Publications
NIBIOs employees contribute to several hundred scientific articles and research reports every year. You can browse or search in our collection which contains references and links to these publications as well as other research and dissemination activities. The collection is continously updated with new and historical material.
2020
Abstract
Sweet potato (Ipomoea batatas (L.) Lam.) is an important root crop for poor farmers in developing countries. Since the late 1980s, viral diseases have increasingly become a threat to sweet potato production in Ethiopia. This review paper presents the role of sweet potato production for ensuring food security, the level of sweet potato virus research, including the types of viral species identified and their current level of incidences in Ethiopia. Sweet potato feathery mottle virus (SPFMV), Sweet potato chlorotic stunt virus (SPCSV), Sweet potato virus 2 (SPV2), Sweet potato virus G (SPVG), and Cucumber mosaic virus (CMV) were reported in Ethiopia, where the first two are the most common and exist at high incidences. In addition, this paper discusses the virus vectors, virus transmission methods to new farms, factors exacerbating the rate of viral incidence and the methods used to reduce the incidences. Moreover, it highlights methods of sweet potato viruses’ detection and cleaning of infected materials in use and the challenges encountered towards the efficient utilization of the methods. Finally, we suggest major intervention techniques that will integrate all key players in managing the impact of the virus on sweet potato production to improve productivity and ensuring food security in Ethiopia. The findings obtained from this review could be an input for the current research on sweet potato improvement (both planting materials and routines) in Ethiopia.
Authors
Yongjie Kuang Shaofang Li Bin Ren Fang Yan Carl Jonas Jorge Spetz Xiangju Li Xueping Zhou Huanbin ZhouAbstract
Recently developed CRISPR-mediated base editors, which enable the generation of numerous nucleotide changes in target genomic regions, have been widely adopted for gene correction and generation of crop germplasms containing important gain-of-function genetic variations. However, to engineer target genes with unknown functional SNPs remains challenging. To address this issue, we present here a base-editing-mediated gene evolution (BEMGE) method, employing both Cas9n-based cytosine and adenine base editors as well as a single-guide RNA (sgRNA) library tiling the full-length coding region, for developing novel rice germplasms with mutations in any endogenous gene. To this end, OsALS1 was artificially evolved in rice cells using BEMGE through both Agrobacterium-mediated and particle-bombardment-mediated transformation. Four different types of amino acid substitutions in the evolved OsALS1, derived from two sites that have never been targeted by natural or human selection during rice domestication, were identified, conferring varying levels of tolerance to the herbicide bispyribac-sodium. Furthermore, the P171F substitution identified in a strong OsALS1 allele was quickly introduced into the commercial rice cultivar Nangeng 46 through precise base editing with the corresponding base editor and sgRNA. Collectively, these data indicate great potential of BEMGE in creating important genetic variants of target genes for crop improvement.
Abstract
Wheat dwarf virus (WDV), a mastrevirus transmitted by the leafhopper Psammotettix alienus, causes a severe disease in cereal crops. Typical symptoms of wheat plants infected by WDV are yellowing and severe dwarfing. In this present study, RNA-Seq was used to perform gene expression analysis in wheat plants in response to WDV infection. Comparative transcriptome analysis indicated that a total of 1042 differentially expressed genes (DEGs) were identified in the comparison between mock and WDV-inoculated wheat plants. Genomes ontology (GO) annotation revealed a number of DEGs associated with different biological processes, such as phytohormone metabolism, photosynthesis, DNA metabolic process, response to biotic stimulus and defense response. Among these, DEGs involved in phytohormone and photosynthesis metabolism and response pathways were further enriched and analyzed, which indicated that hormone biosynthesis, signaling and chloroplast photosynthesis-related genes might play an important role in symptom development after WDV infection. These results illustrate the dynamic nature of the wheat-WDV interaction at the transcriptome level and confirm that symptom development is a complex process, providing a solid foundation to elucidate the pathogenesis of WDV.
