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Diversity 2018, 10(2), 17; https://doi.org/10.3390/d10020017

Genotyping by Sequencing Reasserts the Close Relationship between Tef and Its Putative Wild Eragrostis Progenitors

1
Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
2
Ethiopian Institute of Agricultural Research, National Agricultural Biotechnology Research Center, Holetta P.O. Box 249, Ethiopia
3
Institute of Biotechnology, Addis Ababa University, Addis Ababa P.O. Box 32853, Ethiopia
4
Center for Development and Environment (CDE), University of Bern, 3012 Bern, Switzerland
*
Author to whom correspondence should be addressed.
Received: 5 February 2018 / Revised: 8 March 2018 / Accepted: 15 March 2018 / Published: 21 March 2018
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Abstract

The genus Eragrostis consists of 350 species, including tef (Eragrostis tef (Zucc.) Trotter), the only cultivated species in this genus. Very little is known about the genetic potential of these species for tef improvement and genomics research. Here, we investigated a germplasm panel consisting of 40 Eragrostis species and 42 tef lines with single nucleotide polymorphism (SNP) data generated using the genotyping by sequencing (GBS) protocol. Thousands of SNPs were identified genome-wide from the germplasm panel. High-quality SNPs were used to assess sequence similarity and/or divergence, genetic diversity, population structure, and phylogenetic relationships. Mapping individual reads to the tef reference genome revealed that of the 40 wild Eragrostis species included in this study, E. pilosa, E. aethiopica, E. obtusa, E. ferruginea, E. lugens, and E. lehmanniana had 92% of their sequences represented in the tef reference genome. In the maximum likelihood phylogenetic analysis, these wild species clearly showed grouping in the clade consisting of the entire tef germplasm. Population structure analysis showed two major clusters consistent with the germplasm class information and the inferred phylogenetic relationships. The wild Eragrostis species were more diverse than the tef cultivars and could therefore potentially be used to enrich the tef gene pool. The SNP dataset and the results documented here are taxonomically the most inclusive to date and could be a useful informational tool for the design of genomics-informed tef breeding and research. View Full-Text
Keywords: Eragrostis; genetic diversity; genotyping by sequencing (GBS); phylogenetic relationships; population structure; single nucleotide polymorphism (SNP); sequence similarity; tef Eragrostis; genetic diversity; genotyping by sequencing (GBS); phylogenetic relationships; population structure; single nucleotide polymorphism (SNP); sequence similarity; tef
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Girma, D.; Cannarozzi, G.; Weichert, A.; Tadele, Z. Genotyping by Sequencing Reasserts the Close Relationship between Tef and Its Putative Wild Eragrostis Progenitors. Diversity 2018, 10, 17.

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