Genomic Evaluation of Primiparous High-Producing Dairy Cows: Inbreeding Effects on Genotypic and Phenotypic Production-Reproductive Traits

Abstract

The main objective of this study was to analyze the effects of the inbreeding degree in high-producing primiparous dairy cows genotypically and phenotypically evaluated and its impacts on production and reproductive parameters. Eighty Holstein-Friesian primiparous cows (age: ~26 months; ~450 kg body weight) were previously genomically analyzed to determine the Inbreeding Index (II) and were divided into two groups: low inbreeding group (LI: <2.5; n = 40) and high inbreeding group (HI: ≥2.5 and ≤5.0; n = 40). Genomic determinations of production and reproductive parameters (14 in total), together with analyses of production (12) and reproductive (11) phenotypic parameters (23 in total) were carried out. Statistically significant differences were obtained between groups concerning the genomic parameters of Milk Production at 305 d and Protein Production at 305 d and the reproductive parameter Daughter Calving Ease, the first two being higher in cows of the HI group and the third lower in the LI group (p < 0.05). For the production phenotypic parameters, statistically significant differences were observed between both groups in the Total Fat, Total Protein, and Urea parameters, the first two being higher in the LI group (p < 0.05). Also, significant differences were observed in several reproductive phenotypic parameters, such as Number of Services per Conception, Calving to Conception Interval, Days Open Post Service, and Current Inter-Partum Period, all of which negatively influenced the HI group (p < 0.05). In addition, correlation analyses were performed between production and reproductive genomic parameters separately and in each consanguinity group. The results showed multiple positive and negative correlations between the production and reproductive parameters independently of the group analyzed, being these correlations more remarkable for the reproductive parameters in the LI group and the production parameters in the HI group (p < 0.05). In conclusion, the degree of inbreeding significantly influenced the results, affecting different genomic and phenotypic production and reproductive parameters in high-producing primiparous cows. The determination of the II in first-calf heifers is crucial to evaluate the negative effects associated with homozygosity avoiding an increase in inbreeding depression on production and reproductive traits.

Keywords: dairy cattle; genomic analysis; genotypic parameters; homozygosis; inbreeding index; phenotypic traits; primiparous; production; reproductive performance.

Figure 1

Experimental design map. Dairy cows used for the Inbreeding Index (II) determination (ranges <2.5% and ≥2.5% to ≤5.0) from the total population analyzed (n = 385) by genomic tests (genotypic and phenotypic parameters). For genomic analysis, the sampling was carried out by using the Gene Max kit (TSU, ALLFLEX, Kalamazoo, MI, USA) and next a chip with 12,000 DNA markers (12K; Illumina Bovine SNP50 BeadChip, Clarifide–Zoetis, San Diego, CA, USA) was used for genotyping. The results have a ~70% reliability based on a panel of 50,000 (HD50K) genetic markers from the Animal Improvement Programs Laboratory (AIPL) (Zoetis–Clarifide, SanDiego, CA, USA). Genomic production values: MP305G: Milk Production at 305 days; MPFAT305G: Fat Production at 305 days; MPPROT305G: Protein Production at 305 days; PF305G: Percent of Fat at 305 days; PP305G: Percent of Protein at 305 days; SCCG: Somatic Cell Count; MRG: Mastitis Resistance. Genomic reproductive values: FIG: Fertility Index; HCRG: Nulliparous Cow Conception Rate; DPRG: Daughter Conception Rate; CCRG: Cow Conception Rate; DCEG: Daughter Calving Ease; MTRG: Resistance to Metritis; RPRG: Resistance to Placental Retention.

Figure 2

Effect of the degree of inbreeding (LI versus HI) on the genomic parameters for production traits in high-producing primiparous dairy cows. Production genomic values: MP305G: Milk Production at 305 days; MPFAT305G: Fat Production at 305 days; MPPROT305G: Protein Production at 305 days; PF305G: Percent of Fat at 305 days; PP305G: Percent of Protein at 305 days; SCCG: Somatic Cell Count; MRG: Mastitis Resistance. Different letters show statistical differences between values (p ≤ 0.05). lbs: Pounds; %: Percentage; SEM: Standard Error of the Mean.

Figure 3

Effect of the degree of inbreeding (LI versus HI) on phenotypic parameters for production traits in high-producing primiparous dairy cows. Production phenotypic values: MPJ305: Projected Milk at 305 days; MPJ305ME: Projected Milk 305 days Maturity Equivalent; TLM: Total Liters of Milk; TFAT: Total Fat; TPROT: Total Protein; SCC: Somatic Cell Count; LCCM: Liters of Current Corrected Milk; ALM: Average Liters of Milk; U: Urea; FATP: Percentage of Fat; PROTP: Percentage of Protein; LGSCC: Logarithmic Somatic Cell Count. Different letters show statistical differences between values (p ≤ 0.05). L: Liters; lbs: Pounds; %: Percentage; mg: milligrams; dL: deciliters; SEM: Standard Error of the Mean.

Figure 4

Effect of the degree of inbreeding (LI versus HI) on genomic parameters for reproductive traits in high-producing primiparous dairy cows. Reproductive genomic values: FIG: Fertility Index; DPRG: Daughter Conception Rate; HCRG: Nulliparous Cow Conception Rate; CCRG: Cow Conception Rate; DCEG: Daughter Calving Ease; MTRG: Resistance to Metritis; RPRG: Resistance to Placental Retention; NS: Not Significant; SEM = Standard Error of the Mean. Different letters show statistical differences between values (p ≤ 0.05). pts: points; %: Percentage; SEM: Standard Error of the Mean.

Figure 5

Effect of the degree of inbreeding (LI and HI) on phenotypic parameters for reproductive traits in high producing primiparous dairy cows. Reproductive phenotypic values: WFS: Weight at First Service; DG: Days of Gestation; DMFB: Days in Milk at First Service; DAPVWP: Days of Anestrus Post Voluntary Waiting Time; CCI: Calving to Conception Interval; DOPS: Days Open Post Service; EHD: Efficiency in Heat Detection; MPJIPP: Minimum Projected Inter-Partum Interval; CIPP: Current Inter-Partum Period. NSCNC: Number of Services per Conception: Nulliparous Cow (heifer); NSCC: Number of Services per Conception in Cows Different letters show statistical differences between values (p ≤ 0.05). Kg: Kilograms; uns: Units; d: days; %: Percentage; SEM: Standard Error of the Mean.