Utilization of genomic information

Genomic information, mainly SNP-genotype data, is utilized in genome-wide association studies (GWAS), genomic selection methods and population genetics analyses. We have used Porcine 60K SNP chip data of Finnish pig breeds to investigate genetic basis of pork quality, lethal haplotypes and effective population size.

Currently we exploit gene expression and targeted sequencing to validate our previously found candidate genes for pork quality. This is done in collaboration with the research group at the University of Bologna. In the Ayrshire dairy cattle, imputed 50K SNP-genotypes of over 10,000 Finnish cows have been used for estimating levels of genomic inbreeding.

Selected Publications

Kudinov, A. A., Mäntysaari, E. A., Pitkänen, T. J., Saksa, E. I., Aamand, G. P., Uimari, P., & Strandén, I. 2022. Single-step genomic evaluation of Russian dairy cattle using internal and external information. Journal of Animal Breeding and Genetics 139: 259-270. https://doi.org/10.1111/jbg.12660

Martikainen, K., Koivula, M. & Uimari, P. 2020. Identification of runs of homozygosity affecting female fertility and milk production traits in Finnish Ayrshire cattle. Scientific Reports 10, 3804. https://doi.org/10.1038/s41598-020-60830-9

Kudinov, A.A., Mäntysaari, E.A., Aamand, G.P., Uimari, P. & Strandén, I. 2020. Metafounder approach for single-step genomic evaluations of Red Dairy cattle. Journal of Dairy Science 103: 6299-6310. https://doi.org/10.3168/jds.2019-17483

Noskova, A., Wurmser, C., Crysnanto, D., Sironen, A., Uimari, P., Fries, R., Andersson, M., & Pausch, H. 2020. Deletion of porcine BOLL is associated with defective acrosomes and subfertility in Yorkshire boars. Animal Genetics 51: 945-949. https://doi.org/10.1111/age.12998

Martikainen, K., Sironen, A. & Uimari, P. 2018. Estimation of intrachromosomal inbreeding depression on female fertility using runs of homozygosity in Finnish Ayrshire cattle. Journal of Dairy Science 101: 11097-11107. https://doi.org/10.3168/jds.2018-14805

Smaragdov, M.G., Kudinov, A.A. & Uimari, P. 2018. Assessing the genetic differentiation of Holstein cattle herds in the Leningrad region using Fst statistics. Agricultural and Food Science 27: 96-101. https://journal.fi/afs/article/view/69777

Martikainen K., Tyrisevä A-M., Matilainen K., Pösö J. & Uimari P. 2017. Estimation of inbreeding depression on female fertility in the Finnish Ayrshire population. Journal of Animal Breeding and Genetics 134: 383-392. http://dx.doi.org/10.1111/jbg.12285

Verardo L., Sevon-Aimonen M-L., Serenius T., Hietakangas V. and Uimari, P. 2017. Whole-genome association analysis of pork meat pH revealed three significant regions and several potential genes in Finnish Yorkshire pigs. BMC Genetics 18. http://dx.doi.org/10.1186/s12863-017-0482-x

Häggman J. and Uimari P. 2016. Novel harmful recessive haplotypes for reproductive traits in pigs. Journal of Animal Breeding and Genetics 134: 129-135. http://dx.doi.org/10.1111/jbg.12240