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

Girma, Dejene; Cannarozzi, Gina; Weichert, Annett; Tadele, Zerihun (2018). Genotyping by Sequencing Reasserts the Close Relationship between Tef and Its Putative Wild Eragrostis Progenitors. Diversity, 10(2), p. 17. MDPI AG 10.3390/d10020017

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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.

Item Type:

Journal Article (Original Article)

Division/Institute:

08 Faculty of Science > Department of Biology > Institute of Plant Sciences (IPS) > Plant Development
10 Strategic Research Centers > Centre for Development and Environment (CDE)
08 Faculty of Science > Department of Biology > Institute of Plant Sciences (IPS)

UniBE Contributor:

Kebede, Dejene Girma; Cannarozzi, Gina Michelle; Weichert, Annett and Tadele, Zerihun

Subjects:

500 Science > 580 Plants (Botany)

ISSN:

1424-2818

Publisher:

MDPI AG

Language:

English

Submitter:

Peter Alfred von Ballmoos-Haas

Date Deposited:

02 May 2018 13:46

Last Modified:

22 Oct 2019 21:11

Publisher DOI:

10.3390/d10020017

Uncontrolled Keywords:

Eragrostis; genetic diversity; genotyping by sequencing (GBS); phylogenetic relationships; population structure; single nucleotide polymorphism (SNP); sequence similarity; tef

BORIS DOI:

10.7892/boris.113420

URI:

https://boris.unibe.ch/id/eprint/113420

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