| 1. |
- Bedada Chala, Girma, et al.
(author)
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DNA sequence variation of wild barley Hordeum spontaneum (L.) across environmental gradients in Israel
- 2014
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In: Heredity. - : Springer Science and Business Media LLC. - 0018-067X .- 1365-2540. ; 112, s. 646-655
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Journal article (peer-reviewed)abstract
- Wild barley Hordeum spontaneum (L.) shows a wide geographic distribution and ecological diversity. A key question concerns the spatial scale at which genetic differentiation occurs and to what extent it is driven by natural selection. The Levant region exhibits a strong ecological gradient along the North-South axis, with numerous small canyons in an East-West direction and with small-scale environmental gradients on the opposing North-and South-facing slopes. We sequenced 34 short genomic regions in 54 accessions of wild barley collected throughout Israel and from the opposing slopes of two canyons. The nucleotide diversity of the total sample is 0.0042, which is about two-thirds of a sample from the whole species range (0.0060). Thirty accessions collected at 'Evolution Canyon' (EC) at Nahal Oren, close to Haifa, have a nucleotide diversity of 0.0036, and therefore harbor a large proportion of the genetic diversity. There is a high level of genetic clustering throughout Israel and within EC, which roughly differentiates the slopes. Accessions from the hot and dry South-facing slope have significantly reduced genetic diversity and are genetically more distinct from accessions from the North-facing slope, which are more similar to accessions from other regions in Northern Israel. Statistical population models indicate that wild barley within the EC consist of three separate genetic clusters with substantial gene flow. The data indicate a high level of population structure at large and small geographic scales that shows isolation-by-distance, and is also consistent with ongoing natural selection contributing to genetic differentiation at a small geographic scale.
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| 2. |
- Bedada Chala, Girma
(author)
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Genomic divergence in differentially adapted wild and domesticated barley
- 2014
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Doctoral thesis (other academic/artistic)abstract
- Genomic divergence is responsible for plant differential adaptation to diverse and contrasting environments and different biotic stresses. This thesis focuses on the analyses of the adaptive genomic divergence in wild and domesticated barley and the driving evolutionary forces, and to identify genes and genetic variation with signature of adaptive selection. By applying genome scanning, transcriptome sequencing and customized target-enriched pool sequencing approaches, we found strong adaptive patterns of genomic divergence in wild barley across environmental gradients in Israel, which is about two-thirds of the variation found in samples from the whole species range. Hence, high level of population structure driven by natural selection and neutral evolutionary forces was observed at large and small geographical scales. Strong phenotypic and genomic differentiation was detected between wild barley ecotypes from the desert and Mediterranean environments. The desert ecotype had better water use efficiency and higher leaf relative water content. The majority of the transcripts were non-shared between the ecotypes and hence novel transcripts were identified. The genomic divergence was about 2-fold higher in the desert ecotype and it harbored more deleterious mutations than the Mediterranean ecotype, which is genetically closer to cultivated barley. Novel transcripts from the desert ecotype and genes differentially expressed in another drought-tolerant ecotype showed higher genomic divergence than the average genes. Using the targeted captured pooled sequencing, we identified genes and genetic variation with signature of selection in wild and Ethiopian cultivated barley genotypes. Ethiopian barley had high genomic divergence similar to wild barley, retained large proportion of ancestral variation, and showed low genomic differentiation from the wild ancestor. Using the targeted sequence capturing method, we were able to detect known BARE retroelement insertions and further identify genome-wide novel insertions from pooled sequencing of wild and Ethiopian barley genotypes. Keywords: BARE, drought tolerance, Hordeum, Evolution Canyon, genome divergence, population structure, transcriptome, targeted capture, transposable element, wild barley.
