PDF file: Annual Report 2002/2003 - Scottish Crop Research Institute

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Viruses - evolving organisms ? Cassava is not a native plant to Africa but was introduced from South America, probably by Portuguese traders and settlers. When it first reached Uganda is unclear, but its presence there was noted by Speke during his expedition in 1875. Until the 1920’s it was an unimportant crop, but thereafter its cultivation increased and it is now the main staple in much of the country. Cassava mosaic disease, caused by ACMV, was first recorded in 1928 and subsequently became endemic, although the losses it caused were tolerable. This situation changed from 1988 when an outbreak of severe disease was reported in Luwero district and spread southwards at a rate of 20 km / year, eventually reaching the northern shores of Lake Victoria. In the area affected by the epidemic, which has now spread into all neighbouring countries, cassava yields were virtually nil and people starved. Workers at SCRI contributed to understanding the causes of this epidemic by characterizing a novel form of begomovirus from cassava affected by the severe disease 3 . This virus, called the Uganda variant (UgV), has a DNA-A that is clearly the product of recombination between the DNA-A’s of ACMV and EACMV. Most of the sequence is like that of EACMV but the coat protein gene is like that of ACMV (Fig 1). In both parts, the sequences faithfully match those of the parent viruses, and examination of a range of UgV isolates showed that there was hardly any variation among them. These observations implied that the recombination event that led to the formation of UgV was recent, and that UgV had not yet had time to diversify by the accumulation of mutations. UgV occurred only in the area affected by the epidemic, indicating a causal connection between the new virus and the epidemic. Moreover, in a popular Ugandan cassava variety, UgV reached about 20-fold higher concentration than did an isolate of ACMV typical of those circulating in Uganda before the epidemic. However, the most severe disease appeared in plants infected with both UgV and ACMV 4 (Fig. 2). UgV is therefore an example of a newly evolved virus with increased pathogenic potential. The key event in its evolution was recombination between the DNA- A’s of ACMV and EACMV, which can have taken place only in a cassava plant doubly infected with the two parental viruses. Such double infections are uncommon, and therefore recombination should be a rare event. However, once this particular recombinant had been produced, it was well adapted for transmission by the local strains of whitefly, and therefore it persisted and spread. Figure 2 Mosaic-affected cassava shoots: left, infected with ACMV; right, infected with UgV; centre, doubly infected with both ACMV and UgV. Cotton leaf curl disease in Pakistan. Another example of a disease caused by begomoviruses is leaf curl disease of cotton (Fig. 3), which was first recorded in Pakistan in 1967. The incidence of the disease increased rapidly from 1989, coinciding with the widespread cultivation of S-12, a high-yielding longstaple cultivar that is highly susceptible to infection with cotton leaf curl virus. Another factor in the epidemic was the presence of huge uncontrollable populations of whiteflies that had arisen following the over-use of pesticides and the development of resistance to many of them. By 1993-94, losses of cotton (Pakistan’s principal export) were estimated at about 2 million bales, worth around $400 million. There was a possibility that there might be parallels with the cassava mosaic epidemic in Uganda, but when we examined the DNA-A of viruses in leaf curlaffected cotton, it quickly became clear that the situation was rather different. Instead of a single novel form, we found many different variants 5 . Some included regions whose sequence closely resembled that of parts of the DNA-A of okra yellow vein mosaic virus and thus were obvious recombinants, although the recombinants typically induced leaf curl rather than yellow vein symptoms in okra (Fig. 3). The origin of other variants was less clear. The recent evolution of cotton leaf curl virus in Pakistan had therefore been characterized by an explosion of new variants, perhaps induced by the prevalence of susceptible cotton cultivars and massive populations of the vector. In another contrast with the Ugandan cassava scenario, multiple infections were common in Pakistan. More than half the plants tested contained two or more virus variants 6 . There were therefore plenty of opportunities for recombination to produce new forms, but other processes may also have had a role in their evo- 72
Viruses - evolving organisms ? CLCuV -26 CLCuV -72b OYVMV -301 CLCuV -804a Figure 3 Centre panel: diagrams of the genomes of three recombinant CLCuV variants, showing the regions derived from okra yellow vein mosaic virus (OYVMV) in yellow. Top left: symptoms of CLCuV in cotton. Bottom left: symptoms of OYVMV in okra. Right: symptoms of CLCuV in okra. lution. As in Uganda, the epidemic was brought under control by the introduction of resistant cultivars. But in Pakistan, the evolutionary pressure was so great that in 2001 a strain of virus appeared that could overcome this resistance, something that has thankfully not yet happened in Uganda. Evidence of selection pressures The appearance of new viruses is evidence of the products of evolution, but Darwinian evolution postulates that for new forms to persist they must be well fitted to withstand the selection pressures imposed upon them. For UgV, we can surmise that key factors were its ability to replicate to high concentrations, and its acquisition of the coat protein gene from a local ACMV strain that was presumably already well adapted for transmission by the local whitefly population. In Pakistan it may be that some of the cotton leaf curl virus variants we observed will not survive for long, but that one or two of the best adapted will become dominant. In other cases, the study of patterns of variation among strains of a virus can offer clues to the selection pressures that have operated to bring about the present diversity. In contrast to the multiplicity of begomoviruses, the genus Tobravirus contains only three species 7 : Tobacco rattle virus (TRV) occurs in Europe, North America, Japan, China and New Zealand, and infects more than 400 species of monocots and dicots in over 50 families, including many crops and common weeds. It is best known in Britain as one of the causes of spraing disease of potatoes. Pea early-browning virus (PEBV) occurs in Europe and North Africa, and infects legumes. TRV RNA 1 RNA 2 Pepper ringspot virus occurs in South America, and causes diseases in peppers, tomatoes and artichokes. TMV Rep P1 MP P1a P1b P2a P2b P2c Figure 4 Diagrams of the genomes of tobacco rattle virus (TRV) and tobacco mosaic virus (TMV). Coloured blocks represent genes encoding replication proteins (green), cell-to-cell movement proteins (purple), coat proteins (orange), seed transmission protein (yellow) and nematode transmission proteins (blue). CP All three viruses are spread by free-living nematodes in the genera Trichodorus and Paratrichodorus (trichodorids), which are found mainly in light or sandy soils. The genomes of tobraviruses consist of linear singlestranded RNA, and are bipartite. The larger RNA, RNA-1, codes for replication and intercellular movement functions and for a protein involved in seed transmission (Fig. 4). Although there are large differences between the RNA-1 sequences of the three virus species, there is little difference among those of different strains of TRV. In the three TRV strains whose RNA-1 has been completely sequenced, more than 99% of the 6791 bases in RNA-1 are the same in all 73
