Genetic trends and trade-offs between growth and reproductive traits in a Nellore herd

Genome-wide association and functional annotation analysis for the calving interval in Nellore cattle

Calving interval (CI) measures the number of days between two consecutive calves of the same cow, and previous studies based on phenotype and pedigree data reported low heritability for this trait. However, the genetic architecture of CI in the Nellore breed was not evaluated based on genomic data. Thus, this study aimed to estimate the heritability based on genomic data and carry out a genome-wide association study (GWAS) for CI in the Nellore breed, using 12,599 pedigree records, 5078 CI records, and 3818 animals genotyped with 50k SNPchip panel. Both quality control and GWAS were performed in BLUPF90 family packages, which use the single-step genomic best linear unbiased predictor (ssGBLUP) method. The average CI was 427.6 days, with a standard deviation of 106.9 and a total range of 270-730 days. The heritability estimate was 0.04 ± 0.04. The p-values of GWAS analysis resulted in a genomic inflation factor (lambda) of 1.08. The only significant SNP (rs136725686) at the genome-wide level (p-value = 1.53E-06) was located on BTA13. Other 19 SNPs were significant at the chromosome-wide level, distributed on BTA1, 2, 3, 6, 10, 13, 14, 17, 18, 22, and 26. Functional annotation analysis found thirty-six protein-coding genes, including genes related to cell cycle (RAD21, BCAR3), oocyte function (LHX8, CLPX, UTP23), immune system (TXK, TEC, NFATC2), endocrine function (LRRFIP2, GPR158), estrous cycle (SLC38A7), and female fertility (CCK, LYZL4, TRAK1, FOXP1, STAC). Therefore, CI is a complex trait with small heritability in Nellore cattle, and various biological processes may be involved with the genetic architecture of CI in Nellore cattle.

Unravelling the genetic variability of host resilience to endo- and ectoparasites in Nellore commercial herds

BACKGROUND

Host resilience (HR) to parasites can affect the performance of animals. Therefore, the aim of this study was to present a detailed investigation of the genetic mechanisms of HR to ticks (TICK), gastrointestinal nematodes (GIN), and Eimeria spp. (EIM) in Nellore cattle that were raised under natural infestation and a prophylactic parasite control strategy. In our study, HR was defined as the slope coefficient of body weight (BW) when TICK, GIN, and EIM burdens were used as environmental gradients in random regression models. In total, 1712 animals were evaluated at five measurement events (ME) at an average age of 331, 385, 443, 498, and 555 days, which generated 7307 body weight (BW) records. Of the 1712 animals, 1075 genotyped animals were used in genome-wide association studies to identify genomic regions associated with HR.

RESULTS

Posterior means of the heritability estimates for BW ranged from 0.09 to 0.54 across parasites and ME. The single nucleotide polymorphism (SNP)-derived heritability for BW at each ME ranged from a low (0.09 at ME.331) to a moderate value (0.23 at ME.555). Those estimates show that genetic progress can be achieved for BW through selection. Both genetic and genomic associations between BW and HR to TICK, GIN, and EIM confirmed that parasite infestation impacted the performance of animals. Selection for BW under an environment with a controlled parasite burden is an alternative to improve both, BW and HR. There was no impact of age of measurement on the estimates of genetic variance for HR. Five quantitative trait loci (QTL) were associated with HR to EIM but none with HR to TICK and to GIN. These QTL contain genes that were previously shown to be associated with the production of antibody modulators and chemokines that are released in the intestinal epithelium.

CONCLUSIONS

Selection for BW under natural infestation and controlled parasite burden, via prophylactic parasite control, contributes to the identification of animals that are resilient to nematodes and Eimeria ssp. Although we verified that sufficient genetic variation existed for HR, we did not find any genes associated with mechanisms that could justify the expression of HR to TICK and GIN.

Managing embryonic and calves losses after twin pregnancies induced by transfer of in vitro-produced Nellore embryos

Two farms applying reproductive technology for the Nellore beef cattle were selected. Both farms had the same technology programme of oestrous synchronization and embryo transfer, but management was different, especially regarding twins pregnancies. In the present study, we followed the farms from the moment of oestrous synchronization, embryo transfer (two per cow), until delivery and first care of the calves. In farm A, cows presenting twin pregnancies (5 from 13) were submitted to delivery induction, as well as calves and cows were monitored after birth. In farm B, such management was not followed with the twin pregnant cows (31 from 49). In both farms, freemartinism was detected, but this was not a problem as none of the animals would be selected for breeding. No dystocia was observed in farm A, while 48% of the twin pregnancies in farm B ended up in dystocia. Furthermore, the mortality rate of new-born calves in farm A was 10%, while in farm B it reached 32%. Although twin pregnancies remain a concern, we showed here that proper management during and after delivery minimizes animal and economic losses.

Genetic variances and covariances of live weight traits in Charolais cattle by multi-trait analysis

Live weight traits are economically important for beef cattle production systems. Genetic analysis of live weight traits frequently presents a problem due to animal records, in that matter, not all the animals have complete records as many young animals leave the herd because of sale, transfer to another herd, or culling reasons. Therefore, the use of multi-trait genetic analysis might be of assistance to help overcome any possible loss of information for those animals with incomplete records. In this study, genetic variances and covariances were obtained to estimate genetic parameters for birth (BW), weaning (WW), and yearling (YW) live weights in a registered Charolais beef cattle population using a multivariate model, where a considerable reduction of data from birth weight to year weight was observed. Direct and maternal heritabilities for BW, WW, and YW were 0.50, 0.30, and 0.28, and 0.31, 0.25, and 0.14, respectively. Direct and maternal genetic correlations were negative in all live weight traits. Genetic correlations among direct BW with direct WW and YW were low, while genetic correlations among maternal traits were medium or high (r>0.39). Comparison between univariate and multi-trait models with substantial reduction of information revealed important differences, implying that multi-trait analysis is better for the structure of data allowing a better fitting of genetic effects by covariance among evaluated traits. Results support multi-trait analysis implementation for genetic evaluations for live weight traits of Charolais cattle.