Hostname: page-component-cd9895bd7-gvvz8 Total loading time: 0 Render date: 2024-12-29T14:51:11.717Z Has data issue: false hasContentIssue false
  • English
  • Français

Genetic diversity in East African finger millet (Eleusine coracana (L.) Gaertn) landraces based on SSR markers and some qualitative traits

Published online by Cambridge University Press:  01 May 2014

E. O. Manyasa ,
P. Tongoona ,
P. Shanahan ,
M. A. Mgonja  and
S. de Villiers
E. O. Manyasa*
Affiliation:
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), PO Box 39063, Nairobi00623, Kenya School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg3209, South Africa
P. Tongoona
Affiliation:
School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg3209, South Africa
P. Shanahan
Affiliation:
School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg3209, South Africa
M. A. Mgonja
Affiliation:
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), PO Box 39063, Nairobi00623, Kenya
S. de Villiers
Affiliation:
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), PO Box 39063, Nairobi00623, Kenya School of Pure and Applied Sciences, Pwani University, PO Box 195, Kilifi80108, Kenya
*
*Corresponding author. E-mails: [email protected]; [email protected]
Get access Rights & Permissions [Opens in a new window]

Abstract

In this study, genetic diversity in 340 finger millet accessions from Kenya, Tanzania and Uganda and 15 minicore accessions was assessed using 23 single-sequence repeat markers and five qualitative traits. Nineteen markers were polymorphic with a mean polymorphic information content value of 0.606 and a range of 0.035–0.889, with allele size ranging from 148 to 478. A total of 195 alleles were detected (range of 3–23 and average of 10.3 alleles per locus), with 57.7% being rare and 17.4% being private. Differentiation between the accessions of the three countries was weak, with most of the genetic diversity being explained by variability within the countries and subregions than by that among the countries and subregions. The highest genetic diversity was observed in the Kenyan accessions (0.638 ± 0.283) and the least in the Ugandan accessions (0.583 ± 0.264). The highest differentiation based on Wright's fixation index was observed between the Ugandan and Tanzanian accessions (FST= 0.117; P< 0.001). There was no association between the morphological traits assessed and the genetic classes observed. The low variability between the countries could be attributed to a shared gene pool, as the crop originated from the East African region. Farmers' selection for adaptation and end use could have contributed to the high diversity within the countries. Concerted efforts need to be made to characterize the large germplasm stocks in East Africa for their effective conservation and utilization. The lack of representation of accessions from the three countries in all global minicore diversity clusters points to the need to explore the East African germplasm to identify the diversity not captured earlier to be included in the global repository.

Keywords

East Africafinger millet (Eleusine coracana)genetic diversitymolecular characterizationSSR markers
Type
Research Article
Information
Plant Genetic Resources , Volume 13 , Issue 1 , April 2015 , pp. 45 - 55
Copyright
Copyright © NIAB 2014 

