Keygene NV

Wageningen, Netherlands

Keygene NV

Wageningen, Netherlands
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The invention relates to a method for the high throughput identification of single nucleotide polymorphisms by performing a complexity reduction on two or more samples to yield two or more libraries, sequencing at least part of the libraries, aligning the identified sequences and determining any putative single nucleotide polymorphisms, confirming any putative single nucleotide polymorphism, generating detection probes for the confirmed single nucleotide polymorphisms, subjection a test sample to the same complexity reduction to provide a test library and screen the test library for the presence or absence of the single nucleotide polymorphisms using the detection probe.


Patent
Keygene N.V. | Date: 2017-03-01

The present invention provides a method for improving at least one phenotypic trait of interest in subsequent generation(s) of a population of individuals, preferably crop plants or cattle. Particularly, the method identifies the combination of at least three individuals that gives, upon subsequent intercrossing, the highest estimated probability of improving the at least one phenotypic trait of interest in the subsequent generation(s). Also provided is a computer-readable medium comprising instructions for performing the method.


The invention relates to a method for identifying one or more polymorphisms in nucleic acid samples, comprising: (a) performing a reproducible complexity reduction on a plurality of nucleic acid samples to provide a plurality of libraries of the nucleic acid samples comprising amplified fragments, wherein the reproducible complexity reduction comprises amplifying fragments of the nucleic acid samples using one or more primers to obtain the amplified fragments, and wherein the amplified fragments in each library comprise a unique identifier sequence to indicate origin of each library obtained by the reproducible complexity reduction; (b) combining the plurality of libraries to obtain a combined library and sequencing at least a portion of the combined library to obtain sequences; (c) aligning the sequences to obtain an alignment; and (d) identifying one or more polymorphisms in the plurality of nucleic acid samples.


Patent
Keygene N.V. | Date: 2016-12-01

The invention relates to a method for the high throughput discovery, detection and genotyping of one or more genetic markers in one or more samples, comprising the steps of restriction endonuclease digest of DNA, adaptor-ligation, optional pre-amplification, selective amplification, pooling of the amplified products, sequencing the libraries with sufficient redundancy, clustering followed by identification of the genetic markers within the library and/or between libraries and determination of (co-)dominant genotypes of the genetic markers.


Efficient methods are disclosed for the high throughput identification of mutations in genes in members of mutagenized populations. The methods comprise DNA isolation, pooling, amplification, creation of libraries, high throughput sequencing of libraries, preferably by sequencing-by-synthesis technologies, identification of mutations and identification of the member of the population carrying the mutation and identification of the mutation.


Patent
Keygene N.V. | Date: 2016-12-20

The invention relates to a method for the introduction of one or more molecules of interest in a plant cell protoplast by providing plant cell protoplasts, performing a first transfection of the plant cell protoplast with a composition that is capable of altering the regulation of one or more pathways selected from the group consisting of Mismatch Repair System and Non-Homologous End Joining and/or a composition that is capable of introducing DSBs, performing a second transfection of the plant cell protoplast with one or more molecules of interest such as mutagenic oligonucleotides and allowing the cell wall to form.


Efficient methods are disclosed for the high throughput identification of mutations in genes in members of mutagenized populations. The methods comprise DNA isolation, pooling, amplification, creation of libraries, high throughput sequencing of libraries, preferably by sequencing-by-synthesis technologies, identification of mutations and identification of the member of the population carrying the mutation and identification of the mutation.


Patent
Keygene N.V. | Date: 2016-11-07

The current invention relates to a method for targeted alteration of acceptor DNA, for example duplex acceptor DNA. The method comprises use of at least two oligonucleotides, each oligonucleotide having at least one mismatch relative to the targeted (duplex) acceptor DNA. The mismatch of the first oligonucleotide is directed to a nucleotide at a position in the first strand of the duplex and the mismatch of the second oligonucleotide is directed to the nucleotide in the second strand that occupies the complementary position in the duplex acceptor DNA (e.g. forms a base-pair with the nucleotide in the first strand). These mismatches are located at specific positions within said oligonucleotides. Also provided is a kit that comprises instructions for performing the method according to the inventions, and in a preferred embodiment, comprises oligonucleotides suitable for use in the method.


Efficient methods are disclosed for the high throughput identification of mutations in genes in members of mutagenized populations. The methods comprise DNA isolation, pooling, amplification, creation of libraries, high throughput sequencing of libraries, preferably by sequencing-by-synthesis technologies, identification of mutations and identification of the member of the population carrying the mutation and identification of the mutation.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-IP | Phase: KBBE.2013.3.3-01 | Award Amount: 7.01M | Year: 2014

Natural rubber (NR) is an essential renewable material for more than 40,000 products essential to building (adhesives, sealants), medicine (gloves, tubing), and transportation (matting, tyres) industries. In many applications NR cannot be replaced by synthetic rubbers. At the moment NR is harvested exclusively from the rubber tree (Hevea brasiliensis) of which 90% is grown in South East Asia. Worldwide NR consumption is forecasted to increase significantly. At the moment the EU is completely dependent on imports of NR. The successful EU-PEARLS project, which finished in 2012, demonstrated the viability of a new NR producing concept: Russian dandelion (Taraxacum koksaghyz , abbreviated TKS). Not demonstrated in the EU-PEARLS project, but of equal importance in the construction of the TKS business case, is the fact that TKS is also a promising new crop for biomass derived building blocks for the chemical industry via the production of inulin. The strategic objective of EU-DRIVE is to demonstrate the economic potential of a European production chain for natural rubber and inulin as building block for green chemicals, using TKS as a dual purpose production platform. The main deliverables of DIRVE4EU are: (1) plant genotypes with high root biomass, high rubber and inulin yield, (2) seed batches for agronomic tests and large scale demo field trials, (3) optimized cultivation and harvest methods for TKS, (4) ecological analysis of the gene flow between TKS and wild dandelions, (5) scaled-up and optimised extraction and refinery protocol for TKS NR and inulin, (6) testing and application of TKS NR and inulin in end product uses, (7) demonstration of the economic viability of the TKS production chain for NR and inulin. To reach the objective a strong consortium of 8 industrial partners and 5 research organisations from 7 EU countries and Kazakhstan is constructed with a very broad background from bioscience to the rubber industry.

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