Authors
Lang Liu Yongjie Kuang Fang Yan Shaofang Li Bin Ren Gokul Gosavi Carl Jonas Jorge Spetz Xiangju Li Xifeng Wang Xueping Zhou Huanbin ZhouAbstract
No abstract has been registered
Abstract
Sweet potato (Ipomoea batatas L. Lam) has become one of the staple crops in Africa in the last 20 years. In Ethiopia, sweet potato is the second most widely grown root crop and is the first regarding the production per hectare. Thus, there is a great demand of planting material throughout the country. Currently, planting material is usually obtained from own previous season harvest, local markets or from the neighboring fields since no certified clean planting material production scheme has been established in Ethiopia yet. Unfortunately, this practice has contributed to the spread of viral diseases throughout the country. Elimination of viruses from infected plants is a tedious job, which requires efficient methods to eliminate the virus and also to verify that the plants are indeed virus-free. In the case of sweet potato, it was observed that heat treatment, combined with meristem tip culture is an efficient method for virus elimination. Previous findings indicate that reverse transcription (RT) PCR is more efficient than ELISA to verify the efficiency of virus elimination. In this study, the use of next generation sequencing (NGS) was explored as a verification method and compared with RT-PCR. The results show that NGS seems to be more efficient than RT-PCR, although also prone to inconclusive results.
Authors
Meixia Wang Ziyan Xu Gokul Gosavi Bin Ren Yongsen Cao Yongjie Kuang Changyong Zhou Carl Jonas Jorge Spetz Fang Yan Xueping Zhou Huanbin ZhouAbstract
No abstract has been registered
Authors
Harrison Mburu Laura Cortada Solveig Haukeland Wilson Ronno Moses Nyongesa Zachary Kinyua Joel L. Bargul Danny CoyneAbstract
Potato cyst nematodes (PCN), such as Globodera rostochiensis and Globodera pallida, are quarantine restricted pests of potato causing major yield and financial losses to farmers. G. rostochiensis was first reported from Kenya’s key potato growing area in 2015. We sought to determine the diversity, prevalence and distribution of PCN species across the country by conducting a country-wide survey between 2016 and 2018, which included a more focused, follow-up assessment in three key potato growing counties. A total of 1,348 soil samples were collected from 20 potato growing counties. Information regarding local potato farming practices, potato cultivar use, their diversity and availability was also recorded. PCN cysts were obtained from 968 samples (71.8%) in all the counties surveyed, with Nyandarua County recording the highest PCN field-incidence at 47.6%. The majority of PCN populations, 99.9%, were identified as G. rostochiensis, while G. pallida was recovered from just one field, in a mixed population with G. rostochiensis. Inconsistencies in PCR amplification efficiency was observed for G. rostochiensis using the recommended EPPO primers, compared with ITS primers AB28/TW81, indicating that this protocol cannot be entirely relied upon to effectively detect PCN. Egg density in Nyandarua County varied between 30.6 and 158.5 viable eggs/g soil, with an average egg viability of 78.9 ± 2.8% (min = 11.6%, max = 99.9%). The PCN-susceptible potato cultivar named Shangi was the most preferred and used by 65% of farmers due to its shorter dormancy and cooking time, while imported cultivars (Destiny, Jelly, Manitou, and Markies) with resistance to G. rostochiensis were used by 7.5% of farmers due to unavailability and/or limited access to seeds. Thus, most farmers preferred using their own farm-saved seeds as opposed to purchasing certified seeds. Establishing the distribution and prevalence of PCN and elucidating the local farming practices that could promote the spread of PCN is a necessary precursor to the implementation of any containment or management strategy in the country and ultimately across the region.
