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Association analysis of low-phosphorus tolerance in West African pearl millet using DArT markers

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Abstract

Pearl millet [Pennisetum glaucum (L.) R. Br.] is a food security crop in the harshest agricultural regions of the world. While low soil phosphorus (P) availability is a big constraint on its production, especially in West Africa (WA), information on genomic regions responsible for low-P tolerance in pearl millet is generally lacking. We present the first report on genetic polymorphisms underlying several plant P-related parameters, flowering time (FLO) and grain yield (GY) under P-limiting conditions based on 285 diversity array technology markers and 151 West African pearl millet inbred lines phenotyped in six environments in WA under both high-P and low-P conditions. Nine markers were significantly associated with P-related traits, nine markers were associated with FLO, whereas 13 markers were associated with GY each explaining between 5.5 and 15.9 % of the observed variation. Both constitutive and adaptive associations were observed for FLO and GY, with markers PgPb11603 and PgPb12954 being associated with the most stable effects on FLO and GY, respectively, across locations. There were a few shared polymorphisms between traits, especially P-efficiency-related traits and GY, implying possible colocation of genomic regions responsible for these traits. Our findings help bridge the gap between quantitative and molecular methods of studying complex traits like low-P tolerance in WA. However, validation of these markers is necessary to determine their potential applicability in marker-assisted selection programs targeting low-P environments, which are especially important in WA where resource-poor farmers are expected to be the hardest hit by the approaching global P crisis.

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Acknowledgments

The financial support from the German Federal Ministry for Economic Cooperation and Development (BMZ) through the BMZ-Abiotic Stress project (GIZ Project Number 09.7860.1-001.00) based at ICRISAT West Africa-Niamey, from Foundation ‘Fiat Panis’ through the Food Security Centre at University of Hohenheim to DC Gemenet and from the McKnight Foundation Collaborative Crop Research Program to BIG Haussmann is gratefully appreciated. We thank Mr. Hamadou Adamou, Mr. Ada Abarchi and Mr. Issa Karimou (all at ISC-Sadoré) for preparing and coordinating the field trials within the region. Our sincere appreciation is extended to the technical staff at collaborating NARs in Burkina Faso, Mali and Senegal for conducting trials in their respective countries. The publication is an output of a scholarship from the Food Security Centre from the University of Hohenheim, which is part of the DAAD (German Academic Exchange Service) program ‘exceed’ and is supported by DAAD and BMZ. The work was finalized as part of the CGIAR Research Program on Dryland Cereals.

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Authors and Affiliations

  1. Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Fruwirthstr. 21, 70599, Stuttgart, Germany

    D. C. Gemenet, W. L. Leiser & B. I. G. Haussmann

  2. Kenya Agricultural and Livestock Research Organization, PO Box 57811, Nairobi, 00200, Kenya

    D. C. Gemenet

  3. International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Sahelian Center, Niamey, Niger

    I. I. Angarawai & C. T. Hash

  4. Institut de l’Environnement et de Recherches Agricoles (INERA), Ouagadougou, Burkina Faso

    R. G. Zangre

  5. Institut d’Economie Rurale (IER), Cinzana, Mali

    M. D. Sanogo

  6. Institut Sénégalais de Recherches Agricoles (ISRA), Bambey, Senegal

    O. Sy

  7. The Genomics Service Laboratory, M.S. Swaminathan Center of Excellence in Genomics, ICRISAT, Hyderabad, India

    T. Mahendar

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  1. D. C. Gemenet
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Gemenet, D.C., Leiser, W.L., Zangre, R.G. et al. Association analysis of low-phosphorus tolerance in West African pearl millet using DArT markers. Mol Breeding 35, 171 (2015). https://doi.org/10.1007/s11032-015-0361-y

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