums within Sorghum bicolor ssp. bicolor (L.) Moench using AFLP markers. Euphytica 157: 161–176.Google Scholar
Kong, L, Dong, J and Hart, GE (2000) Characteristics, linkage-map positions and allelic differentiation of Sorghum bicolor (L.) Moench DNA simple-sequence repeats (SSRs). Theoretical and Applied Genetics 101: 438–448.Google Scholar
Levinson, G and Gutman, GA (1987) Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Molecular Biology and Evolution 4: 203–221.Google Scholar
Manzelli, M, Pileri, L, Lacerenza, N, Bendettelli, S and Vecchio, V (2007) Genetic diversity assessment in Somalia sorghum (Sorghum bicolor (L.) Moench) accessions using microsatellite markers. Biodiversity Conservation 16: 1715–1730.Google Scholar
Menkir, A, Goldsbrough, P and Ejeta, G (1997) RAPD based assessment of genetic diversity in cultivated races of sorghum. Crop Science 37: 564–569.Google Scholar
Menz, MA, Klein, RR, Mullet, JE, Obert, JA, Unruh, NC and Klein, PE (2002) A high-density genetic map of Sorghum bicolor (L.) Moench based on 2926 AFLP, RFLP and SSR markers. Plant Molecular Biology 48: 483–499.Google Scholar
Morris, GP, Ramu, P, Deshpande, SP, Hash, CT, Shah, T, Upadhyaya, HD, Lizarazu, OR, Brown, PJ, Acharya, CB, Mitchell, SE, Harriman, J, Glaubitz, JC, Buckler, ES and Kresovich, S (2013) Population genomic and genome-wide association studies of agro-climatic traits in sorghum. Proceedings of the National Academy of Sciences 110: 453–458.Google Scholar
Nei, M (1987) Molecular Evolutionary Genetic. New York: Columbia University Press.Google Scholar
Nei, M and Li, W (1979) Mathematical method for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences 76: 5256–5273.Google Scholar
Nguni, D, Geleta, M and Bryngelsson, T (2011) Genetic diversity in sorghum (Sorghum bicolor (L.) Moench) accessions of Zambia as revealed by simple sequence repeats (SSR). Hereditas 148: 52–68.CrossRefGoogle ScholarPubMed
Peakall, R and Smouse, PE (2007) GENALEX6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6: 288–295.Google Scholar
Perrier, X and Jacquemoud-Collet, JP (2006) DARwin software. Available at http://www.darwin.cirad.fr/darwin.html.Google Scholar
Perumal, R, Krishnaramanujam, R, Menz, MA, Katile, S, Dahlberg, J, Magill, CW and Rooney, WL (2007) Genetic diversity among sorghum races and working groups based on AFLPs and SSRs. Crop Science 47: 1375–1383.Google Scholar
Pritchard, JK, Stephens, M and Donnelly, P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945–959.Google Scholar
Rieseberg, LH, Archer, MA and Wayne, RK (1999) Transgressive segregation, adaptation and speciation. Heredity 83: 363–372.Google Scholar
Rogstad, SH (2003) Plant DNA extraction using silica. Plant Molecular Biology Reporter 21: 463–464.Google Scholar
Rosenberg, NA (2002) Distruct: a programme for the graphical display of structure results. Available at http://rosenberglab.bioinformatics.med.umich.edu/distruct.html.Google Scholar
Smith, JSC, Kresovich, S, Hopkins, MS, Mitchell, SE, Dean, RE, Woodman, WL, Lee, M and Poster, K (2000) Genetic diversity among elite sorghum inbred lines assessed with simple sequence repeats. Crop Science 40: 226–232.Google Scholar
Teshome, A, Baum, BR, Fahrig, L, Torrance, JK, Arnasson, TJ and Lambert, JD (1997) Sorghum (Sorghum bicolor (L.) Moench) landraces variation in North Shewa and South Welo. Euphytica 97: 255–263.Google Scholar
Teshome, A, Patterson, D, Asfaw, Z, Torrance, JK and Arnsan, JT (2007) Changes of Sorghum bicolor landraces diversity and farmers' selection criteria over space and time, Ethiopia. Genetic Resources and Crop Evolution 54: 1219–1233.Google Scholar
Weir, BS and Cockerham, CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38: 1358–1370.Google Scholar
Zongo, JD, Gouyon, PH, Sarr, A and Sandmeier, M (2005) Genetic diversity and phylogenetic relations among Sahelian sorghum accessions. Genetic Resources and Crop Evolution 52: 869–878.CrossRefGoogle Scholar