Development and Genotyping Potentials of EST-SSRs in Finger Millet (E. Coracana (L.) Gaertn.)

Oscar Nnaemeka Obidiegwu; Heiko Parzies; Jude Ejikeme Obidiegwu

doi:doi:10.11648/j.ijgg.20140203.12

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Development and Genotyping Potentials of EST-SSRs in Finger Millet (E. Coracana (L.) Gaertn.)

Oscar Nnaemeka Obidiegwu, Heiko Parzies, Jude Ejikeme Obidiegwu

Published in International Journal of Genetics and Genomics (Volume 2, Issue 3)

Received: 14 May 2014 Accepted: 29 May 2014 Published: 10 June 2014

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Abstract

Finger millet (E. coracana (L.) Gaertn.) provides food for millions of people in Africa and Asia. In this study, sequence data were mined at the database of National Center for Biotechnology Information (NCBI) with the aim of developing polymorphic expressed sequence tags simple sequence repeat (EST-SSRs) markers. Three selected markers which showed clear polymorphism in pre-testing with 5 accessions were used to characterize some randomly selected 48 accessions from the pool of finger millet core set. The polymorphic information content (PIC) of the developed markers gave a value range of 0.6741 for marker UH-Ec-931 to 0.7658 for marker UH-Ec-958. The mean PIC value of 0.7171 was recorded. Marker UH-Ec-958 showed 13 alleles per locus while marker UH-Ec-956 showed 20 alleles per locus. The mean average allele per locus was 17. Following Nei’s approach, the mean gene diversity value of 0.7638 was captured by the three markers. Cluster analysis for the 48 selected accessions of finger millet showed four major clusters. Accessions from Zimbabwe and Zambia are distributed on the cluster I. Accessions from India are mostly found in cluster IV. Accessions from Nepal were found mostly on cluster III while Ugandan accessions are found in cluster II and III respectively. Our investigation showed that the developed EST-SSRs are quite effective in unraveling the nature of diversity in our studied population.

Published in	International Journal of Genetics and Genomics (Volume 2, Issue 3)
DOI	10.11648/j.ijgg.20140203.12
Page(s)	42-46
Creative Commons	This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.
Copyright	Copyright © The Author(s), 2014. Published by Science Publishing Group

Keywords

EST-SSRs, Finger Millet (E. Coracana (L.) Gaertn.), Gene Diversity, Polymorphic Information Content (PIC)

