João Cruz Reis Filho

Bio: João Cruz Reis Filho is an academic researcher from Ministry of Agriculture. The author has contributed to research in topics: Heritability & Dairy cattle. The author has an hindex of 4, co-authored 8 publications receiving 52 citations.

Population structure of Brazilian Gyr dairy cattle

Abstract: The objective of the present study was to evaluate the genetic structure of Gyr cattle selected for milk production. Files of pedigree and production were composed of 27,610 animals. The ENDOG program was used for the calculation of individual inbreeding coefficient (F) and coefficient of average relatedness (AR), effective number of animals(Ne), effective number of founders (fe) and ancestors (fa), and generation interval (GI). Individual inbreeding coefficients and average relatedness in the population were 2.82% and 2.10%, respectively. It was observed a reduction in the effective number of animals, especially after publication of the results of the first progeny test. The estimated effective number of founders was 146 and 75 for the ancestrals. Out of those, only 28 ancestors accounted for the origin of 50% of the population genes. The average generation interval was 8.41 years and it was longer for males than for females. For maintaining genetic variability in future generations, it should be invested mating strategies that reduce inbreeding and which do not use massively only some high breeding value sires.

Genetic parameters and response to selection for post-weaning weight gain, visual scores and carcass traits in Hereford and Hereford × Nellore cattle

Abstract: The objective of this study was to estimate heritability, correlations and response to selection for post-weaning average daily weight gain (ADG), visual scores of conformation (C), precocity (P) and muscling (M), longissimus muscle area (LMA), and backfat thickness (BFT) measured by ultrasound in Brazilian Hereford and Hereford × Nellore cattle. The components of (co)variance were estimated by the Bayesian method in two-trait analysis. The posterior means (± standard deviation) of heritability for ADG (0.164 ± 0.013), C (0.152 ± 0.014), P (0.194 ± 0.015), M (0.198 ± 0.015), LMA (0.232 ± 0.047) and BFT (0.136 ± 0.037) and their corresponding phenotypic standard deviation (standard deviation of posterior density) of 0.076 (0.0003) kg/day, 0.803 (0.003), 0.869 (0.005), 0.883 (0.007), 5.491 (0.069) cm2 and 0.761 (0.009) mm support the utilization of these traits as criteria for selection, as long as the selection is done based on predicted breeding values. The genetic correlations (± standard deviation) between M and LMA (0.483 ± 0.098) and between P and BFT (0.403 ± 0.108) were favorable and indicate that part of the genes with additive effect on the visual scores also influenced the traits measured by ultrasound. The genetic correlations between M and P (0.814 ± 0.025) and between LMA and BFT (0.286 ± 0.200) suggest that the selection of animals with more developed muscle mass does not necessarily result in animals with less fat cover.

Inbreeding on productive and reproductive traits of dairy Gyr cattle

Abstract: The objective of this study was to estimate genetic parameters and to evaluate the effects of inbreeding on productive and reproductive traits of dairy Gyr cattle. Single-trait animal models were used to estimate genetic parameters and solutions for inbreeding coefficients for milk (milk 305-d), fat (fat 305-d), protein (protein 305-d), lactose (lactose 305-d), and total solids (TS 305-d) yield up to 305 days of lactation, days in milk (DIM), age at first calving (AFC) and calving intervals (CI). The mean inbreeding coefficient was 2.82%. The models with linear and quadratic effects of inbreeding coefficients fitted the data better than the models without or with only linear effect of inbreeding coefficient for all traits. The increase in inbreeding coefficient caused several losses in productive and reproductive traits of dairy Gyr cattle. Estimates of heritability for milk 305-d, fat 305-d, protein 305-d, lactose 305-d, TS 305-d, DIM, AFC, and CI were 0.28, 0.27, 0.22, 0.21, 0.22, 0.17, 0.20, and 0.10, respectively. It is possible to achieve genetic progress in productive traits (especially in milk 305-d and fat 305-d) and age at first calving in dairy Gyr cattle through selection.

