Assessment of runs of homozygosity, heterozygosity-rich regions and genomic inbreeding estimates in a subpopulation of Guzerá (Bos indicus) dual-purpose cattle

For decades, inbreeding in cattle has been evaluated using pedigree information. Nowadays, inbreeding coefficients can be obtained using genomic information such as runs of homozygosity (ROH). The aims of this study were to quantify ROH and heterozygosity-rich regions (HRR) in a subpopulation of Guzerá dual-purpose cattle, to examine ROH and HRR islands, and to compare inbreeding coefficients obtained by ROH with alternative genomic inbreeding coefficients. A subpopulation of 1733 Guzerá animals genotyped for 50k SNPs was used to obtain the ROH and HRR segments. Inbreeding coefficients by ROH (FROH ), by genomic relationship matrix based on VanRaden's method 1 using reference allele frequency in the population (FGRM ), by genomic relationship matrix based on VanRaden's method 1 using allele frequency fixed in 0.5 (FGRM_0.5 ), and by the proportion of homozygous loci (FHOM ) were calculated. A total of 15,660 ROH were identified, and the chromosome with the highest number of ROH was BTA6. A total of 4843 HRRs were identified, and the chromosome with the highest number of HRRs was BTA23. No ROH and HRR islands were identified according to established criteria, but the regions closest to the definition of an island were examined from 64 to 67 Mb of BTA6, from 36 to 37 Mb of BTA2 and from 0.50 to 1.25 Mb of BTA23. The genes identified in ROH islands have previously been associated with dairy and beef traits, while genes identified on HRR islands have previously been associated with reproductive traits and disease resistance. FROH was equal to 0.095 ± 0.084, and its Spearman correlation with FGRM was low (0.44) and moderate-high with FHOM (0.79) and with FGRM_0.5 (0.80). The inbreeding coefficients determined by ROH were higher than other cattle breeds' and higher than pedigree-based inbreeding in the Guzerá breed obtained in previous studies. It is recommended that future studies investigate the effects of inbreeding determined by ROH on the traits under selection in the subpopulation studied.

Pedigree analysis and inbreeding effects over morphological traits in Campolina horse population

Genetic improvement, without control of inbreeding, can go to loss of genetic variability, reducing the potential for genetic gains in the domestic populations. The aim of this study was to analyze the population structure and the inbreeding depression in Campolina horses. Phenotype information from 43 465 individuals was analyzed, data provided by the Campolina Breeders Association. A pedigree file containing 107 951 horses was used to connected the phenotyped individuals. The inbreeding coefficient was performed by use of the diagonal of the relationship matrix and the genealogical parameters were computed using proper softwares. The effective population size was estimated based on the rate of inbreeding and census information, and the stratification of the population was verified by the average relationship coefficient between animals born in different regions of Brazil. The effects of inbreeding on morphological traits were made by the use of inbreeding coefficient as a covariate in the model of random regression. The inbreeding coefficient increased from 1990 on, impacting effective population size and, consequently, shrinking genetic variability. The paternal inbreeding was greater than maternal, which may be attributed to the preference for inbred animals in reproduction. The average genetic relationship coefficient of animals born in different states was lower than individuals born within the same state. The increase in the inbreeding coefficient was negatively associated with all studied traits, showing the importance to avoid genetic losses in the long term. Although results do not indicate a severe narrowing of the population until the present date, the average relationship coefficient shows signs of increase, which could cause a drastic reduction in genetic variability if inbred mating is not successfully controlled in the Campolina horse population.

Red Sindhi cattle in Brazil: population structure and distribution

The Red Sindhi cattle breed was imported to Brazil in small numbers. Nowadays, the herds of this breed are distributed in the Northeast, Southeast and Midwest regions of the country. In this study, DNA samples of animals originating from 15 herds in the Northeast and Southeast regions have been analyzed to obtain the ancestry proportions, and to gain a better understanding of the current population structure of this breed in Brazil. Samples were genotyped using three different single nucleotide polymorphism (SNP) marker panels. Those markers have been used with the approach of unsupervised hierarchical clustering of individuals, and consequently, the ancestry of the population was divided into six different subpopulations. Three of those ancestry subpopulations were identified to be present in various different herds, while the other three were restricted to only one or two herds each. One of those herds has been kept isolated for more than 30 years, and it was identified to contain two almost exclusive subpopulations. To avoid important losses in the genetic diversity within the Red Sindhi breed in Brazil, we recommend the identification of superior sires from every subpopulation in the establishment of a breeding program for this breed.

