Dataset Information

Comparative analyses of 32 complete plastomes of Tef (Eragrostis tef ) accessions from Ethiopia: phylogenetic relationships and mutational hotspots.

ABSTRACT: Eragrostis tef is an important cereal crop in Ethiopia with excellent storage properties, high-quality food, and the unique ability to thrive in extreme environmental conditions. However, the application of advanced molecular tools for breeding and conservation of these species is extremely limited. Therefore, developing chloroplast genome resources and high-resolution molecular markers are valuable to E. tef population and biogeographic studies. In the current study, we assembled and compared the complete plastomes of 32 E. tef accessions. The size of the plastomes ranged from 134,349 to 134,437 bp with similar GC content (?38.3%). Genomes annotations revealed 112 individual genes, including 77 protein-coding, 31 tRNA, and 4 rRNA genes. Comparison of E. tef plastomes revealed a low degree of intraspecific sequence variations and no structural differentiations. Furthermore, we found 34 polymorphic sites (13 cpSSRs, 12 InDels, and 9 SNPs) that can be used as valuable DNA barcodes. Among them, the majority (88%) of the polymorphic sites were identified in the noncoding genomic regions. Nonsynonymous (ka) and synonymous (ks) substitution analysis showed that all PCGs were under purifying selection (ka/ks <1). The phylogenetic analyses of the whole plastomes and polymorphic region sequences were able to distinguish the accession from the southern population, indicating its potential to be used as a super-barcode. In conclusion, the newly generated plastomes and polymorphic markers developed here could be a useful genomic resource in molecular breeding, population genetics and the biogeographical study of E. tef.

SUBMITTER: Teshome GE

PROVIDER: S-EPMC7307559 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Comparative analyses of 32 complete plastomes of Tef (Eragrostis tef ) accessions from Ethiopia: phylogenetic relationships and mutational hotspots.

Teshome Girma Eshetu GE Mekbib Yeshitila Y Hu Guangwan G Li Zhi-Zhong ZZ Chen Jinming J

PeerJ 20200619

Eragrostis tef is an important cereal crop in Ethiopia with excellent storage properties, high-quality food, and the unique ability to thrive in extreme environmental conditions. However, the application of advanced molecular tools for breeding and conservation of these species is extremely limited. Therefore, developing chloroplast genome resources and high-resolution molecular markers are valuable to E. tef population and biogeographic studies. In the current study, we assembled ...[more]

PMID: 32596045

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Project description:Tef (Eragrostis tef), a staple crop that originated in the Horn of Africa, has been introduced to multiple countries over the last several decades. Crop cultivation in new geographic regions raises questions regarding the molecular basis for biotic stress responses. In this study, we aimed to classify the insect abundance on tef crop in Israel, and to elucidate its chemical and physical defense mechanisms in response to insect feeding. To discover the main pests of tef in the Mediterranean climate, we conducted an insect field survey on three selected accessions named RTC-144, RTC-405, and RTC-406, and discovered that the most abundant insect order is Hemiptera. We compared the differences in Rhopalosiphum padi (Hemiptera; Aphididae) aphid performance, preference, and feeding behavior between the three accessions. While the number of aphid progeny was lower on RTC-406 than on the other two, the aphid olfactory assay indicated that the aphids tended to be repelled from the RTC-144 accession. To highlight the variation in defense responses, we investigated the physical and chemical mechanisms. As a physical barrier, the density of non-granular trichomes was evaluated, in which a higher number of trichomes on the RTC-406 than on the other accessions was observed. This was negatively correlated with aphid performance. To determine chemical responses, the volatile and central metabolite profiles were measured upon aphid attack for 4 days. The volatile analysis exposed a rich and dynamic metabolic profile, and the central metabolism profile indicated that tef plants adjust their sugars and organic and amino acid levels. Overall, we found that the tef plants possess similar defense responses as other Poaceae family species, while the non-volatile deterrent compounds are yet to be characterized. A transcriptomic time-series analysis of a selected accession RTC-144 infested with aphids revealed a massive alteration of genes related to specialized metabolism that potentially synthesize non-volatile toxic compounds. This is the first report to reveal the variation in the defense mechanisms of tef plants. These findings can facilitate the discovery of insect-resistance genes leading to enhanced yield in tef and other cereal crops.

Project description:Teff [Eragrostis tef (Zuccagni) Trotter] is a small-sized cereal grain and an indigenous crop in Ethiopia. The Amhara region is one of the major teff producers regions in the country. However, information on the phenolic content of the region's teff varieties is limited. Seventy-two teff samples were collected from three administrative zones (West Gojjam zone, Awi zone, and East Gojjam zone) of the Amhara region of Ethiopia. The samples' total polyphenol and flavonoid contents were determined using colorimetric methods. The total flavonoid contents expressed as catechin equivalent, CE (i.e., under alkaline conditions) and quercetin equivalent, Q.E (i.e., under the methanolic solution of AlCl3) were found to be in the range of 7.66 ± 0.60-57.36 ± 3.87 mg C.E and 15.45 ± 0.15-113.12 ± 3.09 mg Q.E per 100 g of teff samples, respectively. The corresponding total polyphenol content (TPC), described as gallic acid equivalent (G.A.E.), was in the range of 46.21 ± 1.20-133.32 ± 5.44 mg G.A.E. The results showed that the mean TPC value of the teff samples from the West Gojjam zone was enriched with polyphenol than samples from the Awi zone and East Gojjam. Furthermore, it was noted that the mean TPC and TFC values did not vary significantly between samples of the East Gojjam and Awi zone (p > 0.05). In contrast, a significant difference in mean TPC and TFC-Q.E were noted between the sampling zone of East Gojjam and West Gojjam and between West Gojjam and Awi zones (p < 0.05). These significant variations in TPC and TFC might be due to observable variations in the agroecological zones and the genetic-make-up of the samples. Person correlation indicated a significant positive correlation matrix between the three variables (p = 0.01). The teff samples were trying to be classified based on their geographical origin using hierarchical cluster analysis (HCA) and biplots. Accordingly, the variance explained by component 1 (PC1) is 67.2%, and the variance explained by component 2 (PC2) is 20.0%.

Dataset Information

Comparative analyses of 32 complete plastomes of Tef (Eragrostis tef ) accessions from Ethiopia: phylogenetic relationships and mutational hotspots.

Publications

Comparative analyses of 32 complete plastomes of Tef (<i>Eragrostis tef</i> ) accessions from Ethiopia: phylogenetic relationships and mutational hotspots.

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