Inter-species Transferability of Microsatellite Markers Derived from Wild Relatives to Cultivated Species of Finger Millet

Nagabhushana Kotrappa; Shailaja Hittalmani; Krishna Venkatarangaiah

doi:doi:10.11648/j.ijgg.20170504.12

| Peer-Reviewed

Inter-species Transferability of Microsatellite Markers Derived from Wild Relatives to Cultivated Species of Finger Millet

Nagabhushana Kotrappa, Shailaja Hittalmani, Krishna Venkatarangaiah

Published in International Journal of Genetics and Genomics (Volume 5, Issue 4)

Received: 16 June 2017 Accepted: 3 July 2017 Published: 1 August 2017

Views: Downloads:

Download PDF

Share This Article

Twitter
Linked In
Facebook

Abstract

The accessibility to public sequence information has paved the way for development of new genomic resources and its cross transferability among closely related genera. In the present study, the nucleotide and EST sequences derived from nine different species of Eleusine were utilized for identifying microsatellite markers and their transferability in E. coracana. The frequency and distribution of repeat motifs of Di, tri, tetra and penta-nucleotide repeats were compared across species. The nucleotide/EST sequences, classified based on their function, were majorly involved in abiotic stress followed by carbohydrate biosynthesis in all the species. Of 2133 primers designed, tri-nucleotide repeats were more abundant (1043) followed by repeats in compound format (963). A highest number of 1660 primer pairs were identified in E. coracana subsp. coracana and nearly 50% of which contained compound repeats, majorly comprising of di-nucleotides. The frequency of microsatellite repeats and the number of primers designed per sequence were maximum in E. kigeziensis (138%) followed by E. floccifolia (126%) while the same was minimum in E. coracana subsp. africana (53%). While the transferability of microsatellites derived from other Eleusine species to cultivated coracana species ranged from 50 to 100%, the primers derived from cultivated species were more informative than from that of wild relatives.

Published in	International Journal of Genetics and Genomics (Volume 5, Issue 4)
DOI	10.11648/j.ijgg.20170504.12
Page(s)	42-48
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), 2017. Published by Science Publishing Group

