Skip to main content
SpringerLink
Log in

Construction of a genetic map for pearl millet, Pennisetum glaucum (L.) R. Br., using a genotyping-by-sequencing (GBS) approach

  • Published:
Molecular Breeding Aims and scope Submit manuscript

Abstract

Pearl millet is the main component of traditional farming systems and a staple grain in the diet of sub-Saharan Africa and India. To facilitate breeding work in this crop, a genetic map consisting of single nucleotide polymorphism (SNP) markers was constructed using an F2 population of 93 progenies, from a wild × cultivated pearl millet cross. We used a modified genotyping-by-sequencing (GBS) protocol involving two restriction enzymes (PstI–MspI) and PCR amplification with primers including three selective bases to generate 3,321 SNPs. Of these, 2,809 high-quality SNPs exhibited a minor allele frequency ≥0.3. In total, 314 non-redundant haplotypes and 85 F2 individuals were used to construct a genetic map spanning a total distance of 640 cM. These SNPs were evenly distributed over seven linkage groups ranging considerably in size (62–123 cM). The average density for this map was 0.51 SNP/cM, and the average interval between SNP markers was 2.1 (±0.6) cM. Finally, to establish bridges between the linkage groups of this and previous maps, 19 SSR markers were examined for polymorphism between the parents of this population. We could only tentatively suggest a correspondence between four of our linkage groups and those of previous maps. Overall, GBS enabled us to quickly produce a genetic map with a density and uniformity of markers greater than previously published maps. The availability of such a map will be useful for the identification of genomic regions associated with Striga resistance and other important agronomic traits.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Amusan IO, Rich PJ, Menkir A, Housley T, Ejeta G (2008) Resistance to Striga hermonthica in a maize inbred line derived from Zea diploperennis. New Phytol 178:157–166

    Article  PubMed  Google Scholar 

  • Bidinger FR, Nepolean T, Hash CT, Yadav RS, Howarth CJ (2007) Identification of QTLs for grain yield of pearl millet [Pennisetum glaucum (L.) R. Br.] in environments with variable moisture during grain filling. Crop Sci 47:969–980

    Article  Google Scholar 

  • Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635

    Article  CAS  PubMed  Google Scholar 

  • Chemisquy MA, Giussani LM, Scataglini MA, Kellogg EA, Morrone O (2010) Phylogenetic studies favour the unification of Pennisetum, Cenchrus and Odontelytrum (Poaceae): a combined nuclear, plastid and morphological analysis, and nomenclatural combinations in Cenchrus. Ann Bot (Oxford, UK) 106:107–130

    Article  Google Scholar 

  • Devaux P, Kilian A, Kleinhofs A (1995) Comparative mapping of the barley genome with male and female recombination-derived, doubled haploid populations. Mol Gen Genet 249:600–608

    Article  CAS  PubMed  Google Scholar 

  • Dhuppe MV, Chavan AA, More AW, More SS, Choudhary LM (2005) Heterosis in pearl millet. J Soils Crops 15(2):343–351

    Google Scholar 

  • Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6(5):e19379. doi:10.1371/journal.pone.0019379

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Gowda CLL, Rai KN (2006) Evolution of hybrid parents research. In: Gowda CLL, Rai KN, Freddy BVS, Sana KB (eds) Hybrid parents research at ICRISAT. ICRISAT Center, Patancheru, pp 1–10

    Google Scholar 

  • Gurney AL, Slate J, Press MC, Scholes JD (2006) A novel form of resistance in rice to the angiosperm parasite Striga hermonthica. New Phytol 169:199–208

    Article  CAS  PubMed  Google Scholar 

  • Hash CT, Yadav RS, Cavan GP, Howarth CJ, Liu H, Qi X, Sharma A, Kolesnikova-Allen MA, Bidinger FR, Witcombe JR (2000) Marker-assisted backcrossing to improve terminal drought tolerance in pearl millet. In: Ribaut J-M, Poland D (eds) Molecular approaches for the genetic improvement of cereals for stable production in water-limited environments, a strategic planning workshop held at CIMMYT, El Batan, Mexico, 21–25 June 1999, International Maize and Wheat Improvement Center (CIMMYT), Mexico, pp 114–119

  • Haussmann BIG, Hess DE, Omanya GO, Folkertsma RT, Reddy BVS, Kayentao M, Welz HG, Geiger HH (2004) Genomic regions influencing resistance to the parasitic weed Striga hermonthica in two recombinant inbred populations of sorghum. Theor Appl Genet 109:1005–1016

    Article  CAS  PubMed  Google Scholar 

  • Jauhar PP, Rai KN, Ozias-Akins P, Chen Z, Hanna WW (2006) Genetic improvement of pearl millet for grain and forage production: cytogenetic manipulation and heterosis breeding. In: Singh RJ, Jauhar PP (eds) Genetic resources, chromosome engineering, and crop improvement, 2nd edn. CRC Press, Taylor & Francis Group, Boca Raton, pp 281–307

