Development of molecular selection methods

Last changed: 06 July 2017
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The most common means of selecting the best individual in plant and livestock breeding are to examine the traits you are looking for. However, this is time-consuming and the traits can be affected by external factors such as weather. By looking at variations in the genetic material and the proteins in cells, it may prove easier to make the right choice.

Use of biological information in genomic selection

Genomic selection (selection based on the entire genetic material) involves predicting the breeding value of an individual plant or animal based on genetic markers in the individual's entire genetic material (genome). Traditionally, within genomic selection there has not been any biological information concerning the various markers (the specific bases in the genetic material that varies between individuals: SNP; Single Nucleotide Polymorphism). If, on the other hand, knowledge of biological differences tied to each respective SNP is included, the individual's breeding value can be predicted with greater accuracy.

Models adapted to this exist, but are not especially user-friendly and do not work for larger data volumes. We are developing methods to include biological information in models for genomic selection by evaluating different SNPs based on their biological function. Existing information is supplemented with further biological information from other projects within Mistra Biotech. The objective is a user-friendly model that both researchers and breeders of potatoes and field cress can use.

Contact: Lars Rönnegård and Dirk Jan de Koning

Use of proteomics in plant and livestock breeding

Proteomics means that the proteins in the cells are examined (unlike genomics, where the genome – genetic material is compared). This is an important branch for future plant and livestock breeding in Sweden. Just as with gene sequencing, we can use proteins as markers for selection at an early stage in the individual's development. We have identified nearly 600 proteins in the sperm from Holstein bulls. When we now study a large number of bulls, the composition and levels of proteins can be connected to fertility. In order to verify the results, we compare them with results from other breeds. We also compare proteomic data with results from the genomic studies we have carried out on the same bulls earlier in the programme. As potential breeding bulls are always tested for sperm quality, it should not present a logistic problem to include a proteomic analysis as part of the continual breeding process.

We are also doing work using proteins as markers in plant breeding, with focus on potatoes. We have identified markers for resistance to tuber and leaf late blight, both caused by Phytophthora infestans. However, many more different biological mechanisms seem to control resistance, and so far we have not found any usable specific gene for resistance to tuber late blight. By integrating tissue-specific proteomics with genomic studies on the same potato clones, we can find the places on the chromosomes with the most interesting markers for tuber late blight resistance. One advantage of the protein analysis is that we can study several properties even in organisms with several sets of chromosomes, such as the tetraploid potato. The polyploid organisms have a more complex genetic material and this can make it easier to examine the individuals' protein content than studying the genes.

Contact: Fredrik Levander

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