Keywords

Finger Millet, Wild Relatives, EST-SSRs, Cross-Species Transferability

References

[1]	Paterson AH, Bowers JE, Burow MD, Draye X, Elsik CG, Jiang CX, Katsar CS, Lan TH, Lin YR, Ming R, Wright RJ: Comparative genomics of plant chromosomes. Plant Cell 2000, 12:1523-1540.
[2]	Devos KM, Gale MD: Genome relationships: the grass model in current research. Plant Cell 2000, 12:637-646.
[3]	Goron, TL, Raizada, MN: Genetic diversity and genomic resources available for the small millet crops to accelerate New Green Revolution. Front. Plant Sci. 2015, 6:157.
[4]	Devi PB, Vijayabharathi R, Sathyabama S, Malleshi NG, Priyadarisini VB: Health benefits of finger millet (Eleusine coracana L.) polyphenols and dietary fiber: a review. J. Food Sci. Technol 2014, 51 (6):1021–1040.
[5]	Ramakrishnan, M, Antony Ceasar S, Duraipandiyan V, Al-Dhabi NA, Ignacimuthu S: Assessment of genetic diversity, population structure and relationships in Indian and non-Indian genotypes of finger millet (Eleusine coracana (L.) Gaertn.) using genomic SSR markers. Springer Plus 2016, 5:120.
[6]	Fakrudin B, Kulkarni RS, Shashidhar HE, Hittalmani S: Genetic diversity assessment of finger millet, Eleusine coracana (Gaertn), germplasm through RAPD analysis. Plant Genet. Resour. Newsletter 2004, 138: 50-54.
[7]	Dida M, Srinivasachary M, Ramakrishnan S, Bennetzen JL, Gale MD, Devos KM: The genetic map of finger millet, Eleusine coracana. Theor. Appl. Genet 2007 114:321-332.
[8]	Kalyana Babu B, Pandey D, Agrawal PK., Sood S, Kumar A: Insilico mining, type and frequency analysis of genic microsatellites of finger millet (Eleusine coracana (L.) Gaertn.): a comparative genomic analysis of NBS–LRR regions of finger millet with rice. Mol. Biol. Rep 2014e, 41:3081-3090.
[9]	Gimode D., Odeny DA, deVilliers EP, Wanyonyi S, Dida MM, Mneney EE, etal: Identification of SNP and SSR markers in finger millet using next generation sequencing technologies. PLoSONE 2016, 11:e0159437.
[10]	Srinivasachary RS, Dida MM, Gale MD, Devos KM: Comparative analyses reveal high levels of conserved colinearity between the finger millet and rice genomes. Theor. Appl. Genet 2007, 115:489-499.
[11]	Wang ML, BarkleyNA, Yu JK, Dean RE, Newman ML, Sorrells ME, etal: Transfer of simple sequence repeat (SSR) markers from major cereal crops to minor grass species for germplasm characterization and evaluation. Plant Genet. Resour 2005, 3: 45-57.
[12]	Pandey G, Misra G, Kumari K, Gupta S, Parida SK, Chattopadhyay D, etal: Genome-wide development and use of microsatellite markers for large scale genotyping applications in Foxtail Millet (Setaria italica L.). DNA Res 2013, 20:197-207.
[13]	Hittalmani S, Mahesh HB, Shirke MD, Biradar H, Uday G, Aruna YR, Lohithaswa HC, Mohanrao A: Genome and transcriptome sequence of finger millet (Eeusine coracana (L.) Gaertn.) provides insights in to drought tolerance and nutraceutical properties. 2017, 18:465.
[14]	Dagnachew L, DeVilliers S, Sewalem T, Dida M, Masresha F, Kimani W, etal: Genetic diversity and eco-geographical distribution of Eleusine species collected from Ethiopia. African Crop Sci. J. 2014, 22:45-58.
[15]	Thiel T, Michalek W, Varshney RK, Graner A: Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 2003, 106 (3):411-22.
[16]	Untergrasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG: Primer3 - new capabilities and interfaces. Nucleic Acids Research, 2012, 40 (15):e115.
[17]	Doyle JJ, Doyle JL: Isolation of plant DNA from fresh tissue. Focus 1990, 12:13-15.
[18]	Gupta SM, Arora S, Mirza N, Pande A, Lata C, Puranik S, Kumar J, Kumar A: Finger Millet: A “Certain” Crop for an “Uncertain” Future and a Solution to Food Insecurity and Hidden Hunger under Stressful Environments. Front. Plant Sci 2017, 8:643.
[19]	Selvam JN, Muthukumar M, Rahman H, Senthil N, Raveendran M: Development and validation of SSR markers in Finger millet (Eleusine coracana Gaertn). International Journal of Tropical Agriculture 2015, 33 (3): 2055-2066.
[20]	Varshney RK, Graner A, Sorrels M: Genic microsatellite markers in plants: features and applications. Trends in Biotechnol 2005, 1:48-55.
[21]	Ellis JR, Burke JM: EST-SSRs as a resource for population genetic analyses. Heredity 2007, 99:125-132.
[22]	Sood S, Kumar A, Babu BK, Gaur VS, Pandey D, Kant L. Pattnayak A: Gene Discovery and Advances in Finger Millet [Eleusine coracana (L.) Gaertn.] Genomics - An Important Nutri-Cereal of Future. Front. Plant Sci 2016, 7:1634.

