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Genetic diversity in tef [Eragrostis tef (Zucc.) Trotter].

Assefa K, Cannarozzi G, Girma D, Kamies R, Chanyalew S, Plaza-Wüthrich S, Blösch R, Rindisbacher A, Rafudeen S, Tadele Z - Front Plant Sci (2015)

Bottom Line: These germplasm accessions appear to have huge variability with regard to key agronomic and nutritional traits.In order to properly utilize the variability in developing new tef cultivars, various techniques have been implemented to catalog the extent and unravel the patterns of genetic diversity.In this review, we show some recent initiatives investigating the diversity of tef using genomics, transcriptomics and proteomics and discuss the prospect of these efforts in providing molecular resources that can aid modern tef breeding.

View Article: PubMed Central - PubMed

Affiliation: National Tef Research Program, Debre Zeit Agricultural Research Center, Ethiopian Institute of Agricultural Research Debre Zeit, Ethiopia.

ABSTRACT
Tef [Eragrostis tef (Zucc.) Trotter] is a cereal crop resilient to adverse climatic and soil conditions, and possessing desirable storage properties. Although tef provides high quality food and grows under marginal conditions unsuitable for other cereals, it is considered to be an orphan crop because it has benefited little from genetic improvement. Hence, unlike other cereals such as maize and wheat, the productivity of tef is extremely low. In spite of the low productivity, tef is widely cultivated by over six million small-scale farmers in Ethiopia where it is annually grown on more than three million hectares of land, accounting for over 30% of the total cereal acreage. Tef, a tetraploid with 40 chromosomes (2n = 4x = 40), belongs to the family Poaceae and, together with finger millet (Eleusine coracana Gaerth.), to the subfamily Chloridoideae. It was originated and domesticated in Ethiopia. There are about 350 Eragrostis species of which E. tef is the only species cultivated for human consumption. At the present time, the gene bank in Ethiopia holds over five thousand tef accessions collected from geographical regions diverse in terms of climate and elevation. These germplasm accessions appear to have huge variability with regard to key agronomic and nutritional traits. In order to properly utilize the variability in developing new tef cultivars, various techniques have been implemented to catalog the extent and unravel the patterns of genetic diversity. In this review, we show some recent initiatives investigating the diversity of tef using genomics, transcriptomics and proteomics and discuss the prospect of these efforts in providing molecular resources that can aid modern tef breeding.

No MeSH data available.


Phylogenetic tree showing the relationship among natural accessions and improved varieties of tef. The ∗ represents improved varieties. The phylogenetic tree was constructed from ∼200 bp surrounding an SSR marker located on linkage group nine (Zeid et al., 2011). Quncho, the most popular variety in Ethiopia was produced from a cross between the high-yielding Dukem variety and the white-seeded Magna variety.
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Figure 2: Phylogenetic tree showing the relationship among natural accessions and improved varieties of tef. The ∗ represents improved varieties. The phylogenetic tree was constructed from ∼200 bp surrounding an SSR marker located on linkage group nine (Zeid et al., 2011). Quncho, the most popular variety in Ethiopia was produced from a cross between the high-yielding Dukem variety and the white-seeded Magna variety.

Mentions: Finding and exploiting DNA sequence variation within a genome is of utmost importance for crop genetics and breeding (Varshney et al., 2009). Over the last three decades, different methods have been developed to detect and quantify the genetic diversity of tef. The first techniques employed were flow cytometry, sequencing of single genes or regions and genotyping using AFLP, RAPD, RFLP, inter-simple sequence repeat (ISSR), and simple sequence repeat (SSR) markers, and these have all shed light on the structure of allelic diversity within selected tef germplasm collections (Girma et al., 2014). As shown in Figure 2, an SSR marker was used successfully to study the relationships among diverse tef genotypes, including natural accessions and improved varieties. However, only a small part of the diversity has been studied, and many of the essential questions still remain unanswered. Currently high-throughput single nucleotide polymorphism (SNP) genotyping is one of the methods that has been used to detect and exploit the genetic diversity of several crops. Genetic diversity analysis in some of the agriculturally important food crops such as sorghum (Nelson et al., 2011) and (Morris et al., 2013), barley (Close et al., 2009), rice (Thomson et al., 2012), bread wheat and emmer wheat (Akhunov et al., 2009), durum wheat (Trebbi et al., 2011), and maize (Yan et al., 2010) have been carried out with SNP genotyping methods employing next generation sequencing technologies.