Polymorphisms and alternative splicing of the luteinizing hormone receptor of dairy cattle

The aim of this study was to screen for variability in the luteinizing hormone/choriogonadotropin receptor (LHCGR) and to determine the occurrence of LHCGR mRNA isoforms in two dairy breeds of cattle. Granulosa cells from dominant ovarian follicles were recovered from 16 Gir and 16 Holstein cows, and total RNA was extracted. Complementary DNA was synthesized and PCR was used to generate amplicons for sequencing. Chromatograms were evaluated, and multiple sequences were aligned and analyzed for the presence of polymorphisms, allele frequency, polymorphic information content (PIC), and Hardy-Weinberg equilibrium (HWE). Twenty-one single nucleotide polymorphisms (SNPs) were identified in LH receptor mRNA. Seventeen SNPs were identified in Gir cattle (seven exclusively), and 14 were found in Holstein cattle (four exclusively). Seven of the 21 polymorphisms found did not alter which amino acid was translated. Eight SNPs caused a change to an amino acid in a different chemical group. Classification of SNPs according to PIC values identified 12 as being highly informative in Gir cattle and five in Holstein. Eight SNPs deviated from HWE in Gir compared with 11 in Holstein, and eight in both breeds. Two isoforms were also identified, one in exon 1, which lacks 30 nucleotides beginning at position 118, and the other in exon 10. Taken together, these data show that LHCGR in dairy cattle breeds has a high frequency of polymorphism and exists in multiple isoforms resulting from alternative splicing.

Genetic parameters of test-day milk yield in Guzerá cattle under tropical conditions

The objective of this study was to estimate genetic parameters for test-day milk yield (TDMY) in Guzerá cows using random regression models. Additive and permanent environmental random effects were modeled by random regression on fourth- and fifth-order orthogonal Legendre polynomials, respectively. The residual variances were heterogeneous, with seven classes. Heritability estimates for TDMY ranged from 0.24 to 0.52, with higher heritabilities for yields during early lactation. Genetic correlations between TDMYs ranged from -0.03 to 0.95. The phenotypic and permanent environmental correlations were all positive, and the highest estimates were between adjacent TDMYs. The results suggest that TDMYs obtained with random regression models may be used as selection criteria for Guzerá cattle.

Genetic parameters for milk production traits and breeding goals for Gir dairy cattle in Brazil

To implement an animal breeding program, it is important to define the production circumstances of the animals of interest to determine which traits of economic interest will be selected for the breeding goal. The present study defined breeding goals and proposed selection indices for milk production and quality traits of Gir dairy cattle. First, a bioeconomic model was developed to calculate economic values. The genetic and phenotypic parameters were estimated based on records from 22,468 first-lactation Gir dairy cows and their crosses for which calving occurred between 1970 and 2011. Statistical analyses were carried out for the animal model, with multitrait analyses using the restricted maximum likelihood method. Two situations were created in the present study to define the breeding goals: 1) including only milk yield in the breeding goal (HGL1) and 2) including fat and protein in addition to the milk yield (HGL2). The heritability estimates for milk, protein, and fat production were 0.33 ± 0.02, 0.26 ± 0.02, and 0.24 ± 0.02, respectively. All phenotypic and genetic correlations were highly positive. The economic values for milk, fat, and protein were US$0.18, US$0.27, and US$7.04, respectively. The expected economic responses for HGL2 and for HGL1 were US$126.30 and US$79.82, respectively. These results indicate that milk component traits should be included in a selection index to rank animals evaluated in the National Gir Dairy Breeding Program developed in Brazil.