Authors
Susanne von Bargen Rim Al Kubrusli Thomas Gaskin Stephanie Fürl Florian Hüttner Dag-Ragnar Blystad David G. Karlin Risto Jalkanen Carmen BüttnerAbstract
Since Emaraviruses have been discovered in 2007 several new species were detected in a range of host plants. Five genome segments of a novel Emaravirus from mosaic‐diseased Eurasian aspen (Populus tremula) have been completely determined. The monocistronic, segmented ssRNA genome of the virus shows a genome organisation typical for Emaraviruses encoding the viral RNA‐dependent RNA polymerase (RdRP, 268.2 kDa) on RNA1 (7.1 kb), a glycoprotein precursor (GPP, 73.5 kDa) on RNA2 (2.3 kb), the viral nucleocapsid protein (N, 35.6 kDa) on RNA3 (1.6 kb), and a putative movement protein (MP, 41.0 kDa) on RNA4 (1.6 kb). The fifth identified genome segment (RNA5, 1.3 kb) encodes a protein of unknown function (P28, 28.1 kDa). We discovered that it is distantly related to proteins encoded by Emaraviruses, such as P4 of European mountain ash ringspot‐associated virus. All proteins from this group contain a central hydrophobic region with a conserved secondary structure and a hydrophobic amino acid stretch, bordered by two highly conserved positions, thus clearly representing a new group of homologues of Emaraviruses. The virus identified in Eurasian aspen is closely associated with observed leaf symptoms, such as mottle, yellow blotching, variegation and chloroses along veins. All five viral RNAs were regularly detectable by RT‐PCR in mosaic‐diseased P. tremula in Norway, Finland and Sweden (Fennoscandia). Observed symptoms and testing of mosaic‐diseased Eurasian aspen by virus‐specific RT‐PCR targeting RNA3 and RNA4 confirmed a wide geographic distribution of the virus in Fennoscandia. We could demonstrate that the mosaic‐disease is graft‐transmissible and confirmed that the virus is the causal agent by detection in symptomatic, graft‐inoculated seedlings used as rootstocks as well as in the virus‐infected scions used for graft‐inoculation. Owing to these characteristics, the virus represents a novel species within the genus Emaravirus and was tentatively denominated aspen mosaic‐associated virus.
Authors
Anna Filipiak Solveig Haukeland Kamila S. Zając Dorota Lachowska-Cierlik Bjørn Arild HattelandAbstract
A survey of helminths associated with terrestrial slugs focusing on the invasive Arion vulgaris and the native A. ater was conducted on populations from France, Germany, Netherlands, Norway and Poland. In total, 648 terrestrial slugs were collected from 18 sample sites, and identified by means of morphological examination, dissection of genitalia and molecular analysis using mitochondrial DNA. In addition to A. vulgaris and A. ater, also A. vulgaris/A. rufus hybrids and A. ater/A. rufus hybrids were collected. Helminth species were identified based on morphological features and sequencing of the 18S and ITS rDNA regions. The parasites included four nematode species: Alloionema appendiculatum, Angiostoma sp., Phasmarhabditis hermaphrodita, Entomelas sp., two trematode species: Brachylaima mesostoma, Eurytrema sp., and one cestode (tapeworm) species: Skrjabinia sp. Alloionema appendiculatum was the most common helminth in the investigated slug populations. Furthermore, we found higher prevalence of trematodes in the invasive A. vulgaris compared with the native A. ater, while differences in the prevalence for nematodes were not as clear.
Authors
Iben M. Thomsen Håvard Kauserud Paal Krokene Mogens Nicolaisen Per Hans Micael Wendell Beatrix Alsanius Christer Magnusson Johan A. Stenberg Sandra A .I. Wright Trond RafossAbstract
Key words: VKM, risk assessment, Norwegian Scientific Committee for Food and Environment, Norwegian Environment Agency, mycorrhiza. Mycorrhiza is a beneficial association between plant roots and fungi. This mutualistic symbiosis is essential for plant growth in most natural terrestrial ecosystems and in agriculture. Commercial mycorrhizal products containing fungi and bacteria may promote plant growth, especially on sites without a natural microbial community. Due to the risk of unintended negative effects, introduction of new species or genetically different isolates of native species should always be considered carefully. This report assesses the risk of establishment and spread of six fungal species and six bacterial species included in different commercial mycorrhizal products, as well as the species’ potential impact on Norwegian biodiversity. Most of the evaluated fungi and bacteria are probably present in Norway, even though presence at present data only exist for two of the six fungal species. Establishment of the assessed fungi on the plants and sites where they are applied is considered moderately likely, with medium uncertainty, while establishment of the bacterial species is considered to range from very unlikely to very likely depending on the bacterial group, with low uncertainty. The probability of spread to the wider environment ranges from unlikely (four fungal species), to moderately likely (two fungal species), to very likely (five of the six bacterial species). However, for all species it is considered unlikely that establishment and spread would have negative effects on other native species, habitats and ecosystems in Norway.