In component project 2 we will provide methods and tools to facilitate the use of whole genome sequence data in the breeding of animals and plants, including sequencing strategies, data mining software, tools for improved genomic selection. We will also explore the potential for protein-assisted breeding and generate a vast amount of sequencing data for Lepidium campestre (Field pepperweed) and the Swedish Red cattle.
New challenges are appearing with a changing environment and breeding of plants and animals that contribute to a sustainable agriculture needs to be accelerated. Thus we need to be able to screen for and select suitable plants and animals at an early stage in the breeding process. The majority of economically important traits in crops and livestock, whether it is product yield, quality or disease resistance, are so called complex traits that reflect the actions and interactions of many genes and environmental factors. Traditional breeding approaches use pedigree information and apply statistical tools to estimate the proportion of variation that is inherited from ancestors. While these approaches have successfully improved agricultural productivity, using DNA information facilitates further advantages such as the selection of the best individuals earlier, more independent from the relevant phenotype and considering the complexity of traits.
The availability of whole genome sequences (WGS) of some major livestock and crop species allowed to identify variations between individuals at the DNA level, also called single nucleotide polymorphisms (SNP). This enables so called ‘genomic selection’ where selection is performed using information of SNP alleles of an individual across the genome. The advantage of this method is that, once markers are identified and their genetic merit determined you can look for many traits at the same time and across multiple populations. This also opens the potential to detect additional mechanisms (for example epistasis and genotype-environment interactions) which influence the development of an individual. Genomic selection is used in the breeding of dairy cattle worldwide and is also a very active area of research for other livestock and crop species. Additional to the application of this technique in Swedish red cattle and different plant species, we will develop a decision support tool that will evaluate the requirements and potential for genomic selection in a new target species, L. campestre.
As the ultimate function of living organisms is determined by proteins, we are also aiming at analysing the complex of proteins (so called proteomics) and to incorporate gained information into the selection process. Data collected from cattle and potato will provide a starting point.
Furthermore, an important question is whether genetic modification is acceptable and how such modification and other genetic selection methods do impact the individual. We will compare the protein profiles of material obtained by different breeding methods (in CP1) to determine the alterations to the ultimate function.
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