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Scottish Crop Research Institute ®
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The Scottish Crop Research Institut
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Contents Biomathematics and Statist
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Introduction upon the Commissioner
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Introduction ® Scottish Crop Resea
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Report of the Director John R. Hill
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Director’s Report tion from dismi
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Director’s Report paper A revised
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Director’s Report and the relatio
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Director’s Report Member States A
Page 21 and 22: Director’s Report US subsidies fr
Page 23 and 24: Director’s Report regions of the
Page 25 and 26: Director’s Report of silver and m
Page 27 and 28: Director’s Report tions. Obscenel
Page 29 and 30: Director’s Report participation.
Page 31 and 32: Director’s Report heads of state
Page 33 and 34: Director’s Report Philippines (2.
Page 35 and 36: Director’s Report Food Aid Famine
Page 37 and 38: Director’s Report adoption of unh
Page 39 and 40: Director’s Report economy propose
Page 41 and 42: Director’s Report (herbicides, in
Page 43 and 44: Director’s Report by a combinatio
Page 45 and 46: Director’s Report mended a study
Page 47 and 48: Director’s Report notes, bulletin
Page 49 and 50: Director’s Report research instit
Page 51 and 52: Director’s Report Ireland. Also i
Page 53 and 54: Director’s Report tats, most nota
Page 55 and 56: Director’s Report shares of total
Page 57 and 58: Director’s Report tonnes in 1999.
Page 59 and 60: Director’s Report Relative Import
Page 61 and 62: Director’s Report cheap food-stuf
Page 63 and 64: Director’s Report culturally-rela
Page 65 and 66: Director’s Report on large parts
Page 67 and 68: Director’s Report minimum input s
Page 69 and 70: Director’s Report organic farming
Page 71: Viruses - evolving organisms ? Viru
Page 75 and 76: Viruses - evolving organisms ? a) b
Page 77 and 78: Barley Crop Development formation o
Page 79 and 80: Barley Crop Development Year Total
Page 81 and 82: Barley Crop Development on a year t
Page 83 and 84: GM herbicide-tolerant crops Some pe
Page 85 and 86: GM herbicide-tolerant crops and som
Page 87 and 88: GM herbicide-tolerant crops mitted
Page 89 and 90: GM herbicide-tolerant crops 12 Squi
Page 91 and 92: Mechanisms & Processes Peronospora
Page 93 and 94: Mechanisms & Processes Proteomic an
Page 95 and 96: Mechanisms & Processes High-through
Page 97 and 98: Mechanisms & Processes Studying pla
Page 99 and 100: Mechanisms & Processes Phytoene pea
Page 101 and 102: Mechanisms & Processes New discover
Page 103 and 104: Mechanisms & Processes in these cel
Page 105 and 106: Mechanisms & Processes d). This dat
Page 107 and 108: Genes to Products ic enzymes (use o
Page 109 and 110: Genes to Products Carotenogenesis i
Page 111 and 112: Genes to Products accumulation in s
Page 113 and 114: Genes to Products Retrotransposons
Page 115 and 116: SH43 SL03 SH44 SH12 B20 SL22 B47 B0
Page 117 and 118: Management of genes and organisms i
Page 119 and 120: Environment Functional diversity in
Page 121 and 122: Environment Plant root biomechanics
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Environment Microbial and microfaun
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Environment The role and importance
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Environment duced from barley mixtu
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Environment IOBC GMO Guidelines Pro
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Environment Mathematical modelling
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Biomathematics and Statistics Scotl
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Research services Analytical facili
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Research services Division of Finan
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Research services Information Techn
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Research services Estate, Glasshous
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Research services Engineering and M
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Research services MRS will: strengt
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Research services Health and Safety
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Publications Blok, V.C. 2002. Progr
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Publications Phenotype/genotype ass
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Publications for virus-transmitting
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Publications Muckenschnabel, I., Go
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Publications rich grassland. Procee
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Publications Woodford, J.A.T., Fent
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Statement of health & safety policy
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The Governing Body The Governing Bo
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The Governing Body development and
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Staff Theme 2 - Genes to Products T
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Staff Division of Finance and Admin
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Staff Resignations Name Unit Band M
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Staff Editorial Duties Name Positio
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Staff Name Position Committee or Or
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SCRI Research Programme 2002-2003 S
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Research Projects SCR/587/02 SCR/58
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Meteorological Records D. Petrie &
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List of Abbreviations AAB ACRE ADAS
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