Genome-wide association study for milk production and reproduction traits in Russian Holstein cattle population

Genome-wide association study (GWAS) has been proven as a powerful tool for identifying genomic variants associated with economically important traits in domestic animal species. Development of the methods for genomic evaluation opens the new opportunities in improvement of milk production and fertility traits of livestock. The objective of our study was to evaluate the whole-genome associations between single nucleotide polymorphisms (SNPs) and estimated breeding values (EBVs) for milk production and reproduction traits in Russian Holsteins. SNPs screening was performed in 195 progeny-tested and 61 young bulls using Illumina Bovine SNP50 v2 BeadChip. EBVs were calculated for milk production traits (305-d milk yield (MY), milk fat content (FC), milk protein content (PC), milk fat yield (FY) and milk protein yield (PY)) and reproduction performances (age at fist calving (CA), calving difficulty (CD), conception rate (CR), days open (DO), gestation length (GL) and interval between calving (CI)) using BLUP Sire Model approach. In total, 41370 SNPs were selected for the association analysis based on the quality control results. Direct genomic values (DGV) were calculated by GBLUP approach using genomic relationship matrix (G). Genomic EBVs (GEBVs) were calculated as combination of residual polygenic effects (EBV) with the DGV. To increase the probabilities of GWAS values we used the GEBV values for young bulls, whereas deregressed DGV values were used for progeny-tested bulls. The Bonferroni correction test for detection of significant associations and local false discovery rate (LocFdr) were used to check a type I errors in -cases hypothesis. Heritability coefficient values for reproduction traits ranged from 0.035 for CR to 0.221 CA, whereas for milk production traits they were higher, i.e. from 0.250 for MY to 0.401 for PC. According to the Bonferroni and LocFdr tests, we have identified several high-significant SNPs, which were associated both with milk production and with fertility traits. Two SNPs with the most significant effect on MY were located on BTA17 ( ARS-BFGLNGS-50172 ) and BTA13 ( Hapmap54246-rs29017970 ). The association analysis for milk components revealed four SNPs at conservative regions, which were significantly associated with FC, i.e. BTA-104917-no-rs and BTB-01604502 (58 Mb, BTA9), ARS-BFGL-NGS-107379 and ARS-BFGL-NGS-4939 (1.8-2.0 Mb, BTA14), and one SNP, which was significantly associated with PC - Hapmap 43278-BTA-50082 (BTA20). Polymorphisms ARS-BFGL-BAC-7205 (BTA1) and Hapmap48395-BTA-583 82 (BTA5) were associated with PY. Several SNPs were found to be associated with reproduction traits, i.e. BTB-01622929 on BTA1 for CA, ARS-BFGL-NGS-89711 on BTA27 for CR, ARS-BFGL-NGS-117881 on BTA5 for DO, BTA-31636-no-rs on BTA1 and Hapmap26774-BTA-163037 on BTA27 for CI. The significant effects of SNPs explained up to more than 9.0 % of additive genetic variances. Some of the referent mutations with most significant effect were located within or close to the genes TRAFD1, DGAT1, SLC16A7, DUSP26 and CCDC58. Thus, application of a genome-wide analysis allows with high accuracy to detect the QTL for medium and low heritable productive and reproductive traits in Russian Holsteins.