Genetic diversity in tef [Eragrostis tef (Zucc.) Trotter].

Assefa K, Cannarozzi G, Girma D, Kamies R, Chanyalew S, Plaza-Wüthrich S, Blösch R, Rindisbacher A, Rafudeen S, Tadele Z - Front Plant Sci (2015)

Phylogenetic tree showing the relationship among natural accessions and improved varieties of tef. The ∗ represents improved varieties. The phylogenetic tree was constructed from ∼200 bp surrounding an SSR marker located on linkage group nine (Zeid et al., 2011). Quncho, the most popular variety in Ethiopia was produced from a cross between the high-yielding Dukem variety and the white-seeded Magna variety.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4374454&req=5

Figure 2: Phylogenetic tree showing the relationship among natural accessions and improved varieties of tef. The ∗ represents improved varieties. The phylogenetic tree was constructed from ∼200 bp surrounding an SSR marker located on linkage group nine (Zeid et al., 2011). Quncho, the most popular variety in Ethiopia was produced from a cross between the high-yielding Dukem variety and the white-seeded Magna variety.
Mentions: Finding and exploiting DNA sequence variation within a genome is of utmost importance for crop genetics and breeding (Varshney et al., 2009). Over the last three decades, different methods have been developed to detect and quantify the genetic diversity of tef. The first techniques employed were flow cytometry, sequencing of single genes or regions and genotyping using AFLP, RAPD, RFLP, inter-simple sequence repeat (ISSR), and simple sequence repeat (SSR) markers, and these have all shed light on the structure of allelic diversity within selected tef germplasm collections (Girma et al., 2014). As shown in Figure 2, an SSR marker was used successfully to study the relationships among diverse tef genotypes, including natural accessions and improved varieties. However, only a small part of the diversity has been studied, and many of the essential questions still remain unanswered. Currently high-throughput single nucleotide polymorphism (SNP) genotyping is one of the methods that has been used to detect and exploit the genetic diversity of several crops. Genetic diversity analysis in some of the agriculturally important food crops such as sorghum (Nelson et al., 2011) and (Morris et al., 2013), barley (Close et al., 2009), rice (Thomson et al., 2012), bread wheat and emmer wheat (Akhunov et al., 2009), durum wheat (Trebbi et al., 2011), and maize (Yan et al., 2010) have been carried out with SNP genotyping methods employing next generation sequencing technologies.

Bottom Line: These germplasm accessions appear to have huge variability with regard to key agronomic and nutritional traits.In order to properly utilize the variability in developing new tef cultivars, various techniques have been implemented to catalog the extent and unravel the patterns of genetic diversity.In this review, we show some recent initiatives investigating the diversity of tef using genomics, transcriptomics and proteomics and discuss the prospect of these efforts in providing molecular resources that can aid modern tef breeding.

View Article: PubMed Central - PubMed

Affiliation: National Tef Research Program, Debre Zeit Agricultural Research Center, Ethiopian Institute of Agricultural Research Debre Zeit, Ethiopia.

ABSTRACT
Tef [Eragrostis tef (Zucc.) Trotter] is a cereal crop resilient to adverse climatic and soil conditions, and possessing desirable storage properties. Although tef provides high quality food and grows under marginal conditions unsuitable for other cereals, it is considered to be an orphan crop because it has benefited little from genetic improvement. Hence, unlike other cereals such as maize and wheat, the productivity of tef is extremely low. In spite of the low productivity, tef is widely cultivated by over six million small-scale farmers in Ethiopia where it is annually grown on more than three million hectares of land, accounting for over 30% of the total cereal acreage. Tef, a tetraploid with 40 chromosomes (2n = 4x = 40), belongs to the family Poaceae and, together with finger millet (Eleusine coracana Gaerth.), to the subfamily Chloridoideae. It was originated and domesticated in Ethiopia. There are about 350 Eragrostis species of which E. tef is the only species cultivated for human consumption. At the present time, the gene bank in Ethiopia holds over five thousand tef accessions collected from geographical regions diverse in terms of climate and elevation. These germplasm accessions appear to have huge variability with regard to key agronomic and nutritional traits. In order to properly utilize the variability in developing new tef cultivars, various techniques have been implemented to catalog the extent and unravel the patterns of genetic diversity. In this review, we show some recent initiatives investigating the diversity of tef using genomics, transcriptomics and proteomics and discuss the prospect of these efforts in providing molecular resources that can aid modern tef breeding.

No MeSH data available.