References

[1]	MM. Dida, N. Wanyera, MLH. Dunn, JL. Bennetzen, KM. Devos, "Population structure and diversity in finger millet (Eleusine coracona) germplasm". Trop. Plant. Biol. Vol. 1, pp.131–141, 2008
[2]	HD. Upadhyaya, NDRK. Sarma, CR. Ravishankar, T. Albrecht, Y. Narasimhudu, SK. Singh, SK. Varshney, VG. Reddy, S. Singh, SL. Dwivedi, N. Wanyera, COA. Oduri, MA. Mgonja, DB. Kisandu, HK. Parzies, CLL. Gowda, " Developing minicore collection in finger millet using mul-ti-location data". Crop. Sci. Vol. 50, pp. 1924-1931, 2010
[3]	National Research Council, "Finger millet, In FR Ruskin, eds, Lost crops of Africa, Grains" Nat. Acad. Press. USA. Vol. 1, pp. 39–58,1996
[4]	KW. Hilu, JMJ. deWet, "Domestication of Eleusine coracana" Econ. Bot. Vol. 30, pp. 199–208, 1979
[5]	B. Babu, N. Senthil, S. Gomez, K. Biji, N. Rajendraprasad, S. Kumar, R. Babu, "Assessment of genetic diversity among finger millet (E. coracana (L.) Gaertn.) acces-sions using molecular markers". Genet. Resour. Crop. Evol. Vol. 54, pp. 399–404, 2007
[6]	M. Dida, M. Srinivasachary, S. Ramakrishnan, JL. Bennetzen, MD. Gale, KM. Devos, "The genetic map of finger millet, Eleusine coracana" Theor. Appl. Genet. Vol. 114, pp. 321–332, 2007
[7]	R. Gupta, K. Verma, DC. Joshi, D. Yadav, M. Singh, "Assessment of genetic related-ness among three varieties of finger millet with variable seed coat color using RAPD and ISSR markers". Genet. Eng. Biotech. J. Vol. 2, pp. 1-5, 2010
[8]	K. Bezaweletaw, "Genetic diver-sity of finger millet (E. coracana (L.) Gaertn.) landraces characterized by random amplified poly-morphic DNA analysis" Inn. Sys. Des. Eng. Vol. 2(4), pp. 207-217, 2011
[9]	KD. Scott, P. Eggler, G. Seaton, M. Rossetto, EM. Ablett, LS. Lee, RJ. Henry, "Analysis of SSRs derived from grape ESTs" Theor. Appl. Genet. Vol. 100, pp. 723-726, 2000
[10]	C. Chen, P. Zhou, YA. Choi, S. Huang, FG. Jr. Gmitter, "Mining and characterizing microsatelites from Citrus ESTs" Theor. Appl. Genet. Vol.112, pp. 1248-1257, 2006
[11]	HD. Upadhyaya, CLL. Gowda, RPS. Pundir, VG. Reddy, S. Singh, "Development of core subset of finger millet germplasm using geographical origin and data on 14 quantitative traits" Genet. Resour. and Crop Evol. Vol. 53, pp. 679–685, 2006
[12]	JJ. Doyle "DNA protocols for plants-CTAB total DNA isolation", In molecular techniques in Taxonomy, GM Hewitt , eds , Springer, Germany, 1991
[13]	AFA. Smit, R. Hubley, P. Green, "Repeat-Masker Open-3.0. http://www.repeatmasker.org", 2004
[14]	P. Miller, "Tools for population genetic analysis (TFPGA) 1.3, a windows program for the analysis of allozyme and molecular pop-ulation genetic data", 1997
[15]	M. Nei, "Analysis of gene diversity in subdivided populations" Proc. Nat. Acad. Sci. Vol.70 (12), pp. 3321-3323, 1973
[16]	D. Botstein, RL. White, M. Skolnick, RW. Davis, "Construction of a genetic linkage map in man using restriction fragment length poly-morphisms" Am. J. Hum. Genet. Vol. 32, pp. 314-331, 1980
[17]	P. Panwar, M. Nath, VK.Yadav, A. Kumar, "Comparative evaluation of genetic diversity using RAPD, SSR and cytochome P450 gene based markers with respect to calcium content in ﬁnger millet (Eleusine coracana L. Gaertn.)". J. Genet. Vol. 89, pp. 121–133, 2010
[18]	M. Nirgude, BB. Kalyana, Y. Shambhavi, UM. Singh, HD. Upadhyaya, A. Kumar, "Development and molecular characterization of genic molecular markers for grain protein and calcium content in finger millet (Eleusine coracana (L.) Gaertn.)" Mol. Biol. Rep. DOI-10.1007/s11033-013-2825-7.
[19]	KW. Hilu, JMJ. de Wet, JR. Harlan, " Archaeobotanical studies of Eleusine coracana". Am. J. Bot. Vol. 66, pp. 330- 333, 1976

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APA Style

Oscar Nnaemeka Obidiegwu, Heiko Parzies, Jude Ejikeme Obidiegwu. (2014). Development and Genotyping Potentials of EST-SSRs in Finger Millet (E. Coracana (L.) Gaertn.). International Journal of Genetics and Genomics, 2(3), 42-46. https://doi.org/10.11648/j.ijgg.20140203.12

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ACS Style

Oscar Nnaemeka Obidiegwu; Heiko Parzies; Jude Ejikeme Obidiegwu. Development and Genotyping Potentials of EST-SSRs in Finger Millet (E. Coracana (L.) Gaertn.). Int. J. Genet. Genomics 2014, 2(3), 42-46. doi: 10.11648/j.ijgg.20140203.12