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| 3. |
- Bedada Chala, Girma
(author)
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Meristem culture of selected sweet potato (Ipomoea batatas L. Lam.) cultivars to produce virus-free planting material
- 2012
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In: Journal of Horticultural Science and Biotechnology. - : Informa UK Limited. - 1462-0316 .- 2380-4084. ; 87, s. 255-260
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Journal article (peer-reviewed)abstract
- Sweet potato (Ipomoea batatas L. Lam.) is a staple root crop, consumed as a carbohydrate-rich food source in many tropical countries. The production and productivity of sweet potato is limited by several factors, mainly virus infections. This study was conducted to produce virus-free sweet potato planting material using meristem culture. Meristems without leaf primordia were excised from four virus-positive field-grown local sweet potato cultivars 'Bellela', 'Temesgen', 'LO-323', and 'Zapallo'. Meristems were cultured in Murashige and Skoog (MS) medium supplemented with different combinations and concentrations of 6-benzylaminopurine (BAP), alpha-naphthaleneacetic acid (NAA), and gibberellic acid (GA(3)) for shoot initiation. 'Bellela' and 'Temesgen' exhibited 100% shoot initiation on 5 mg l(-1) BAP, 0.01 mg l(-1) NAA, and 1 mg l(-1) GA(3), although the shoots were bushy. 'LO-323' showed 90% shoot initiation with the best shoot quality on 2 mg l(-1) BAP, 0.01 mg l(-1) NAA, and 1 mg l(-1) GA(3). Shoot tips and nodes from in vitro-grown plantlets were cultured on BAP (0, 0.5, 1.0, or 2.0 mg l(-1)) or on BAP (0, 0.5, 1.0, or 2.0 mg l(-1)) + kinetin (Kin; 0, 0.1, 0.5 or 1.0 mg l(-1)) for multiple shoot formation. The best shoot proliferation was obtained on MS + 0.5 mg l(-1) BAP + 0.5 mg l(-1) Kin. In vitro-grown shoots were cultured on MS medium containing 0.0, 0.01, 0.1, 0.5, or 1.0 mgl(-1) indole-3-butyric acid (IBA). The best root formation was obtained on IBA-free medium. The plantlets thus produced were tested for the presence of ten sweet potato viruses [Sweet potato chlorotic stunt virus (SPCSV), Sweet potato feathery mottle virus (SPFMV), Sweet potato mild mottle virus (SPMMV), Sweet potato chlorotic fleck virus (SPCFV), Sweet potato caulimo-like virus (SPCaLV), Sweet potato mild speckling virus (SPMSV), C-6 (a flexuous rod virus), Sweet potato latent virus (SwPLV), Sweet potato virus G (SPVG), and Cucumber mosaic virus (CMV)] using nitrocellulose membrane enzyme-linked immunosorbent assay (NCM-ELISA). Ninety-nine percent of plantlets were free from all viruses.
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| 4. |
- Bedada Chala, Girma, et al.
(author)
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Transcriptome sequencing of two wild barley (Hordeum spontaneum L.) ecotypes differentially adapted to drought stress reveals ecotype-specific transcripts
- 2014
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In: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 15
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Journal article (peer-reviewed)abstract
- Background: Wild barley is adapted to highly diverse environments throughout its geographical distribution range. Transcriptome sequencing of differentially adapted wild barley ecotypes from contrasting environments contributes to the identification of genes and genetic variation involved in abiotic stress tolerance and adaptation.Results: Two differentially adapted wild barley ecotypes from desert (B1K2) and Mediterranean (B1K30) environments were analyzed for drought stress response under controlled conditions. The desert ecotype lost more water under both irrigation and drought, but exhibited higher relative water content (RWC) and better water use efficiency (WUE) than the coastal ecotype. We sequenced normalized cDNA libraries from drought-stressed leaves of both ecotypes with the 454 platform to identify drought-related transcripts. Over half million reads per ecotype were de novo assembled into 20,439 putative unique transcripts (PUTs) for B1K2, 21,494 for B1K30 and 28,720 for the joint assembly. Over 50% of PUTs of each ecotype were not shared with the other ecotype. Furthermore, 16% (3,245) of B1K2 and 17% (3,674) of B1K30 transcripts did not show orthologous sequence hits in the other wild barley ecotype and cultivated barley, and are candidates of ecotype-specific transcripts. Over 800 unique transcripts from each ecotype homologous to over 30 different stress-related genes were identified. We extracted 1,017 high quality SNPs that differentiated the two ecotypes. The genetic distance between the desert ecotype and cultivated barley was 1.9-fold higher than between the Mediterranean ecotype and cultivated barley. Moreover, the desert ecotype harbored a larger proportion of non-synonymous SNPs than the Mediterranean ecotype suggesting different demographic histories of these ecotypes.Conclusions: The results indicate a strong physiological and genomic differentiation between the desert and Mediterranean wild barley ecotypes and a closer relationship of the Mediterranean to cultivated barley. A significant number of novel transcripts specific to wild barley were identified. The higher SNP density and larger proportion of SNPs with functional effects in the desert ecotype suggest different demographic histories and effects of natural selection in Mediterranean and desert wild barley. The data are a valuable genomic resource for an improved genome annotation, transcriptome studies of drought adaptation and a source of new genetic markers for future barley improvement.
