143 GENOMIC ASSESSMENT ASSOCIATIONS OF THE PATERNAL EFFECT FOR DAUGHTER FERTILITY TRAITS IN HOLSTEIN CATTLE
Authors: Sermyagin A. A. , Gladyr E. A. , Romanenkova O. S. , Ermilov A. N. , Brem G. , Zinovieva N. A. 
Published: December 2015

A worldwide decline of fertility in Holsteins requires the reliable evaluation of fertility traits. Because of the low heritability of most fertility traits, the reliabilities of bull estimated breeding values (EBV) for these traits are usually low. Recent developments in molecular genetics have opened the possibilities of identifying and using genomic variation that can significantly boost the reliabilities of EBV. Furthermore, some of the fertility problems can be caused by embryonic lethality due to LoF (loss of function) mutations. The objective of our study was to identify loci associated with fertility-related traits in Russian Holstein cattle and to evaluate the distribution of several LoF mutations associated with fertility in the Russian Holstein bull population. A genome-wide scan was performed on 195 progeny-tested and 61 young bulls genotyped with the 50K Illumina BeadChip (Illumina Inc., San Diego, CA, USA). The analysis was carried out using EBV for gestation length (GL), calving interval (CI), conception rate (CR), and days to the first insemination (DI) calculated by best linear unbiased prediction (BLUP) SM methodology. To increase the prediction reliability of associations, genomic EBV (GEBV) for young bulls were obtained using an genomic BLUP (GBLUP) approach. Furthermore, the bulls were genotyped by PCR or PCR-RFLP for LoF mutations in FANCI, APAF1, and GART genes, which are associated with brachyspina (BY) and fertility haplotypes HH1 and HH3. The single nucleotide polymorphism (SNP) quality check and association analysis was performed using Plink (1.09) software. In total, 43 101 SNP passed quality control. The average number of daughters per sire was ~215. Bonferroni correction test for detection significant associations was applied as P < 1.2E × 10–6. The values for heritability were 0.036, 0.063, 0.035, and 0.068 for GL, CI, CR, and DI, respectively. Frequencies of the late abortions and stillbirths were 1.7 and 3.6% respectively. We identified some SNP with direct significant effects for fertility-related traits: BTA-31636-no-rs on BTA1 for GL (P = 1.2E × 10–6), Hapmap26774-BTA-163037 on BTA27 for CI (P = 1.1E × 10–6), and ARS-BFGL-NGS-89711 on BTA27 for CR (P = 2.1E × 10–7). One SNP (ARS-BFGL-NGS-92135) was found on BTA10 that was close to being significant for DI (P = 2.8E × 10–6). The direct EBV effect of SNP (R2) ranged from 8.4 to 9.0% of additive genetic variances. Genotyping bulls for LoF mutations revealed carrier frequencies of 2.0% for BY, 2.0% for HH1, and 4.3% for HH3. Our results will be useful to improve cow fertility traits in Holstein dairy herds in Russia. Furthermore, they allow selection of donor cows and bulls with more reliable EBV for fertility-related traits and that are free of LoF mutations associated with embryonic death for application in embryo transfer programs.
The study was supported by the Federal Agency for Scientific Organizations and by the Russian Ministry of Education and Science, project no. RFMEFI60414X0062.