Industry: Agriculture and forestry Region: Germany Transaction price: US$ 1 million Transaction method: equity investment
Project introduction:
The University of Gö ttingen in Germany invented a new genotyping method for plant breeding and research. It is based on sequencing part of the genome (shallow depth) and filling the missing data by inputting sequence data based on haplotype library. Software-aided interpolation increases the reading coverage of haplotypes and allows parallel genotyping of a large number of variants of a large number of individuals. Therefore, this method is superior to array genotyping in cost, simplicity, performance and accuracy. Because the cost of each data point is several times lower, this method may replace array-based genotyping in the next few years and may become the "gold standard" of plant breeding.
Challenge:
Complex but economically important traits, such as yield or pest resistance, are difficult to reproduce because they are affected by several genes at the same time. By selecting variants based on effective genotyping, it is hoped that clearer selection and higher reliability can be achieved in selecting suitable hybridization partners. At present, high-throughput genotyping mainly uses single nucleotide polymorphism (SNP) arrays. They are relatively easy to use and generally produce robust representations with relatively few errors. Therefore, they are usually used for diversity analysis, genome selection or genome-wide association studies. However, the limitations of this technology include the complexity and cost of array design, the inability to classify polymorphism from scratch, the inflexibility of markers and the cost of genotyping, and the cost of genotyping increases significantly with the number of SNP in the array. In addition, SNPs are usually selected as array markers located in conserved regions of the genome, that is, by design, they provide little information about structural variation.
Solution:
The new genotyping method is to sequence the genome at a very shallow depth (1x instead of 30x) and supplement the missing data by inputting sequence data based on haplotypes. The key aspect of the invention is to use haplotype library, that is, the set of starting and ending coordinates of genome blocks as the basis of genotype interpolation. The program determines which individuals carry the same haplotype allele and then combines their sequencing readings. This leads to an increase in the reading coverage of haplotypes, which allows the missing data points of the whole population sharing the same haplotype to be interpolated. The innovative method is to use haplotype library to artificially increase the reading coverage in haplotype blocks. The accuracy and efficiency of this genotyping are similar to those at high reading depth, and it can be achieved by low coverage sequencing.
Advantages:
+Economical and efficient
+Read coverage is greatly improved.
+Information about new structural variants
+Very easy to implement
Application:
The present invention allows parallel genotyping of a very large number of variants of a large number of individuals sequenced with low coverage (e.g., less than 1x), so it is of interest for application in plant breeding. Although so far, this method is only applied to haploid plant genomes, the same method can also be applied to non-haploid organisms by considering their haplotypes after appropriate stage division.
+Plant breeding
+Animal reproduction
Cooperation mode:
This technology has applied for patent, which can provide technical authorization cooperation. Welcome to discuss.