Collaborative and Knowledge-building Project, NFR
13 mill NOK
Use long read sequencing technology to construct pan-genomes, including structural variants (SV’s), for Norwegian Red cattle and Landrace pigs. Utilize these in modern breeding strategies to improve imputation and calculation of breeding values and explore the relationship between SV’s and key phenotypes to improve our functional understanding of traits related to sustainability.
In recent decades, specialized breeding companies have utilized information about genetic variation in cattle and pigs to transform traditional approaches. By comparing the genetic signatures from animals displaying different biological qualities (disease resistance, milk production etc) it is possible to identify desirable variants and deliberately select for these when choosing which animals to mate; this strategy has been very successful and lead to rapid and sustainable genetic gain. In this project we will increase the power of this approach and replace our reliance on references from other foreign breeds by developing custom reference genomes for Norwegian Red cattle and Landrace pigs. In contrast to linear, homogenized genomes, these will be pan-genomes and a single unified genome graph will represent the majority of genetic variation contained in each of these breeds. Furthermore, we will make special effort to use long-read technologies so that structural variation is captured and represented in the graphs so that we can better understand the role of SV’s in trait development.
Outcomes and impacts
Pan-genomes are rapidly becoming the new gold-standard for accurately representing the genome of a species or breed, and this project will deliver breed specific reference genomes for Norwegian Red cattle and Landrace pigs. Breeding companies involved in the project will use these to increase the accuracy of imputation and allow structural variation to be accounted for when calculating breeding values. Furthermore, existing data relating genetic variation with traits will be re-examined in the light of SV data to specifically explore the functional role of SVs in key traits. We believe this project will help to ensure that cattle and pig farming remains competitive, viable and profitable in Norway and that we avoid a situation of dependency on imported meat and dairy products predictive power and accuracy.