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AMA Style

Oscar Nnaemeka Obidiegwu, Heiko Parzies, Jude Ejikeme Obidiegwu. Development and Genotyping Potentials of EST-SSRs in Finger Millet (E. Coracana (L.) Gaertn.). Int J Genet Genomics. 2014;2(3):42-46. doi: 10.11648/j.ijgg.20140203.12

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@article{10.11648/j.ijgg.20140203.12,
  author = {Oscar Nnaemeka Obidiegwu and Heiko Parzies and Jude Ejikeme Obidiegwu},
  title = {Development and Genotyping Potentials of EST-SSRs in Finger Millet (E. Coracana (L.) Gaertn.)},
  journal = {International Journal of Genetics and Genomics},
  volume = {2},
  number = {3},
  pages = {42-46},
  doi = {10.11648/j.ijgg.20140203.12},
  url = {https://doi.org/10.11648/j.ijgg.20140203.12},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ijgg.20140203.12},
  abstract = {Finger millet (E. coracana (L.) Gaertn.) provides food for millions of people in Africa and Asia. In this study, sequence data were mined at the database of National Center for Biotechnology Information (NCBI) with the aim of developing polymorphic expressed sequence tags simple sequence repeat (EST-SSRs) markers. Three selected markers which showed clear polymorphism in pre-testing with 5 accessions were used to characterize some randomly selected 48 accessions from the pool of finger millet core set. The polymorphic information content (PIC) of the developed markers gave a value range of 0.6741 for marker UH-Ec-931 to 0.7658 for marker UH-Ec-958. The mean PIC value of 0.7171 was recorded. Marker UH-Ec-958 showed 13 alleles per locus while marker UH-Ec-956 showed 20 alleles per locus. The mean average allele per locus was 17. Following Nei’s approach, the mean gene diversity value of 0.7638 was captured by the three markers. Cluster analysis for the 48 selected accessions of finger millet showed four major clusters. Accessions from Zimbabwe and Zambia are distributed on the cluster I. Accessions from India are mostly found in cluster IV. Accessions from Nepal were found mostly on cluster III while Ugandan accessions are found in cluster II and III respectively. Our investigation showed that the developed EST-SSRs are quite effective in unraveling the nature of diversity in our studied population.},
 year = {2014}
}

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TY - JOUR
T1 - Development and Genotyping Potentials of EST-SSRs in Finger Millet (E. Coracana (L.) Gaertn.)
AU - Oscar Nnaemeka Obidiegwu
AU - Heiko Parzies
AU - Jude Ejikeme Obidiegwu
Y1 - 2014/06/10
PY - 2014
N1 - https://doi.org/10.11648/j.ijgg.20140203.12
DO - 10.11648/j.ijgg.20140203.12
T2 - International Journal of Genetics and Genomics
JF - International Journal of Genetics and Genomics
JO - International Journal of Genetics and Genomics
SP - 42
EP - 46
PB - Science Publishing Group
SN - 2376-7359
UR - https://doi.org/10.11648/j.ijgg.20140203.12
AB - Finger millet (E. coracana (L.) Gaertn.) provides food for millions of people in Africa and Asia. In this study, sequence data were mined at the database of National Center for Biotechnology Information (NCBI) with the aim of developing polymorphic expressed sequence tags simple sequence repeat (EST-SSRs) markers. Three selected markers which showed clear polymorphism in pre-testing with 5 accessions were used to characterize some randomly selected 48 accessions from the pool of finger millet core set. The polymorphic information content (PIC) of the developed markers gave a value range of 0.6741 for marker UH-Ec-931 to 0.7658 for marker UH-Ec-958. The mean PIC value of 0.7171 was recorded. Marker UH-Ec-958 showed 13 alleles per locus while marker UH-Ec-956 showed 20 alleles per locus. The mean average allele per locus was 17. Following Nei’s approach, the mean gene diversity value of 0.7638 was captured by the three markers. Cluster analysis for the 48 selected accessions of finger millet showed four major clusters. Accessions from Zimbabwe and Zambia are distributed on the cluster I. Accessions from India are mostly found in cluster IV. Accessions from Nepal were found mostly on cluster III while Ugandan accessions are found in cluster II and III respectively. Our investigation showed that the developed EST-SSRs are quite effective in unraveling the nature of diversity in our studied population.
VL - 2
IS - 3
ER -