    Google Scholar 

  • Kountche BA, Hash CT, Dodo H, Oumarou L, Sanogo MD, Amadou T, Vigouroux Y, This D, Nijkamp R, Haussmann BIG (2013) Development of a pearl millet Striga-resistant genepool: response to five cycles of recurrent selection under Striga-infested field conditions in West Africa. Field Crop Res 154:82–90

    Article  Google Scholar 

  • Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newberg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181

    Article  CAS  PubMed  Google Scholar 

  • Liu CJ, Witcombe JR, Pittaway TS, Nash M, Busso CS, Hash CT, Gale MD (1994) An RFLP-based genetic map of pearl millet (Pennisetum glaucum). Theor Appl Genet 89:481–487

    CAS  PubMed  Google Scholar 

  • Lu H, Romero-Severson J, Bernardo R (2002) Chromosomal regions associated with segregation distortion in maize. Theor Appl Genet 105:622–628

    Article  CAS  PubMed  Google Scholar 

  • Lu F, Lipka AE, Glaubitz J, Elshire R, Cherney JH, Casler MD, Buckler ES, Costich DE (2013) Switchgrass genomic diversity, ploidy, and evolution: novel insights from a network-based SNP discovery protocol. PLoS Genet 9(1):e1003215. doi:10.1371/journal.pgen.1003215

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Manning K, Pelling R, Higham T, Schwenniger JL, Fuller DQ (2011) 4500-Year old domesticated pearl millet (Pennisetum glaucum) from the Tilemsi Valley, Mali: new insights into an alternative cereal domestication pathway. J Archaeol Sci 38(2):312–322

    Article  Google Scholar 

  • Mariac C, Luong V, Kapran I, Mamadou A, Sagnard F, Deu M, Chantereau J, Gerard B, Ndjeunga J, Bezançon G, Pham J, Vigouroux Y (2006) Diversity of wild and cultivated pearl millet accessions [Pennisetum glaucum (L.) R. Br.] in Niger assessed by microsatellite markers. Theor Appl Genet 114:49–58

    Article  CAS  PubMed  Google Scholar 

  • Omanya GO, Haussmann BIG, Hess DE, Reddy BVS, Kayentao M, Welz HG, Geiger HH (2004) Utility of indirect and direct selection traits for improving striga resistance in two sorghum recombinant inbred populations. Field Crop Res 89:237–252

    Article  Google Scholar 

  • Pedraza-Garcia F, Specht JE, Dweikat I (2010) A new PCR-based linkage map in pearl millet. Crop Sci 50:1754–1760. doi:10.2135/cropsci2009.10.0560

    Article  CAS  Google Scholar 

  • Poland JA, Brown PJ, Sorrells ME, Jannink JL (2012) Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS ONE 7(2):e32253. doi:10.1371/journal.pone.0032253

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Presterl T, Weltzien E (2003) Exploiting heterosis in pearl millet for population breeding in arid environments. Crop Sci 43:767–776. doi:10.2135/cropsci2003.7670

    Article  Google Scholar 

  • Qi X, Pittaway TS, Lindup S, Liu H, Waterman E, Padi FK, Hash CT, Zhu J, Gale MD, Devos KM (2004) An integrated genetic map and a new set of simple sequence repeat markers for pearl millet Pennisetum glaucum. Theor Appl Genet 109:1485–1493

    Article  CAS  PubMed  Google Scholar 

  • Quarrie SA, Steed A, Calestani C, Semikhodskii A, Lebreton C, Chinoy C, Steele N, Pljevljakusic D, Waterman E, Weyen EJ, Schondelmaier J, Habash DZ, Farmer P, Saker L, Clarkson DT, Abugalieva A, Yessimbekova M, Turuspekov Y, Abugalieva S, Tuberosa R, Sanguineti M-C, Hollington PA, Aragués R, Royo A, Dodig D (2005) A high-density genetic map of hexaploid wheat (Triticum aestivum L.) from the cross Chinese Spring 9 SQ1 and its use to compare QTLs for grain yield across a range of environments. Theor Appl Genet 110:865–880

    Article  CAS  PubMed  Google Scholar 

  • Rai KN, Govindaraj M, Rao AS (2012) Genetic enhancement of grain iron and zinc content in pearl millet. Qual Assur Saf Crops Foods 4(3):119–125. doi:10.1111/j.1757-837X.2012.00135.x

    Article  CAS  Google Scholar 

  • Rajaram V, Nepolean T, Senthilvel S, Varshney RK, Vadez V, Srivastava RK, Shah TM, Supriya A, Kumar S, Kumari BR, Bhanuprakash A, Narasu ML, Riera-Lizarazu O, Hash CT (2013) Pearl millet [Pennisetum glaucum (L.) R. Br.] consensus linkage map constructed using four RIL mapping populations and newly developed EST-SSRs. BMC Genom 14:159

