Patent Application
20120331582
The present invention relates to a method to control spider mites on plants. More specifically, the invention relates to plants, expressing RNAi of one or more essential genes of the spider mite, and the use of those plants to control the spider mite proliferation into pest proportions. In a preferred embodiment, the spider mite is Tetranychus urticae.
Spider mites are arthropods, belonging to the subphylum of chelicerates (scorpions, horseshoe crabs, spiders, mites and ticks). The mites include different species that can be parasitic on vertebrate and invertebrate hosts, predators, or plant feeding. Within the mites, the spider mites group the web-spinning species that feed on plants.
Spider mites, and particularly T. urticae (two-spotted spider mite) is one of the major pests in agriculture. It is extremely polyphagous and feed on over 1000 plant species. Moreover, it shows a rapid development (generation time of seven days in a hot season). T. urticae represent a key pest for greenhouse crops, annual field crops and many horticultural crops, such as peppers, tomatoes, potatoes, beans, corn, strawberries and roses. It is widespread all over the world, and occurs freely in nature in regions with a warm and dry climate.
Spider mites cause yellow flecks on the leaf surface, and upon heavy infestation, leaves become pale, brittle and covered in webbing. This damage can cause severe reduction in yield.
Spider mites are particularly important pests for vegetables. Spider mites cause significant damage to greenhouse tomato, cucumber and pepper crops.
Given the short generation time and high reproduction rate of spider mites, it is expected that spider mites, with the climate change, will become one of the major pests for crops as well. Devastating effects of spider mites are already creating enormous problems for the agricultural production in Southern Europe.
Spider mite control, currently, is mainly done by specific miticides, as normal insecticides have normally little effect on mites. Miticides have been disclosed, amongst others, in WO03014048 and in WO2007000098. However, miticides are polluting chemicals, and the application may not always be efficient, as spider mites are often protected by a web under the leaves.
Recently, the RNA interference (RNAi) technology was developed as an attractive alternative in the control of insect pests (Gordon and Waterhouse, 2007; Baum et al., 2007; Mao et al., 2007). RNAi is based on sequence-specific gene silencing that is triggered by the presence of double-stranded RNA (dsRNA). RNAi can be used in plants, animals and insects, but the mechanism depends upon endogenous enzymes present and the efficacy depends upon the host organism used (Gordon and Waterhouse, 2007). Khila and Grbic (2007) demonstrated that dsRNA and short interfering RNA (siRNA) can be used for gene silencing in T. urticae, by using a maternal injection protocol to deliver interfering RNAs into the maternal abdomen. This methodology has been used to silence Distal-less, a conserved gene involved in appendage specification in metazoans.
However, gene silencing has never been used in pest control for spider mites. One reason is the uncertainty whether RNAi, supplied in the food, would be functional. Another reason is the lack of sequence data of spider mites, making a selection of mite-specific genes that are lethal when knocked out by RNAi impossible.
We sequenced and annotated the genome of T. urticae. This effort allowed us to pinpoint a set of essential mite-specific genes without relevant plant or mammalian orthologs. From these sequences, RNAi loops were designed that were specific for one essential mite gene, without interfering with the expression in plants or in mammals. Surprisingly, we found that expressing RNAi in a plant derived from those genes, is sufficient to interfere with the spider mite's development and physiology that is feeding on this plant, resulting in death as a consequence.
A first aspect of the invention is a transgenic plant expressing RNAi derived from a spider mite. Preferably, RNAi is derived from an essential gene of the spider mite. Even more preferably, the RNAi is derived from a gene-specific region (GSR) of the essential genes. A “transgenic plant” can be any plant that is, as wild-type, sensitive to spider mite infection, including, but not limited to, members of the citrus family (lemon, oranges, . . . ), grapefruit, different varieties of Vitis, corn, as well as Solanaceae like tomatoes, cucumber, . . . and ornamental flowers. “Derived” as used here, means that the gene region that is transcribed (including the non-coding regions) is used to design the RNAi; preferably, the RNAi comprises an antisense fragment of the transcribed region. Even more preferably, it consists of an antisense region of the transcribed region. The RNAi comprises only a part of the transcribed mRNA. A “GSR” is a gene region without homology with other mite genes and without homology with the host genome, as determined according to Example 1. A GSR allows the design of RNAi that is specific for the target gene, without interfering with other mite genes or with plant or mammalian genes. An “essential gene” as used here means that the inactivation of the gene is blocking growth and/or development of the mite and may result in the death of the mite. Preferably, the essential gene is selected from the group consisting of GABA receptor gene, stem cell gene, neutralized gene, HOX gene, DEV gene, Cytochrome C gene, Hedgehog gene, NADH dehydrogenase gene, Ryanoid receptor gene, sodium channel gene, acetylcholine esterase gene, son of sevenless gene, prospero gene, acetyl choline receptor gene and distal-less gene (Dll). Preferably, the spider mite is T. urticae. In one preferred embodiment, the RNAi is derived from the T. urticae distal-less gene (RNAi indicated as Tetur17g02200-SEQ ID NO:86); preferably, it is comprising the sequence between the primers as shown in
Although, preferably, the inactivation of the mites is obtained by expressing a single RNAi species, it is clear for the person skilled in the art that the same effect may be obtained by expressing more than one RNAi species, in order to obtain a stronger inhibition.