A new tetra-primer ARMS-PCR for genotyping bovine kappa-casein polymorphisms

Kappa-casein (κ-casein) is one of the most abundant milk proteins. Its main function is to avoid the aggregation of casein micelles, keeping them, and therefore calcium phosphate, in pockets in solution. In bovines, a κ-casein functional polymorphism has been associated with fat, calcium, and protein milk contents and faster curd contraction in cheese production. Quicker curd contraction reduces the loss of milk solids, enhancing cheese yield. This polymorphism induces a double amino acid substitution (Thr136Ile and Ala148Asp). The polymorphism is normally detected by PCR-RFLP, which is a laborious method. An interesting methodological alternative is the tetra-primer amplification refractory mutation system PCR (tetra-primer ARMS-PCR). A tetra-primer ARMS-PCR for the detection of this κ-casein polymorphism has been described. However, specificity was not achieved, probably due to problems with primer design. We developed a new tetra-primer ARMS-PCR for the detection of the κ-casein polymorphism. This new method was validated in a double-blind test, by comparison with the results obtained for 50 Guzerá bulls formerly genotyped by PCR-RFLP. This new method achieved 100% sensitivity and specificity. We conclude that this method is a useful, cost-efficient alternative for the detection of functional κ-casein polymorphisms.

Comparison of random regression models to estimate genetic parameters for milk production in Guzerat (Bos indicus) cows

Random regression models have been widely used to estimate genetic parameters that influence milk production in Bos taurus breeds, and more recently in B. indicus breeds. With the aim of finding appropriate random regression model to analyze milk yield, different parametric functions were compared, applied to 20,524 test-day milk yield records of 2816 first-lactation Guzerat (B. indicus) cows in Brazilian herds. The records were analyzed by random regression models whose random effects were additive genetic, permanent environmental and residual, and whose fixed effects were contemporary group, the covariable cow age at calving (linear and quadratic effects), and the herd lactation curve. The additive genetic and permanent environmental effects were modeled by the Wilmink function, a modified Wilmink function (with the second term divided by 100), a function that combined third-order Legendre polynomials with the last term of the Wilmink function, and the Ali and Schaeffer function. The residual variances were modeled by means of 1, 4, 6, or 10 heterogeneous classes, with the exception of the last term of the Wilmink function, for which there were 1, 3, 6, or 10 classes. The models gave similar hereditability estimates, ranging from 0.20 to 0.33. Genetic correlations between adjacent records were high values (0.83-0.99), but they declined when the interval between the test-day records increased, and were negative between the first and last records. The model employing the Ali and Schaeffer function with six residual variance classes was the most suitable for fitting the data.

Quantitative trait loci affecting lactose and total solids on chromosome 6 in Brazilian Gir dairy cattle

Fourteen Brazilian Gir sire families with 657 daughters were analyzed for quantitative trait loci (QTL) on chromosome 6 affecting lactose and total solids. Cows and sires were genotyped with 27 microsatellites with a mean spacing between markers of 4.9 cM. We used a 1% chromosome-wide threshold for QTL qualification. A QTL for lactose yield was found close to marker MNB66 in three families. A QTL for total solid yield was identified close to marker BMS2508 in three families. A QTL for lactose percentage, close to marker DIK1182, was identified in two families. A QTL for total solid percentage, close to marker MNB208, was identified in four families. These QTLs could be used for selection of animals in dairy production systems.

Logistic regression analysis of pregnancy rate following transfer of Bos indicus embryos into Bos indicus × Bos taurus heifers

Factors affecting pregnancy rate of 5627 Zebu embryos in crossbred females with unknown proportions of Holstein and Zebu breeding were examined. After evaluation for developmental stage, quality, and viability, embryos were immediately transferred to recipients. Pregnancy diagnosis was conducted approximately 53 d after transfer; pregnancy rate was coded as a binomial event and analyzed using logistic regression models. Maximum likelihood methodology and the likelihood ratio statistic were used to estimate regression coefficients and test hypotheses. Explanatory variables were year of transfer (1992-1999), season of transfer (summer, autumn, winter and spring), breed of the embryo (Guzerat, Gyr or Nellore), stage of the embryo (morula, early blastocyst, blastocyst, expanded blastocyst, and hatching blastocyst), quality of the embryo (excellent, good or regular), and donor-recipient synchrony (estrus in the recipient occurred 2-3 d before, 1 d before, the day of, 1 d after, or 2-3 d after estrus in the donor). Average pregnancy rate was 63.7%. Pregnancy rates were not significantly affected by breed of embryo. The best multiple-logistic model to explain the pregnancy result included the effects of year and season of transfer, embryo stage and quality, and estrous synchrony between donor and recipient (P<or=.01). High pregnancy rates occurred when transfers occurred in autumn, early blastocysts or morulae were transferred, and excellent quality embryos were chosen. In addition, pregnancy rates were highest when estrus in the recipient began 1 d earlier than that of the donor.