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| 5. |
- Hu, Jia, et al.
(author)
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Fumarate reductase drives methane emissions in the genus Oryza through differential regulation of the rhizospheric ecosystem
- 2024
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In: Environment International. - 0160-4120 .- 1873-6750. ; 190
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Journal article (peer-reviewed)abstract
- The emergence of waterlogged Oryza species similar to 15Mya (million years ago) supplied an anoxic warm bed for methane-producing microorganisms, and methane emissions have hence accompanied the entire evolutionary history of the genus Oryza. However, to date no study has addressed how methane emission has been altered during Oryza evolution. In this paper we used a diverse collection of wild and cultivated Oryza species to study the relation between Oryza evolution and methane emissions. Phylogenetic analyses and methane detection identified a co-evolutionary pattern between Oryza and methane emissions, mediated by the diversity of the rhizospheric ecosystems arising from different oxygen levels. Fumarate was identified as an oxygen substitute used to retain the electron transport/energy production in the anoxic rice root, and the contribution of fumarate reductase to Oryza evolution and methane emissions has also been assessed. We confirmed the between-species patterns using genetic dissection of the traits in a cross between a low and high methane-emitting species. Our findings provide novel insights on the evolutionary processes of rice paddy methane emissions: the evolution of wild rice produces different Oryza species with divergent rhizospheric ecosystem attributing to the different oxygen levels and fumarate reductase activities, methane emissions are comprehensively assessed by the rhizospheric environment of diversity Oryza species and result in a co-evolution pattern.
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| 6. |
- Moreno, Silvana, et al.
(author)
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Response to Waterlogging Stress in Wild and Domesticated Accessions of Timothy (Phleum pratense) and Its Relatives P. alpinum and P. nodosum
- 2023
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In: Plants. - 2223-7747. ; 12
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Journal article (peer-reviewed)abstract
- Timothy (Phleum pratense) is a cool-season perennial forage grass widely grown for silage and hay production in northern regions. Climate change scenarios predict an increase in extreme weather events with fluctuating periods of high rainfall, requiring new varieties adapted to waterlogging (WL). Wild accessions could serve as germplasm for breeding, and we evaluated the responses of 11 wild and 8 domesticated accessions of timothy, P. nodosum and P. alpinum from different locations in northern Europe. Young plants at tillering stage were exposed to WL for 21 days in a greenhouse, and responses in growth allocation and root anatomy were studied. All accessions produced adventitious roots and changed allocation of growth between shoot and root as a response to WL, but the magnitude of these responses varied among species and among accessions. P. pratense responded less in these traits in response to WL than the other two species. The ability to form aerenchyma in the root cortex in response to WL was found for all species and also varied among species and among accessions, with the highest induction in P. pratense. Interestingly, some accessions were able to maintain and even increase root growth, producing more leaves and tillers, while others showed a reduction in the root system. Shoot dry weight (SDW) was not significantly affected by WL, but some accessions showed different and significant responses in the rate of production of leaves and tillers. Overall correlations between SDW and aerenchyma and between SDW and adventitious root formation were found. This study identified two wild timothy accessions and one wild P. nodosum accession based on shoot and root system growth, aerenchyma formation and having a root anatomy considered to be favorable for WL tolerance. These accessions are interesting genetic resources and candidates for development of climate-resilient timothy varieties.
