Molecular genetic diversity and population structure of Ethiopian white lupin landraces: Implications for breeding and conservation

PLoS One. 2017 Nov 30;12(11):e0188696. doi: 10.1371/journal.pone.0188696. eCollection 2017.

Abstract

White lupin is one of the four economically important species of the Lupinus genus and is an important grain legume in the Ethiopian farming system. However, there has been limited research effort to characterize the Ethiopian white lupin landraces. Fifteen polymorphic simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure of 212 Ethiopian white lupin (Lupinus albus) landraces and two genotypes from different species (Lupinus angustifolius and Lupinus mutabilis) were used as out-group. The SSR markers revealed 108 different alleles, 98 of them from 212 landraces and 10 from out-group genotypes, with an average of 6.5 alleles per locus. The average gene diversity was 0.31. Twenty eight landraces harbored one or more private alleles from the total of 28 private alleles identified in the 212 white lupin accessions. Seventy-seven rare alleles with a frequency of less than 5% were identified and accounted for 78.6% of the total alleles detected. Analysis of molecular variance (AMOVA) showed that 92% of allelic diversity was attributed to individual accessions within populations while only 8% was distributed among populations. At 70% similarity level, the UPGMA dendrogram resulted in the formation of 13 clusters comprised of 2 to 136 landraces, with the out-group genotypes and five landraces remaining distinct and ungrouped. Population differentiation and genetic distance were relatively high between Gondar and Ethiopian white lupin populations collected by Australians. A model-based population structure analysis divided the white lupin landraces into two populations. All Ethiopian white lupin landrace populations, except most of the landraces collected by Australians (77%) and about 44% from Awi, were grouped together with significant admixtures. The study also suggested that 34 accessions, as core collections, were sufficient to retain 100% of SSR diversity. These accessions (core G-34) represent 16% of the whole 212 Ethiopian white lupin accessions and populations from West Gojam, Awi and Australian collections contributed more accessions to the core collection.

MeSH terms

  • Conservation of Natural Resources*
  • Ethiopia
  • Genes, Plant
  • Genetic Variation*
  • Lupinus / genetics*
  • Polymerase Chain Reaction

Grants and funding

The study was part of PhD research work of the first author (MA) and he is grateful to the Ethiopian Institute of Agricultural Research (EIAR) for giving him study leave. The study was supported by the BecA-ILRI Hub through the Africa Biosciences Challenge Fund (ABCF) program. The ABCF Program is funded by the Australian Department for Foreign Affairs and Trade (DFAT) through the BecA-CSIRO partnership; the Syngenta Foundation for Sustainable Agriculture (SFSA); the Bill & Melinda Gates Foundation (BMGF); the UK Department for International Development (DFID) and; the Swedish International Development Cooperation Agency (Sida). The landrace accessions were kindly provided by the Ethiopian Biodiversity Institute (EBI).MA would also like to thank Elena Hidalgo (Professor in molecular biology, University of Valladolid, Spain) and Belayneh Admasu (Former director of Holeta National biotechnology laboratory of the Ethiopian Institute of Agricultural Research) for their assistance during the initial stage of this work. Authors would like to thank Helen Altshul for her assistance in language proof reading. This work was approved by EIAR as part of its research activities. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.