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Genetic diversity of indigenous Bradyrhizobium nodulating promiscuous soybean [Glycine max (L) Merr.] varieties in Kenya: Impact of phosphorus and lime fertilization in two contrasting sites

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Abstract

While soybean is an exotic crop introduced in Kenya early last century, promiscuous (TGx) varieties which nodulate with indigenous rhizobia have only recently been introduced. Since farmers in Kenya generally cannot afford or access fertilizer or inoculants, the identification of effective indigenous Bradyrhizobium strains which nodulate promiscuous soybean could be useful in the development of inoculant strains. Genetic diversity and phylogeny of indigenous Bradyrhizobium strains nodulating seven introduced promiscuous soybean varieties grown in two different sites in Kenya was assayed using the Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) of the 16S-23S rDNA intergenic spacer region and 16S rRNA gene sequencing. PCR-RFLP analysis directly applied on 289 nodules using Msp I distinguished 18 intergenic spacer groups (IGS) I–XVIII. Predominant IGS groups were I, III, II, IV and VI which constituted 43.9%, 24.6%, 8.3% 7.6% and 6.9% respectively of all the analyzed nodules from the two sites while IGS group VII, IX, X, XI, XII, XIV, XVI, XVII, XVIII each constituted 1% or less. The IGS groups were specific to sites and treatments but not varieties. Phylogenetic analysis of the 16S rRNA gene sequences showed that all indigenous strains belong to the genus Bradyrhizobium. Bradyrhizobium elkanii, Bradyrhizobium spp and Bradyrhizobium japonicum related strains were the most predominant and accounted for 37.9%, 34.5%, and 20.7% respectively while B. yuanmigense related accounted for 6.9% of all strains identified in the two combined sites. The diversity identified in Bradyrhizobium populations in the two sites represent a valuable genetic resource that has potential utility for the selection of more competitive and effective strains to improve biological nitrogen fixation and thus increase soybean yields at low cost.

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Acknowledgement

This research was funded by the Rockefeller Foundation Project: “Exploring the multiple potentials of soybeans in enhancing rural livelihoods and small industry in east Africa” through Tropical Soil Biology and Fertility of International Centre for Tropical Agriculture (TSBF-CIAT) and Kenya Agricultural Productivity Project and both are gratefully acknowledged.

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Authors and Affiliations

  1. Kenya Agricultural Research Institute (KARI), P.O. Box 57811-00200, Nairobi, Kenya

    V. W. Wasike

  2. Tropical Soil Biology and Fertility Institute of the International Centre for Tropical Agriculture (TSBF-CIAT), United Nations Avenue, P.O. Box 30677, Nairobi, Kenya

    V. W. Wasike, N. Sanginga, H. N. Mburu, D. Mugadi, P. Wango & B. Vanlauwe

  3. Department of Crops Horticulture and Soils, Egerton University, P.O. Box 536, Njoro, Kenya

    V. W. Wasike, N. W. Mungai & L. M. Mumera

  4. Department of Biochemistry and Molecular Biology, Egerton University, P.O. Box 536, Egerton, Kenya

    F. N. Wachira

  5. CIRAD, PERSYST Department, UPR Ecosystems of Plantations, Tropical Soil Biology and Fertility Institute of the International Centre for Tropical Agriculture (TSBF-CIAT), United Nations Avenue, P.O. Box 30677, Nairobi, Kenya

    D. Lesueur

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  1. V. W. Wasike
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Correspondence to D. Lesueur.

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Wasike, V.W., Lesueur, D., Wachira, F.N. et al. Genetic diversity of indigenous Bradyrhizobium nodulating promiscuous soybean [Glycine max (L) Merr.] varieties in Kenya: Impact of phosphorus and lime fertilization in two contrasting sites. Plant Soil 322, 151–163 (2009). https://doi.org/10.1007/s11104-009-9902-7

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