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| 7. |
- Rahimi, Yousef, et al.
(author)
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Phenotypic Diversity in Domesticated and Wild Timothy Grass, and Closely Related Species for Forage Breeding
- 2023
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In: Plants. - 2223-7747. ; 12
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Journal article (peer-reviewed)abstract
- Timothy grass (Phleum pratense L.) is one of the most important forage crops in temperate regions. Forage production, however, faces many challenges, and new cultivars adapted to a changing climate are needed. Wild populations and relatives of timothy may serve as valuable genetic resources in the breeding of improved cultivars. The aim of our study is to provide knowledge about the phenotypic diversity in domesticated (cultivars, breeding lines and landraces) and wild timothy and two closely related species, P. nodosum (lowland species) and P. alpinum, (high altitude species) to identify potential genetic resources. A total of 244 accessions of timothy and the two related species were studied for growth (plant height, fresh and dry weight) and plant development (days to stem elongation, days to booting and days to heading) in the field and in a greenhouse. We found a large diversity in development and growth between the three Phleum species, as well as between the accessions within each species. Timothy showed the highest growth, but no significant difference was found between wild accessions and cultivars of timothy in fresh and dry weight. However, these two groups of accessions showed significant differences in plant development, where timothy cultivars as a group reached flowering earlier than the wild accessions. This suggests that there has not been a strong directional selection towards increased yield during the domestication and breeding of timothy; rather, timothy has been changed for other traits such as earlier heading. Principal component analysis and cluster analysis based on all traits revealed distinct clusters. Accessions falling within the same cluster showed similarities in the development and growth rather than the type of accession. The large diversity found in this study shows the potential of using timothy accessions as genetic resources in crosses with existing cultivars. Also, accessions of P. nodosum with favorable traits can be candidates for the domestication of a novel forage crop, and the high-altitude relative P. alpinum may be a source of genes for the development of more cold and stresstolerant cultivars.
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| 8. |
- Westerbergh, Anna, et al.
(author)
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Towards the Development of Perennial Barley for Cold Temperate Climates—Evaluation of Wild Barley Relatives as Genetic Resources
- 2018
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In: Sustainability. - : MDPI AG. - 2071-1050. ; 10
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Journal article (peer-reviewed)abstract
- Perennial cereal crops could limit the negative impacts of agriculture on the environment and climate change. In cold temperate climates, perennial plants must be adapted to seasonal changes and abiotic stresses, such as frost, to be able to regrow for several years. Wild crop relatives that are perennials and already adapted to cold temperate climates may provide genetic resources for breeding new perennial cereal grain crops. Barley (Hordeum vulgare) is one of the most important cereals in northern agricultural areas, and its related perennial species may be good candidates for the development of perennial cereals. We evaluated a diverse set of 17 wild perennial Hordeum species represented by 67 accessions in field conditions with a cold winter climate and long days during summer in Central Sweden (latitude 60 degrees N). Six species (H. brevisubulatum, H. bulbosum, H. fuegianum, H. jubatum, H. lechleri and H. secalinum) showed regrowth and formation of spikes for four seasons. The most distant perennial relative of barley, H. stenostachys, showed weak regrowth. H. bulbosum, the closest perennial barley relative, had a large number of accessions with wide geographic origins that showed good regrowth. Together with its storage bulbs and its cross-compatibility with barley, this makes H. bulbosum an important genetic resource for the development of perennial Hordeum grains using either the domestication or the wide-hybridization strategy.
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