Another aspect of the invention is a method to improve mite resistance in plants, comprising the expression of RNAi derived from spider mite. Preferably; the RNAi is derived from an essential gene from spider mite; even more preferably, the RNAi is derived from a gene-specific region (GSR) of the essential gene. Preferably, the essential gene is selected from the group consisting of GABA receptor gene, stem cell gene, neutralized gene, HOX gene, DEV gene, Cytochrome C gene, Hedgehog gene, NADH dehydrogenase gene, Ryanoid receptor gene, sodium channel gene, acetylcholine esterase gene, son of sevenless gene, prospero gene, acetyl choline receptor and distal-less gene (Dll). Preferably, the spider mite is T. urticae. In one preferred embodiment, the RNAi is derived from the T. urticae distal-less gene; preferably it is comprising the sequence between the primers as shown in
The T. urticae ortholog of the drosophila Dll distal-less gene was identified in the genomic sequence, using the motifs of the distal-less family (Fonseca et al., 2009). Distal-less is a transcription factor that plays an important role in neuronal development (Cobos et al., 2005). An RNAi fragment is designed on the base of its specificity (no significant homology with other T. urticae genes, neither with the Arabidopsis genome). The RNAi fragment, as well as the primers used to isolate it, is shown in
From a list of candidate Tetranychus urticae target genes, coding sequences (CDS, from start-to-stop codons) were collected from the available predicted genes. For each of those genes, overlapping 21mer sequences were designed covering the whole CDS sequences. This was done by extracting, starting from the first nucleotide of the CDS, sub-sequences of 21 nt, with a sliding window, with steps of one nt. For each CDS from the target genes, n−20 oligos of 21 nt were designed, whereby n is the length of the CDS.
Each of these 21mers was blasted (using BLASTN) against the whole Tetranychus urticae genome. In the case of a perfect match, an e-value of 1e−4 is obtained. To allow some mismatch the threshold was set at 0.01. The threshold was lowered to ensure that no 21mer would hit another region on the genome with a small sequence difference of 1 or 2 nt, thereby ensuring the gene specificity for the RNAi.
Gene-specific regions (GSR), ideally being between 150 and 500 nt, were identified as regions for which, over the whole region, none of the consecutive 21mers derived from this region gave a hit with another sequence from the T. urticae (using the threshold as described above).
The GSR that did meet the above conditions were subsequently blasted (BLASTN, same thresholds) against the Arabidopsis genome. Arabidopsis was chosen, as it is used as host in the proof of principle experiments. This step is to make sure that no Arabidopsis genes could be targeted by the RNAi constructs introduced and that might thus affect Arabidopsis directly; GSR can be blasted against other genomes for optimizing the RNAi in other plant hosts.
All GSR that fulfilled the above criteria (SEQ ID NOS:1-85) were then used as input for primer design. The primers where designed using the OSP perl package, and as a parameter, the melting temperature was set at the 55° C. to 65° C. range in a first run (Table 1). Those targeted GSR that did not succeed in obtaining a primer pair were submitted again to the same design procedure, with slightly more relaxed primer lengths allowed (Table 2). If, with those conditions, still no primers could be designed, melting temperature range was relaxed (50° C. to 70° C.) for a third attempt (Table 3).
Similar to the RNAi distal-less construct, RNAi constructs of the other essential genes are placed under control of the CaMV 35 S promoter, in pB-Agrikola. The plasmid map of pB Agrikola (carrying the RNAi construct of Tetur17g02200-SEQ ID NO:86) is given in
Arabidopsis plants expressing dsRNA from the selected genes are used in spider mite food tests, and the effect on mite development is measured, as described in Example 1. A reduction in living mites, as well in eggs, on the plants is obtained.
| Number | Date | Country | Kind |
|---|---|---|---|
| 09173040.8 | Oct 2009 | EP | regional |
This is a national phase entry under 35 U.S.C. §371 of international Patent Application PCT/EP2010/065311 filed on Oct. 13, 2010, published in English as International Patent Publication No. WO 2011/045333, which claims the benefit under Article 8 of the Patent Cooperation Treaty to European Patent Application Serial No. 09173040.8, filed Oct. 14, 2009.
| Filing Document | Filing Date | Country | Kind | 371c Date |
|---|---|---|---|---|
| PCT/EP2010/065311 | 10/13/2010 | WO | 00 | 7/25/2012 |
