Patterns of Molecular Diversity in Current and Previously Developed Hybrid Parents of Pearl Millet [Pennisetum glaucum (L.) R. Br.]


ICRISAT’s pearl millet (Pennisetum glaucum (L.) R. Br.) breeding program at Patancheru, India, has developed genetically diverse hybrid parents since 1980s. The present study investigated genetic diversity pattern between two groups of parents in this program, bred till 2004 and developed during 2004-2010. Combined analysis of 379 hybrid parents (current 166 parents and 213 previously developed hybrid parents) carried out using a set of highly polymorphic 28 SSRs detected 12.7 alleles per locus. An average of 8.5 and 8.7 SSR alleles per locus were found in previously developed and current parents, respectively, indicating marginal improvement in the levels of genetic diversity of hybrid parents in this program. Distance matrix differentiated these current and previously developed hybrid parents into 2 separate clusters, indicating infusion of new genetic variability over time as reflected by development of more genotype-specific alleles. Also, the seed and restorer parents were found clearly separated from each other in both the sets with few crossovers, indicating existence of two diverse and broad-based pools in hybrid parents of pearl millet. Restorer parents (R-lines) were found more diverse than seed parents (B-lines), as higher average gene diversity was detected among R-lines (0.70) than B-lines (0.56), though variation between B- and R-lines was found reduced in newly developed lines to 9.22% from 16.98% in previously developed lines. Results suggested that newly developed lines were as much divergent when compared with previously developed lines, indicating that current ICRISAT pearl millet breeding program was moving towards development of diverse new hybrid parental lines. The study suggested use of trait-specific donors in B- and R-lines separately to maintain sufficient genetic distance between seed and restorer breeding lines. It was pointed out to cross parents having higher genetic distance within the seed (B-lines) and restorer (R-lines) breeding programs to derive diverse and productive hybrid parental lines in future.

Share and Cite:

Gupta, S. , Nepolean, T. , Sankar, S. , Rathore, A. , Rani Das, R. , Rai, K. and Hash, C. (2015) Patterns of Molecular Diversity in Current and Previously Developed Hybrid Parents of Pearl Millet [Pennisetum glaucum (L.) R. Br.]. American Journal of Plant Sciences, 6, 1697-1712. doi: 10.4236/ajps.2015.611169.

Conflicts of Interest

The authors declare no conflicts of interest.