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Author Information

Oscar Nnaemeka Obidiegwu

Institute of Plant Production and Agroecology in the Tropics and Subtropics, University of Hohenheim, Stuttgart, 70593, Germany
Heiko Parzies

Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, 70593, Germany
Jude Ejikeme Obidiegwu

National Root Crops Research Institute, Umudike, PMB 7006, Abia State, Nigeria

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APA Style

Oscar Nnaemeka Obidiegwu, Heiko Parzies, Jude Ejikeme Obidiegwu. (2014). Development and Genotyping Potentials of EST-SSRs in Finger Millet (E. Coracana (L.) Gaertn.). International Journal of Genetics and Genomics, 2(3), 42-46. https://doi.org/10.11648/j.ijgg.20140203.12

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Oscar Nnaemeka Obidiegwu; Heiko Parzies; Jude Ejikeme Obidiegwu. Development and Genotyping Potentials of EST-SSRs in Finger Millet (E. Coracana (L.) Gaertn.). Int. J. Genet. Genomics 2014, 2(3), 42-46. doi: 10.11648/j.ijgg.20140203.12

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AMA Style

Oscar Nnaemeka Obidiegwu, Heiko Parzies, Jude Ejikeme Obidiegwu. Development and Genotyping Potentials of EST-SSRs in Finger Millet (E. Coracana (L.) Gaertn.). Int J Genet Genomics. 2014;2(3):42-46. doi: 10.11648/j.ijgg.20140203.12

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@article{10.11648/j.ijgg.20140203.12,
  author = {Oscar Nnaemeka Obidiegwu and Heiko Parzies and Jude Ejikeme Obidiegwu},
  title = {Development and Genotyping Potentials of EST-SSRs in Finger Millet (E. Coracana (L.) Gaertn.)},
  journal = {International Journal of Genetics and Genomics},
  volume = {2},
  number = {3},
  pages = {42-46},
  doi = {10.11648/j.ijgg.20140203.12},
  url = {https://doi.org/10.11648/j.ijgg.20140203.12},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ijgg.20140203.12},
  abstract = {Finger millet (E. coracana (L.) Gaertn.) provides food for millions of people in Africa and Asia. In this study, sequence data were mined at the database of National Center for Biotechnology Information (NCBI) with the aim of developing polymorphic expressed sequence tags simple sequence repeat (EST-SSRs) markers. Three selected markers which showed clear polymorphism in pre-testing with 5 accessions were used to characterize some randomly selected 48 accessions from the pool of finger millet core set. The polymorphic information content (PIC) of the developed markers gave a value range of 0.6741 for marker UH-Ec-931 to 0.7658 for marker UH-Ec-958. The mean PIC value of 0.7171 was recorded. Marker UH-Ec-958 showed 13 alleles per locus while marker UH-Ec-956 showed 20 alleles per locus. The mean average allele per locus was 17. Following Nei’s approach, the mean gene diversity value of 0.7638 was captured by the three markers. Cluster analysis for the 48 selected accessions of finger millet showed four major clusters. Accessions from Zimbabwe and Zambia are distributed on the cluster I. Accessions from India are mostly found in cluster IV. Accessions from Nepal were found mostly on cluster III while Ugandan accessions are found in cluster II and III respectively. Our investigation showed that the developed EST-SSRs are quite effective in unraveling the nature of diversity in our studied population.},
 year = {2014}
}

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