Cite This Article

Plain Text BibTeX RIS

APA Style

Nagabhushana Kotrappa, Shailaja Hittalmani, Krishna Venkatarangaiah. (2017). Inter-species Transferability of Microsatellite Markers Derived from Wild Relatives to Cultivated Species of Finger Millet. International Journal of Genetics and Genomics, 5(4), 42-48. https://doi.org/10.11648/j.ijgg.20170504.12

Copy | Download

ACS Style

Nagabhushana Kotrappa; Shailaja Hittalmani; Krishna Venkatarangaiah. Inter-species Transferability of Microsatellite Markers Derived from Wild Relatives to Cultivated Species of Finger Millet. Int. J. Genet. Genomics 2017, 5(4), 42-48. doi: 10.11648/j.ijgg.20170504.12

Copy | Download

AMA Style

Nagabhushana Kotrappa, Shailaja Hittalmani, Krishna Venkatarangaiah. Inter-species Transferability of Microsatellite Markers Derived from Wild Relatives to Cultivated Species of Finger Millet. Int J Genet Genomics. 2017;5(4):42-48. doi: 10.11648/j.ijgg.20170504.12

Copy | Download

@article{10.11648/j.ijgg.20170504.12,
  author = {Nagabhushana Kotrappa and Shailaja Hittalmani and Krishna Venkatarangaiah},
  title = {Inter-species Transferability of Microsatellite Markers Derived from Wild Relatives to Cultivated Species of Finger Millet},
  journal = {International Journal of Genetics and Genomics},
  volume = {5},
  number = {4},
  pages = {42-48},
  doi = {10.11648/j.ijgg.20170504.12},
  url = {https://doi.org/10.11648/j.ijgg.20170504.12},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ijgg.20170504.12},
  abstract = {The accessibility to public sequence information has paved the way for development of new genomic resources and its cross transferability among closely related genera. In the present study, the nucleotide and EST sequences derived from nine different species of Eleusine were utilized for identifying microsatellite markers and their transferability in E. coracana. The frequency and distribution of repeat motifs of Di, tri, tetra and penta-nucleotide repeats were compared across species. The nucleotide/EST sequences, classified based on their function, were majorly involved in abiotic stress followed by carbohydrate biosynthesis in all the species. Of 2133 primers designed, tri-nucleotide repeats were more abundant (1043) followed by repeats in compound format (963). A highest number of 1660 primer pairs were identified in E. coracana subsp. coracana and nearly 50% of which contained compound repeats, majorly comprising of di-nucleotides. The frequency of microsatellite repeats and the number of primers designed per sequence were maximum in E. kigeziensis (138%) followed by E. floccifolia (126%) while the same was minimum in E. coracana subsp. africana (53%). While the transferability of microsatellites derived from other Eleusine species to cultivated coracana species ranged from 50 to 100%, the primers derived from cultivated species were more informative than from that of wild relatives.},
 year = {2017}
}

Copy | Download

TY - JOUR
T1 - Inter-species Transferability of Microsatellite Markers Derived from Wild Relatives to Cultivated Species of Finger Millet
AU - Nagabhushana Kotrappa
AU - Shailaja Hittalmani
AU - Krishna Venkatarangaiah
Y1 - 2017/08/01
PY - 2017
N1 - https://doi.org/10.11648/j.ijgg.20170504.12
DO - 10.11648/j.ijgg.20170504.12
T2 - International Journal of Genetics and Genomics
JF - International Journal of Genetics and Genomics
JO - International Journal of Genetics and Genomics
SP - 42
EP - 48
PB - Science Publishing Group
SN - 2376-7359
UR - https://doi.org/10.11648/j.ijgg.20170504.12
AB - The accessibility to public sequence information has paved the way for development of new genomic resources and its cross transferability among closely related genera. In the present study, the nucleotide and EST sequences derived from nine different species of Eleusine were utilized for identifying microsatellite markers and their transferability in E. coracana. The frequency and distribution of repeat motifs of Di, tri, tetra and penta-nucleotide repeats were compared across species. The nucleotide/EST sequences, classified based on their function, were majorly involved in abiotic stress followed by carbohydrate biosynthesis in all the species. Of 2133 primers designed, tri-nucleotide repeats were more abundant (1043) followed by repeats in compound format (963). A highest number of 1660 primer pairs were identified in E. coracana subsp. coracana and nearly 50% of which contained compound repeats, majorly comprising of di-nucleotides. The frequency of microsatellite repeats and the number of primers designed per sequence were maximum in E. kigeziensis (138%) followed by E. floccifolia (126%) while the same was minimum in E. coracana subsp. africana (53%). While the transferability of microsatellites derived from other Eleusine species to cultivated coracana species ranged from 50 to 100%, the primers derived from cultivated species were more informative than from that of wild relatives.
VL - 5
IS - 4
ER -