[1] Andrews, D.J. and Anand Kumar, K. (1992) Pearl Millet for Food and Forage. Advances in Agronomy, 48, 89-139.
[2] Bonamigo, L.A. (1999) A cultura do milheto no Brasil, implantação e desenvolvimento no cerrado. In: Lopes de Farias Neto, A., Fernando Amabile, R., Martins Netto, D.A., Yamashita, T. and Gocho, H., Eds., Proceedings of the International Pearl Millet Workshop, Planaltina, 9-10 June 1999, Planaltina, D.F., Embrapa Cerrados, 31-65.
[3] Indiastat (2013)
[4] Yadav, O.P. and Rai, K.N. (2013) Genetic Improvement of Pearl Millet in India. Agricultural Research, 2, 275-292.
[5] ICRISAT (2012) Hybrid Parents Research Consortium. The Jewels of ICRISAT. International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 48-51.
[6] Senthilvel, S., Jayashree, B., Mahalakshmi, V., Kumar, P.S., Nakka, S., Nepolean, T. and Hash, C.T. (2008) Development and Mapping of Simple Sequence Repeat Markers for Pearl Millet from Data Mining of Expressed Sequence Tags. BMC Plant Biology, 8, 119.
[7] Yadav, O.P., Mitchell, S.E., Zamora, A., Fulton, T.M. and Kresovich, S. (2007) Development of New Simple Sequence Repeat Markers for Pearl Millet. SAT eJournal, 3.
[8] Rajaram, V., Nepolean, T., Senthilvel, S., Varshney, R.K., Vadez, V., Srivastava, R.K., Shah, T.M., Supriya, A., Kumar, S., Kumari, B.R., Bhanuprakash, A., Narasu, M.N., Riera-Lizarazu, O. and Hash, C.T. (2013) Pearl Millet [Pennisetum glaucum (L.) R. Br.] Consensus Linkage Map Constructed Using Four RIL Mapping Populations and Newly Developed EST-SSRs. BMC Genomics, 14, 159.
[9] Moumouni, K.H., Kountche, B.A., Jean, M., Hash, C.T., Vigouroux, Y., Haussmann, B.I.G. and Belzile, F. (2015) Construction of a Genetic Map for Pearl Millet, Pennisetum glaucum (L.) R. Br., Using a Genotyping-by-Sequencing (GBS) Approach. Molecular Breeding, 35, 5.
[10] Kapila, R.K., Yadav, R.S., Plaha, P., Rai, K.N., Yadav, O.P., Hash, C.T. and Howarth, C.J. (2008) Genetic Diversity among Pearl Millet Maintainers Using Microsatellite Markers. Plant Breeding, 127, 33-37.
[11] Sumathi, P., Sumanth, M., Vinodhana, N.K. and Sathya, M. (2013) Assessment of Genetic Distance among the Inbred Lines of Pearl Millet (Pennisetum glaucum (L.) R. Br.) Using SSR Markers. IJBAF, 1, 153-162.
[12] Rai, K.N., Gupta, S.K., Bhattacharjee, R., Kulkarni, V.N., Singh, A.K. and Rao, A.S. (2009) Morphological Characteristics of ICRISAT-Bred Pearl Millet Hybrid Seed Parents. Journal of SAT Agricultural Research, 7, 1.
[13] Gupta, S.K., Bhattacharjee, R., Rai, K.N. and Suresh Kumar, M. (2011) Characterization of ICRISAT-Bred Restorer Parents of Pearl Millet. Journal of SAT Agricultural Research, 9, 1-5.
[14] Nepolean, T., Gupta, S.K., Dwivedi, S.L., Bhattacharjee, R., Rai, K.N. and Hash, C.T. (2012) Genetic Diversity in Maintainer and Restorer Lines of Pearl Millet. Crop Science, 52, 2555-2563.
[15] Burton, G.W. (1968) Registration of Pearl Millet Inbreds Tift 23B1, Tift 23A1, Tift 23DB1, and Tift 23D2A1. Crop Science, 9, 397.
[16] Sharp, P.J., Kries, M., Sherry, P.R. and Gale, M.D. (1988) Location of β-Amylase Sequences in Wheat and Its Relatives. Theoretical and Applied Genetics, 75, 286-290.
[17] Qi, X., Pittaway, T.S., Lindup, S., Liu, H., Waterman, E., Padi, F.K., Hash, C.T., Zhu, J., Gale, M.D. and Devos, K.M. (2004) An Integrated Genetic Map and a New Set of Simple Sequence Repeat Markers for Pearl Millet, Pennisetum glaucum. Theoretical and Applied Genetics, 109, 1485-1493.
[18] Applied Biosystems: GeneScan Analysis Software User Manual. Release 3.1 (1998) Applied Biosystems, Foster City.
[19] Applied Biosystems: Genotyper 3.1 (1998) Applied Biosystems, Foster City.
[20] Prasanth, V.P., Chandra, S., Jayashree, B. and Hoisington, D. (1998) AlleloBin—A Program for Allele Binning of Microsatellite Markers Based on the Algorithm of Idury and Cardon (1997). ICRISAT, Patancheru.
[21] Liu, K. and Muse, S.V. (2005) PowerMarker: Integrated Analysis Environment for Genetic Marker Data. Bioinformatics, 21, 2128-2129.
[22] Li, Y.H., Guan, R.X., Liu, Z.X., Ma, Y.S., Wang, L.X., Li, L.H., Lin, F.Y., Luan, W.J., Chen, P.Y., Yan, Z., Guan, Y., Zhu, L., Ning, X.C., Smulders, M.J.M., Li, W., Piao, R.H., Cui, Y.H., Yu, Z.M., Guan, M., Chang, R.Z., Hou, A.F., Shi, A.N., Zhang, B., Zhu, S.L. and Qiu, L.J. (2008) Genetic Structure and Diversity of Cultivated Soybean (Glycine max (L.) Merr.) Landraces in China. Theoretical and Applied Genetics, 117, 857-871.
