1a. Objectives (from AD-416):
The objective of this project is to use gene network analysis to identify core genetic modules associated with dystocia (calving difficulty) in three breeds of U.S. dairy cows that have different phenotypes (low, moderate, and high rates of dystocia). Currently there is little understanding of the genetic mechanisms that drive differences in dystocia rates. The agreement will greatly improve our understanding of the genetic architecture of calving difficulty, and will help to better understand why some breeds have a problem in this area and others do not.
1b. Approach (from AD-416):
Previous research by ARS has identified a genetic marker on chromosome 18 that is associated with calving difficulty in Holsteins, but not Brown Swiss or Jerseys, and no genes with large effects on dystocia have been identified in the Brown Swiss breed. This implies that non-additive gene action is responsible for much of the differences observed between breeds. A systems biology approach based on the adaptive weight matrix (AWM) technique will be used within breed to identify gene pathways that are enriched with SNP having statistically significant effects on dystocia. Data also will be polled into a single data set and the AWM analysis repeated. Gene networks common to all breeds and the pooled dataset can plausibly be said to represent fundamental modules controlling the phenotypic expression of dystocia. Genetic evaluations for Jersey calving ease are not routinely computed, but will be calculated from the national dataset by ARS. The Cooperator and ARS will jointly design the experiment. The methods will be applied by the Cooperator to the data provided by ARS. Results will be interpreted and prepared for publication by ARS and the Cooperator.
3. Progress Report:
The project is related to in-house objective 2 (develop a more accurate genomic evaluation system with advanced, efficient methods to combine pedigrees, genotypes, and phenotypes for all animals). Because genetic evaluations for calving ease (dystocia) are routinely calculated in the United States only for Brown Swiss and Holstein cattle, estimates of genetic merit for Jersey bulls were required. Genetic parameters (covariance components) for calving ease in Jersey cattle were estimated and used to calculate genetic merit (expressed as predicted transmitting ability) of service-sire and daughter calving ease for 3,393 Jersey bulls using information stored in the national dairy database. Because the genetic evaluation program for calving ease is funded by the National Association of Animal Breeders (NAAB), approval was necessary before data could be transferred from ARS to the Cooperator. Approval has been granted, and a material transfer research (MTRA) agreement has been set up between ARS and North Carolina State University (NCSU), the parent organization for the Cooperator, to cover the data transfer. An information copy of the MTRA was also sent to NAAB. The project also requires that Cooperator collaborators have access to dairy bull genotypes from the Cooperative Dairy DNA Repository (CDDR), and NCSU negotiated and executed the necessary agreements with CDDR to cover the genotypes. Data files have been prepared by ARS and transferred to NCSU in accordance with the data transfer agreements. Analysis of those data by Cooperator scientists is currently underway.