Conservation Genetics

, Volume 15, Issue 6, pp 1269–1280 | Cite as

Assessment of genetic diversity among sorghum landraces and their wild/weedy relatives in western Kenya using simple sequence repeat (SSR) markers

  • Maria G. Salas FernandezEmail author
  • James A. Okeno
  • Evans Mutegi
  • Anania Fessehaie
  • Samantha Chalfant
Research Article


Understanding the extent of gene exchange between cultivated sorghum and its wild/weedy relatives and the evolutionary processes (including farmers’ practices) that act to shape the structure of genetic diversity within and between them is an important aspect for germplasm conservation strategies, biosafety risk assessment, and crop improvement programs. In this study, molecular characterization and genetic diversity analyses were conducted on wild, weedy and cultivated sorghums collected at a local-scale in a traditional farming system in the Lambwe Valley of western Kenya. Nine simple sequence repeat (SSR) markers were used to genotype 294 cultivated sorghum and 200 wild sorghum individuals. The nine SSR markers were highly polymorphic with a number of alleles that varied from 2 to 19. Overall, wild sorghums had higher genetic diversity, observed heterozygosity, total number of alleles, polymorphic information content and more genotypes per locus than the cultivated types. A Mantel test demonstrated that there was significant isolation-by-distance for wilds and cultivated materials. STRUCTURE, cluster and principal coordinate analyses consistently assigned wild and cultivated individuals to different groups but failed to place hybrids/weedy types as a single separate group from wilds. Our results provide strong evidence of significant genetic diversity retained within wilds, larger divergence between wild and cultivated materials and reduced gene flow than those previously reported in Kenya. These results demonstrate the value of the Lambwe Valley region as a genetic reservoir and the importance to conduct genetic diversity studies at the local scale to design and execute appropriate in situ conservation programs and policies.


Genetic diversity Sorghum bicolor SSR markers Kenya Local-scale collection 



The funds from the Biosafety Institute for Genetically Modified Agricultural Products, Iowa State University, for the visiting scientist program enabled J. A. Okeno to participate in this study. We also acknowledge Dr. Kendall Lamkey, Chair of the Department of Agronomy, Iowa State University, for providing an Agronomy Endowment travel grant to J. A. Okeno to make a reconnaissance trip to sorghum fields in Lambwe Valley, Kenya. The authors thank Mr. Zachary Muthamia (head National Gene Bank of Kenya) for logistical support obtained from the National Gene Bank of Kenya. We highly appreciate the entry permit and security accorded us by the Kenya Wildlife Services to enter and collect wild sorghum in Ruma National Park. We are equally grateful to Mr. Geoffrey Mugambi and Dr. Santie de Villiers (ICRISAT-Nairobi) for DNA extraction, purification, and shipment. Finally, we are indebted to Jonathan Hirsi, Charles Ndiege, and Richard Otip for participating in all sample collection trips.


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Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Maria G. Salas Fernandez
    • 1
    Email author
  • James A. Okeno
    • 2
    • 3
  • Evans Mutegi
    • 5
  • Anania Fessehaie
    • 6
  • Samantha Chalfant
    • 2
    • 4
  1. 1.Department of AgronomyIowa State UniversityAmesUSA
  2. 2.Seed Science Center/Biosafety Institute of Genetically Modified Agricultural ProductsIowa State UniversityAmesUSA
  3. 3.African Agricultural Technology Foundation (AATF)NairobiKenya
  4. 4.Burns & McDonnellKansas CityUSA
  5. 5.Department of Evolution Ecology and Organismal BiologyOhio State UniversityColumbusUSA
  6. 6.Nunhems Netherlands BV/Bayer CropSciencesHaelenThe Netherlands

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