DGAT1 K232A polymorphism in Brazilian cattle breeds

Recent reports identified DGAT1 (EC 2.3.1.20) harboring a lysine to alanine substitution (K232A) as a candidate gene with a strong effect on milk production traits. Our objective was to estimate the frequency of the DGAT1 K232A polymorphism in the main Zebu and Taurine breeds in Brazil as well as in Zebu x Taurine crossbreds as a potential QTL for marker-assisted selection. Samples of 331 animals from the main Brazilian breeds, Nellore, Guzerat, Red Sindhi, Gyr, Holstein, and Gyr x Holstein F1 were genotyped for DGAT1 K232A polymorphism (A and K alleles) using the PCR-RFLP technique. The highest frequency of the A allele was found in the Holstein sample (73%) followed by Gyr x Holstein F1 (39%). Gyr and Red Sindhi showed low frequencies of A alleles (4 and 2.5%, respectively). The A allele was not found in the Nellore and Guzerat samples. Our results could be used to guide association studies between this locus and milk traits in these breeds.

Genetic trend for milk yield in Guzerat herds participating in progeny testing and MOET nucleus schemes

Genetic trends for 305-day milk yield (P305) in Brazilian Guzerat herds under selection were compared. Data from 4898 lactations of 3179 purebred and crossbred cows from various regions of Brazil were used. Milk yield was adjusted for mature age and the contemporary groups were defined as herd and calving year. Genetic parameters were estimated using the MTDFREML program. The model included the random effects of animals and permanent environment, and herd-calving year, calving season and genetic composition as fixed effects. Genetic trends were estimated by linear regression of weighted average estimated breeding values as a function of calving year. The average P305 was 2065 +/- 922 kg and the heritability was 0.23 +/- 0.03. The annual genetic trend in estimated breeding values of cows for P305 was 7.09 +/- 0.71 kg between 1987 and 2004, and 6.47 +/- 2.35 kg between 1997 and 2004. For cows born and raised in the multiple ovulation and embryo transfer (MOET) nucleus, this trend was 36.46 +/- 24.54 kg/year between 1997 and 2004, 183.14 +/- 47.94 kg/year between 1997 and 2000, and 9.13 +/- 19.19 kg/year between 2001 and 2004. An average inbreeding coefficient of 0.04 was found for inbred MOET cows in 2004. Increasing the size of the family and introducing new progenies changed reliabilities and predicted transmitting ability estimates of MOET sires. In conclusion, there was a positive genetic trend for milk yield in the MOET nucleus at low inbreeding coefficients due to the increased accuracy and estimated genetic merit, but no changes in the average milk yield were observed.

Genetic parameters of multiple ovulation traits in Nellore females

Variability in superovulatory response is a limiting factor for animal breeding programs using Multiple Ovulation and Embryo Transfer (MOET) nucleus schemes. To evaluate genetic factors affecting superovulory response, 1036 multiple ovulation records from 475 Brazilian Nellore embryo donors (daughters of 139 sires), 2.2-20.5-year olds, were analyzed. Traits used to evaluate superovulatory response included the number of palpable corpora lutea (CL), the total number of recovered structures (RS), and the number of viable embryos (VE). Two data sets were used: data from the first flush only or data from the first three flushes. Genetic parameter estimations were carried out using Restricted Maximum Likelihood (REML) methodology, with single- and multiple-trait animal models. According to the data set used, heritability estimates ranged from 0.47 to 0.57 for CL, from 0.20 to 0.65 for VE, and from 0 to 0.34 for RS, and were higher for the data set that used only the first flushing only. For the first flush, genetic correlations were 0.43 between CL and SF, 0.01 between CL and VE, and 0.73 between SF and VE. Repeatability estimates ranged from 0.47 to 0.51. In conclusion, the use of data from the first flush only might result in better estimates of genetic parameters for MOET traits in Nellore females. Furthermore, moderate to high values for repeatability suggested that selection for a high response to superovulation could be made after the first flush.