Copy | Download

Author Information

Nagabhushana Kotrappa

Department of Biotechnology, Jnanasahyadri, Shankaraghatta, Kuvempu University, Shimoga, India
Shailaja Hittalmani

Department of Genetics and Plant Breeding, University of Agricultural Sciences, Bengaluru, India
Krishna Venkatarangaiah

Department of Biotechnology, Jnanasahyadri, Shankaraghatta, Kuvempu University, Shimoga, India

Download PDF

Sections

Plain Text BibTeX RIS

APA Style

Nagabhushana Kotrappa, Shailaja Hittalmani, Krishna Venkatarangaiah. (2017). Inter-species Transferability of Microsatellite Markers Derived from Wild Relatives to Cultivated Species of Finger Millet. International Journal of Genetics and Genomics, 5(4), 42-48. https://doi.org/10.11648/j.ijgg.20170504.12

Copy | Download

ACS Style

Nagabhushana Kotrappa; Shailaja Hittalmani; Krishna Venkatarangaiah. Inter-species Transferability of Microsatellite Markers Derived from Wild Relatives to Cultivated Species of Finger Millet. Int. J. Genet. Genomics 2017, 5(4), 42-48. doi: 10.11648/j.ijgg.20170504.12

Copy | Download

AMA Style

Nagabhushana Kotrappa, Shailaja Hittalmani, Krishna Venkatarangaiah. Inter-species Transferability of Microsatellite Markers Derived from Wild Relatives to Cultivated Species of Finger Millet. Int J Genet Genomics. 2017;5(4):42-48. doi: 10.11648/j.ijgg.20170504.12

Copy | Download

@article{10.11648/j.ijgg.20170504.12,
  author = {Nagabhushana Kotrappa and Shailaja Hittalmani and Krishna Venkatarangaiah},
  title = {Inter-species Transferability of Microsatellite Markers Derived from Wild Relatives to Cultivated Species of Finger Millet},
  journal = {International Journal of Genetics and Genomics},
  volume = {5},
  number = {4},
  pages = {42-48},
  doi = {10.11648/j.ijgg.20170504.12},
  url = {https://doi.org/10.11648/j.ijgg.20170504.12},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ijgg.20170504.12},
  abstract = {The accessibility to public sequence information has paved the way for development of new genomic resources and its cross transferability among closely related genera. In the present study, the nucleotide and EST sequences derived from nine different species of Eleusine were utilized for identifying microsatellite markers and their transferability in E. coracana. The frequency and distribution of repeat motifs of Di, tri, tetra and penta-nucleotide repeats were compared across species. The nucleotide/EST sequences, classified based on their function, were majorly involved in abiotic stress followed by carbohydrate biosynthesis in all the species. Of 2133 primers designed, tri-nucleotide repeats were more abundant (1043) followed by repeats in compound format (963). A highest number of 1660 primer pairs were identified in E. coracana subsp. coracana and nearly 50% of which contained compound repeats, majorly comprising of di-nucleotides. The frequency of microsatellite repeats and the number of primers designed per sequence were maximum in E. kigeziensis (138%) followed by E. floccifolia (126%) while the same was minimum in E. coracana subsp. africana (53%). While the transferability of microsatellites derived from other Eleusine species to cultivated coracana species ranged from 50 to 100%, the primers derived from cultivated species were more informative than from that of wild relatives.},
 year = {2017}
}

Copy | Download