Methods Selection of bulls Straws and ampules of semen were obtained from 550 Holstein bulls born between 1962 and 2010. Bulls were chosen based on their predicted transmitting ability and reliability for DPR. In particular, bulls were chosen to have either a high PTA for DPR or low PTA for DPR with reliability as high as pos sible. The PTA for the low DPR group ranged from ?5. 9 to selleck catalog ?2, and the PTA for the high DPR group ranged from 1. 7 to 5. 3. Reliabilities ranged from 0. 46 to 0. 99. The distribution of re liabilities was similar between the low and high DPR groups. Predicted trans mitting abilities for a variety of traits of the bulls are presented in Additional file 1, Table S1. Semen was obtained from the Cooperative Dairy DNA Repository, Alta Genetics, Genex Cooperative Inc.

Taurus service Inc. Foundation Sires Inc. Accelerated Genetics, Interglobe Genetics, and Nebraska Bull Service. Five bulls were born in the 1960s, 15 in the 1970s, 54 in the 1980s, 154 in the 1990s, and 322 in the 2000s. SNP discovery The choice of 434 SNPs to be used for genotyping was made using a three step process, candidate gene selection, SNP identification, and SNP selection. A list of candidate genes affecting reproduction was compiled using two methods. The first was to include genes commonly known to affect reproductive processes such as steroidogenesis, follicular development, oocyte maturation, and early embryonic development, as well as nutritional genes including orexins and anorexins. Furthermore, genes that were in physical proximity to SNPs related Brefeldin_A genetically to inter val to insemination and 56 d non return rate were included.

In addition, genes reported to be differentially expressed between physiological conditions in a variety of tissues as sociated with reproductive function were incorporated. This list included genes differentially regulated in the following conditions, the brain of cows displaying strong vs.

weak estrus, embryos after cryopreservation, superovulated embryos compared to embryos from unstimulated dams, embryos which survived to term compared to embryos that died in vivo after embryo trans fer, selleck chemicals embryos treated with CSF2 or IGF1 compared to control embryos, embryos cultured in vitro in the well of the well system compared to embryos cultured in groups, oocytes compared to 8 cell embryos and blastocysts, oocytes at different stages of oocyte maturation, endometrium related to embryo survival, endometrium in lactating cows compared to non lactating cows or preg nant cows compared to non pregnant cows, cumulus cells regulated by the LH surge, at different stages of oocyte maturation, or from embryos pro duced in vivo embryos compared to embryos produced in vitro dominant follicles compared to subordinate follicles, liver during the transition period, mammary tissue during lactation, and oviduct at diestrus compared to es trus.