    Article  CAS  Google Scholar 

  • Sehgal D, Rajaram V, Armstead IP, Vadez V, Yadav YP, Hash CT, Yadav RS (2012) Integration of gene-based markers in a pearl millet genetic map for identification of candidate genes underlying drought tolerance quantitative trait loci. BMC Plant Biol 12:9. doi:10.1186/1471-2229-12-9

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Senthilvel S, Jayashree B, Mahalakshmi V, Kumar PS, Nakka S, Nepolean T, Hash CT (2008) Development and mapping of simple sequence repeat markers for pearl millet from data mining of expressed sequence tags. BMC Plant Biol 8:119. doi:10.1186/1471-2229-8-119

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Sharma PC, Singh D, Sehgal D, Singh G, Hash CT, Yadav RS (2014) Further evidence that a terminal drought tolerance QTL of pearl millet is associated with reduced salt uptake. Environ Exp Bot. doi:10.1016/j.envexpbot.2014.01.013

    PubMed Central  PubMed  Google Scholar 

  • Sonah H, Bastien M, Iquira E, Tardivel A, Légaré G et al (2013) An improved genotyping by sequencing (GBS) approach offering increased versatility and efficiency of SNP discovery and genotyping. PLoS ONE 8(1):e54603. doi:10.1371/journal.pone.0054603

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Supriya A, Senthilvel S, Nepolean T, Eshwar K, Rajaram V, Shaw R, Hash CT, Kilian A, Yadav RC, Narasu ML (2011) Development of a molecular linkage map of pearl millet integrating DArT and SSR markers. Theor Appl Genet 123:239–250. doi:10.1007/s00122-011-1580-1

    Article  CAS  PubMed  Google Scholar 

  • Tinker N (2013) Genotype-by-sequence in oat. Agriculture and Agri-Food Canada. Retrieved from http://www.9ioc.net/02-Tinker_Nick.pdf

  • Tostain S, Marchais L (1993) Évaluation de la diversité génétique des mils (Pennisetum glaucum (L.) R. BR.) au moyen de marqueurs enzymatiques et relations entre formes sauvages et cultivées. Laboratoire Ressources Génétiques et Amélioration des Plantes Tropicales. ORSTOM, Montpellier Cedex 1

  • Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93(1):77–78. doi:10.1093/jhered/93.1.77

    Article  CAS  PubMed  Google Scholar 

  • Wilson JP, Hess DE, Hanna WW, Kumar KA, Gupta SC (2004) Pennisetum glaucum subsp. monodii accessions with Striga resistance in West Africa. Crop Prot 23:865–870

    Article  Google Scholar 

  • Xu Y, Zhu L, Xiao J, Huang N, McCouch SR (1997) Chromosomal regions associated with segregation distortion of molecular markers in F2, backcross, doubled haploid and recombinant inbred populations of rice (Oryza sativa L.). Mol Gen Genet 253:535–545

    Article  CAS  PubMed  Google Scholar 

  • Yoshida S, Shirasu K (2009) Multiple layers of incompatibility to the parasitic witchweed, Striga hermonthica. New Phytol 183:180–189

    Article  PubMed  Google Scholar 

Download references

Acknowledgments

The support of the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) and the Institut de Recherche pour le Développement (IRD) are acknowledged. We would like also to thank the Institut de Biologie Intégrative et des Systèmes (IBIS) at Université Laval for their involvement in the process of GBS. This publication was finalized as part of the CGIAR Research Program on Dryland Cereals.

Author information

Authors and Affiliations

  1. Département de Phytologie, Faculté des Sciences de l’Agriculture et de l’Alimentation and Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec, QC, G1V 0A6, Canada

    K. H. Moumouni, M. Jean & F. Belzile

  2. International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), BP 12404, Niamey, Niger

    B. A. Kountche, C. T. Hash & B. I. G. Haussmann

  3. Institut de Recherche pour le Développement (IRD), 34394, Montpellier Cedex 5, France

    B. A. Kountche & Y. Vigouroux

  4. Faculté d’Agronomie, Université Abdou Moumouni, BP 10960, Niamey, Niger

    B. A. Kountche

  5. Institute of Plant Breeding, Seed Science and Population Genetics (350a), University of Hohenheim, 70599, Stuttgart, Germany

    B. I. G. Haussmann

Authors
  1. K. H. Moumouni
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. B. A. Kountche
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. M. Jean
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. C. T. Hash
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Y. Vigouroux
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. B. I. G. Haussmann
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. F. Belzile
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to F. Belzile.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 68 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Moumouni, K.H., Kountche, B.A., Jean, M. et al. Construction of a genetic map for pearl millet, Pennisetum glaucum (L.) R. Br., using a genotyping-by-sequencing (GBS) approach. Mol Breeding 35, 5 (2015). https://doi.org/10.1007/s11032-015-0212-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s11032-015-0212-x

Keywords

Search

Navigation