[23] Upadhyaya, H.D., Dwivedi, S.L., Baum, M., Varshney, R.K., Udupa, S.M., Gowda, C.L.L., Hoisington, D. and Singh, S. (2008) Genetic Structure, Diversity, and Allelic Richness in Composite Collection and Reference Set in Chickpea (Cicer arietinum L.). BMC Plant Biology, 8, 106.
[24] Excoffier, L., Smouse, P. and Quattro, J. (1992) Analysis of Molecular Variance Inferred for Metric Distances among DNA Haplophytes: Applications to Human Mitochondrial DNA Restriction Data. Genetics, 131, 479-491.
[25] Perrier, X., Flori, A. and Bonnot, F. (2003) Data Analysis Methods. In: Hamon, P., Seguin, M., Perrier, X. and Glaszmann, J.C., Eds., Genetic Diversity of Cultivated Tropical Plants, Science Publishers, Enfield, 43-76.
[26] Rai, K.N., Andrews, D.J. and Rao, A.S. (1995) Registration of NCD2 Pearl Millet Germplasm. Crop Science, 35, 1237-1238.
[27] Stegmeier, W.D., Andrews, D.J., Rai, K.N. and Hash, C.T. (1998) Pearl Millet Parental Lines 843A and 843B. International Sorghum and Millets Newsletter, 39, 129-130.
[28] Rai, K.N., Bidinger, F.R., Hussain, K. and Rao, A.S. (1998) Registration of ICMP 94001 Pearl Millet Germplasm. Crop Science, 38, 1411.
[29] Anand Kumar, Andrews, D.J., Jain, R.P. and Singh, S.D. (1984) ICMA-1 and ICMB-1 Pearl Millet Parental Lines with A1 Cytoplasmic-Genic Male Sterility System. Crop Science, 24, 832.
[30] Stich, B., Haussmann, B.I.G., Pasam, R., Bhosale, S., Hash, C.T., Melchinger, A.E. and Parzies, H. (2010) Patterns of Molecular and Phenotypic Diversity in Pearl Millet [Pennisetum glaucum (L.) R. Br.] from West and Central Africa and Their Relation to Geographical and Environmental Parameters. BMC Plant Biology, 10, 216.
[31] van Inghelandt, D., Melchinger, A.E., Lebreton, C. and Stich, B. (2010) Population Structure and Gentic Diversity in a Commercial Maize Breeding Program Assessed with SSR and SNP Markers. Theoretical and Applied Genetics, 120, 1289-1299.
[32] Hallauer, A.R., Russell, W.A. and Lamkey, K.R. (1988) Corn Breeding. In: Sprague, G.F. and Dudley, J.W., Ed., Corn and Corn Improvement, 3rd Edition, Agronomy, American Society of Agronomy-Crop Science Society of America-Soil Science Society of America, Madison, 463-564.
[33] Troyer, A.F. (1990) A Retrospective View of Corn Genetic Resources. Journal of Heredity, 81, 17-24.
[34] Lu, H. and Bernardo, R. (2001) Molecular Marker Diversity among Current and Historical Maize Inbreds. Theoretical and Applied Genetics, 103, 613-617.
[35] Senior, M.L., Murthy, J.P., Goodman, M.M. and Stubber, C.W. (1998) Utility of SSRs for Determining Genetic Similarities and Relationships in Maize Using an Agarose Gel System. Crop Science, 38, 1088-1098.
[36] Matsouka, Y., Mitchell, S.E., Kresovich, S., Goodman, M. and Dobeley, J. (2002) Microsatellite in Zea—Variability, Patterns of Mutations and Use for Evolutionary Studies. Theoretical and Applied Genetics, 104, 436-450.
[37] Hash, C.T., Thakur, R.P., Rao, V.P. and Bhaskar Raj, G. (2006) Evidence for Enhanced Resistance to Diverse Isolates of Pearl Millet Downy Mildew through Gene Pyramiding. International Sorghum and Millets Newsletter, 47, 134-138.
[38] Gupta, S.K., Nepolean, T., Rai, K.N., Hash, C.T., Bhattacharjee, R. and Rathore, A. (2012) Within-Line Genetic Variation for Quantitative Characters and SSRs in Long-Time Maintained Inbreds in Pearl Millet [Pennisetum glaucum (L.) R. Br.]. The European Journal of Plant Science and Biotechnology, 6, 109-113.
[39] Gethi, J.G., Labate, J.A., Lamkey, K.R., Smith, M.E. and Kresovich, S. (2002) SSR Variation in Important U.S. Maize Inbred Lines. Crop Science, 42, 951-957.
[40] Heckenberger, M., Van der Voort, J.R., Melchinger, A.E., Peleman, J. and Bohn, M. (2003) Variation of DNA Fingerprints among Accessions within Maize Inbred Lines and Implications for Identification of Essentially Derived Varieties: II. Genetic and Technical Sources of Variation in AFLP Data and Comparison with SSR Data. Molecular Breeding, 12, 97-106.
[41] Rai, K.N., Kulkarni, V.N., Thakur, R.P., Haussmann, B.I.G. and Mgonja, M.A. (2006) Pearl Millet Hybrid Parent’s Research: Approaches and Achievements. In: Gowda, C.L.L., Rai, K.N., Belum, Reddy, V.S. and Saxena K.B., Eds., Hybrid Parents Research at ICRISAT, International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502 324, Andhra Pradesh, 11-74.

Copyright © 2023 by authors and Scientific Research Publishing Inc.

Creative Commons License

This work and the related PDF file are licensed under a Creative Commons Attribution 4.0 International License.