New method to complete genetic data

Date:
January 3, 2022
Source:
University of Go"ttingen
Summary:
Genome sequencing is now much cheaper than it was, but still
accounts for a large part of the costs in animal and plant
breeding. One trick to reduce these costs is to sequence only
a very small and randomly selected part of the genome and to
complete the remaining gaps using mathematical and statistical
techniques. Researchers have developed a new approach to do this.



FULL STORY ==========================================================================
The use of genetic information is now indispensable for modern plant
breeding.

Even though DNA sequencing has become much cheaper since the human
genome was decoded for the very first time in 2003, collecting the
full genetic information still accounts for a large part of the costs
in animal and plant breeding. One trick to reduce these costs is to
sequence only a very small and randomly selected part of the genome
and to complete the remaining gaps using mathematical and statistical techniques. An interdisciplinary research team from the University of Go"ttingen has developed a new methodological approach for this, which
has been published in the journal PLoS Genetics.


==========================================================================
"The core idea of the method is to recognise `haplotype blocks', by
which we mean longer sections in the genome that are very similar in
different plants due to inheritance, and to use this mosaic structure
for compiling the rest of the information," says Dr Torsten Pook from
the Center for Integrated Breeding Research at Go"ttingen University. "In breeding populations, the sequences completed using this new method have quality comparable to collecting a hundred times as much information
from the DNA strand." The researchers' goal is to breed maize plants
with low susceptibility to frost and drought damage as part of the MAZE project. KWS Saat SE, a partner in the project, is already using the
method in breeding programmes because of its cost efficiency.

"Another advantage is that the method not only allows us to detect
differences in individual nucleotides in the DNA strand, but also to
recognise structural differences that have so far been practically
unusable for breeding purposes," says Pook. As things stand, however,
the method can currently only be used efficiently for inbred lines in
plant breeding. A follow-up study to extend the method to organisms with
a regular double set of chromosomes is already planned. This would mean
their new method could be used for most vertebrates, including humans.

========================================================================== Story Source: Materials provided by University_of_Go"ttingen. Note:
Content may be edited for style and length.


========================================================================== Journal Reference:
1. Torsten Pook, Adnane Nemri, Eric Gerardo Gonzalez Segovia,
Daniel Valle
Torres, Henner Simianer, Chris-Carolin Schoen. Increasing calling
accuracy, coverage, and read-depth in sequence data by the use
of haplotype blocks. PLOS Genetics, 2021; 17 (12): e1009944 DOI:
10.1371/ journal.pgen.1009944 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2022/01/220103121748.htm
--- up 4 weeks, 2 days, 7 hours, 13 minutes
* Origin: -=> Castle Rock BBS <=- Now Husky HPT Powered! (1:317/3)