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

Adoukonou-Sagbadja, H, Wagner, C, Dansi, A, Ahlemeyer, J, Daïnou, O, Akpagana, K, Ordon, F and Friedt, W (2007) Genetic diversity and population differentiation of traditional fonio millet (Digitaria spp.) landraces from different agro-ecological zones of West Africa. Theoretical and Applied Genetics 115: 917–931.Google Scholar
Anderson, JA, Churchill, GA, Autrique, JE, Tanksley, SD and Sorrells, ME (1993) Optimizing parental selection for genetic linkage maps. Genome 36: 181–186.CrossRefGoogle ScholarPubMed
Barro-Kodombo, C, Sagnard, F, Chantereau, J, Deu, M, vom Brocke, K, Durand, P, Gozé, E and Zongo, JD (2010) Genetic structure among sorghum landraces as revealed by morphological variation and microsatellite markers in three agro-climatic regions of Burkina Faso. Theoretical and Applied Genetics 120: 1511–1523.Google Scholar
Belkhir, K, Borsa, P, Chikhi, L, Raufaste, N and Bonhomme, F (2002) GENETIX 4.04, logiciel sous Windows™ pour la génétique des populations. Laboratoire Génome, Populations, Interactions, CNRS UMR 5000, Université de Montpellier II, Montpellier, France. (http://www.univ-montp2.fr/~genetix/genetix/constr.htm#download).Google Scholar
Bezawelataw, K, Sripichitt, P, Wongyai, W and Hongtrakul, V (2007) Phenotypic diversity of Ethiopian finger millet [Eleusine coracana (L.) Gaertn] in relation to geographical regions as an aid to germplasm collection and conservation strategy. Kasetsart Journal (National Science) 41: 7–16.Google Scholar
Bezawelataw, K (2011) Genetic diversity of finger millet [Eleusine coracana (L.) Gaertn] landraces characterized by random amplified polymorphic DNA analysis. Innovative Systems Design and Engineering 2: 207–217.Google Scholar
de Wet, JMJ (1995) Finger millet. In: Smartt, J and Simmonds, NW (eds) Evolution of Crop Plants. 2nd edn. Harlow: Longman Scientific and Technical, pp. 137–140.Google Scholar
de Wet, JMJ, Prasada Rao, KE, Brink, DG and Mengesha, MH (1984) Systemic evolution of Eleusine coracana (Graminea). American Journal of Botany 7: 550–557.CrossRefGoogle Scholar
Dida, MM, Srinivasacary, RS, Ramakrishnan, S, Bennetzen, JL, Gale, MD and Devos, KM (2007) The genetic map of finger millet, Eleusine coracana . Theoretical and Applied Genetics 114: 321–332.Google Scholar
Dida, MM, Wanyera, N, Melanie, L, Dunn, H, Bennetzen, JL and Devos, KM (2008) Population structure and diversity in finger millet (Eleusine coracana) germplasm. Tropical Plant Biology 1: 131–141.CrossRefGoogle Scholar
Excoffier, L, Laval, G and Schneider, S (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 1: 47–50.Google Scholar
Fakrudin, B, Kulkarni, RS, Shashidhar, HE and Hittalmani, S (2004) Genetic diversity assessment of finger millet, Eleusine coracana (Gaertn), germplasm through RAPD analysis. Plant Genetic Resources Newsletter 138: 50–54.Google Scholar
Fitzpatrick, BM (2009) Power and sample size for nested analysis of molecular variance. Molecular Ecology 18: 3961–3966.Google Scholar
Guo, SW and Thompson, EA (1992) Performing the exact test of Hardy–Weinberg proportion for multiple alleles. Biometrics 48: 361–372.Google Scholar
Harlan, JR (1971) Agricultural origins: centres and non-centres. Science 174: 468–474.CrossRefGoogle Scholar
Hilu, KW and de Wet, JMJ (1976) Domestication of Eleusine coracana . Economic Botany 30: 199–208.Google Scholar
IBPGR(1985) Descriptors for Finger Millet. Rome: International Board for Plant Genetic Resources Secretariat, pp. 22.Google Scholar
Jain, SK, Qualset, CO, Bhatt, GM and Wu, KK (1975) Geographic patterns of phenotypic diversity in a world collection of durum wheats. Crop Science 15: 700–704.Google Scholar
Kimani, EN, Wachira, FN and Kinyua, GM (2012) Molecular diversity of Kenyan lablab bean (Lablab purpureus (L.) Sweet) accessions using amplified fragment length polymorphism markers. American Journal of Plant Sciences 3: 313–321.Google Scholar
Kumari, K and Pande, A (2010) Study of genetic diversity in finger millet (Eleusine coracana (L.) Gaertn using RAPD markers. African Journal of Biotechnology 9: 4542–4549.Google Scholar
Kuomi, P, Green, HE, Hartley, S, Jordan, D, Lahec, S, Livett, RJ, Tsang, KW and Ward, DM (2004) Evaluation and validation of the ABI 3700, ABI 3100, and the MegaBACE 1000 capillary array electrophoresis instruments for use with short tandem repeat microsatellite typing in a forensic environment. Electrophoresis 25: 2227–2241.Google Scholar
Lapitan, VC, Brar, DS, Abe, T and Redona, ED (2007) Assessment of genetic diversity of Philippine rice carrying good quality traits using SSR markers. Breeding Science 57: 263–270.CrossRefGoogle Scholar
Liu, K and Muse, SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics Applications Note 21: 2128–2129.Google Scholar
Mace, ES, Buhariwalla, KK, Buhariwalla, HK and Crouch, JH (2003) A high-throughput DNA extraction protocol for tropical molecular breeding programs. Plant Molecular Biology Reporter 21: 459–460.Google Scholar
Naga, BLRI, Mangamoori, LN and Subramanyam, S (2011) Identification and characterization of EST-SSRs in finger millet (Eleusine coracana (L.) Gaertn.). Journal of Crop Science and Biotechnology 15: 9–16.Google Scholar
Pande, S (1992) Biology of and resistance to finger millet blast. Trip Report of Work Done by ICRISAT/NARS Collaborative Project on Blast Disease of Finger Millet in Kenya and Uganda. Hyderabad, India: ICRISAT, pp. 68.Google Scholar
Panwar, P, Saini, RK, Sharma, N, Yadav, D and Kumar, A (2010) Efficiency of RAPD, SSR and Cytochrome P450 gene based markers in accessing genetic variability amongst finger millet (Eleusine coracana) accessions. Molecular Biology Reports 37: 4075–4082.Google Scholar
Perrier, X and Jacquemoud-Collet, JP (2006) DARwin software Available at: DARwin software. http://darwin.cirad.fr/darwin (accessed accessed 12 February 2012).Google Scholar
Ramu, P, Billot, C, Rami, JF, Senthilvel, S, Upadhyaya, HD, Ananda Reddy, L and Hash, CT (2013) Assessment of genetic diversity in the sorghum reference set using EST-SSR markers. Theoretical and Applied Genetics 126: 2051–2064.Google Scholar
Roux, KH (2009) Optimization and troubleshooting in PCR. Cold Spring Harbour Protocols 4: 1–6. doi:10.1101/pdb.ip66.CrossRefGoogle Scholar
Saitou, N and Nei, M (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4: 406–425.Google Scholar
Sharma, R, Deshpande, SP, Senthilvel, S, Rao, VP, Rajaram, V, Hash, CT and Thakur, RP (2010) SSR allelic diversity in relation to morphological traits and resistance to grain mold on sorghum. Crop and Pasture Science 61: 230–240.Google Scholar
Sheulke, M (2000) An economic method for the fluorescent labeling of PCR fragments. Nature Biotechnology 18: 233–234.Google Scholar
Sreenivasaprasad, S, Takan, JP, Obilana, AB, Manyasa, E, Brown, AE, Bandyopadhyay, R and Muthumeenakshi, S (2004) Finger millet blast in East Africa: pathogen diversity and disease management strategies. Final Technical Report R8030. Warwick HRI, University of Warwick, Wellesbourne, Warwickshire: DFID-CPP, pp. 118.Google Scholar
Takan, JP, Akello, B, Esele, JP, Manyasa, EO, Obilana, BA, Audi, PO, Kibuka, J, Odendo, M, Oduori, CA, Ajanga, S, Bandyopadhyay, R, Muthumeenakshi, S, Coll, R, Brown, AE, Talbot, NJ and Sreenivasaprasad, S (2004) Pathogen diversity and management of finger millet blast in East Africa: a summary of project activities and outputs. International Sorghum and Millets Newsletter 45: 66–69.Google Scholar
Tsehaye, Y and Kebebew, F (2002) Morphological diversity and geographical distribution of adaptive traits in finger millet (Eleusine coracana (L.) Gaertn. Subsp. coracana (poaceae) population from Ethiopia. Ethiopian Journal of Biological Sciences 1: 37–62.Google Scholar
Upadhyaya, HD, Gowda, CLL, Pundir, RPS, Reddy, VG and Singh, S (2006) Development of core subset of finger millet germplasm using geographical origin and data on 14 morpho-agronomic traits. Genetic Resources and Crop Evolution 53: 679–685.Google Scholar
Upadhyaya, HD, Gowda, CLL and Sastry, DVSSR (2008) Plant genetic resources management: collection, characterization, conservation and utilization. Journal of SAT Agricultural Research 6: 16.Google Scholar
Upadhyaya, HD, Sarma, NDRK, Ravishankar, CR, Albrecht, T, Narasimhudu, Y, Singh, SK, Varshney, SK, Reddy, VG, Dwivedi, SL, Wanyera, N, Oduori, COA, Mgonja, MA, Kisandu, DB, Parzies, HK and Gowda, CLL (2010) Developing a mini-core collection in finger millet using multi-location data. Crop Science 50: 1924–1931.Google Scholar
Wright, S (1965) The interpretation of population structure by F-statistics with special regard to systems of mating. Evolution 19: 395–420.CrossRefGoogle Scholar
Supplementary material: File

Manyasa Supplementary Material

Tables

Download Manyasa Supplementary Material(File)
File 182.2 KB