Modeling the effect of the age of dam at calving on the weaning weight of Charolais-Zebu crossbred calves

Abstract: The objective of this study was to evaluate alternatives for modeling the age of dam at calving (AOD) effect on the weaning weight of Charolais-Zebu crossbred calves. Data from 56,965 calves were analyzed, using statistical models considering the fixed effects of the contemporary groups, sire and dam genetic groups, and AOD. The AOD effect was fitted to models using annual age classes, and ordinary quadratic to quintic-ordered polynomials (OP) or segmented polynomials (SP) with two, three, four, six and twelve evenly spaced intervals. In the case of segmented polynomials, general linear and quadratic effects and only one quadratic additional term from each knot were considered. The AOD effects were nested within sex of calf in all cases. According to the fitting criteria, the F-test for the reduction of residual sum of squares, coefficient of determination, residual sum of squares and mean of squared residuals, the three interval segmented polynomial (two knots) fitted to the data as well as the more complex polynomials.

Modelos para avaliação genética da produção de leite em múltiplas lactações

Abstract: The objective of this work was to evaluate covariance components and breeding values for 305‑day cumulative milk yield with data from the first three lactations of Gyr cows. A total of 14,659 lactations of 9,079 cows were evaluated, using the models of repeatability, multiple‑trait (MT), and random regression with residual homoscedasticity (RRMHo) or heteroscedasticity (RRMHe). Milk yield was considered as a different trait in each lactation, in the MT model. Linear polynomials were used in random regression models to fit the mean trajectories and the additive genetic and permanent environment individual effects, according to calving order. Posteriori means for heritability were similar among different models and lactations, and varied from 0.24 to 0.29. The MT and RRMHe models had a better fit to the data, since heterogeneity was observed for genetic and residual variances between lactations. The genetic correlations of cumulative milk yield up to 305 days in the first three lactations were close to 1.0; therefore, the selection of reproducers can be made with data already from the first lactation. Random regression models with heterogenous genetic and residual variances allow for proper modeling of the covariances in cumulative milk yields in multiple lactations and for obtaining the genetic values to be used in the selection of reproducers, based on data already from the first lactation.

Human biochemical genetics

Abstract: So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to

Assessment of runs of homozygosity islands and estimates of genomic inbreeding in Gyr (Bos indicus) dairy cattle

Abstract: Runs of homozygosity (ROH) are continuous homozygous segments of the DNA sequence. They have been applied to quantify individual autozygosity and used as a potential inbreeding measure in livestock species. The aim of the present study was (i) to investigate genome-wide autozygosity to identify and characterize ROH patterns in Gyr dairy cattle genome; (ii) identify ROH islands for gene content and enrichment in segments shared by more than 50% of the samples, and (iii) compare estimates of molecular inbreeding calculated from ROH (FROH), genomic relationship matrix approach (FGRM) and based on the observed versus expected number of homozygous genotypes (FHOM), and from pedigree-based coefficient (FPED). ROH were identified in all animals, with an average number of 55.12 ± 10.37 segments and a mean length of 3.17 Mb. Short segments (ROH1–2 Mb) were abundant through the genomes, which accounted for 60% of all segments identified, even though the proportion of the genome covered by them was relatively small. The findings obtained in this study suggest that on average 7.01% (175.28 Mb) of the genome of this population is autozygous. Overlapping ROH were evident across the genomes and 14 regions were identified with ROH frequencies exceeding 50% of the whole population. Genes associated with lactation (TRAPPC9), milk yield and composition (IRS2 and ANG), and heat adaptation (HSF1, HSPB1, and HSPE1), were identified. Inbreeding coefficients were estimated through the application of FROH, FGRM, FHOM, and FPED approaches. FPED estimates ranged from 0.00 to 0.327 and FROH from 0.001 to 0.201. Low to moderate correlations were observed between FPED-FROH and FGRM-FROH, with values ranging from −0.11 to 0.51. Low to high correlations were observed between FROH-FHOM and moderate between FPED-FHOM and FGRM-FHOM. Correlations between FROH from different lengths and FPED gradually increased with ROH length. Genes inside ROH islands suggest a strong selection for dairy traits and enrichment for Gyr cattle environmental adaptation. Furthermore, low FPED-FROH correlations for small segments indicate that FPED estimates are not the most suitable method to capture ancient inbreeding. The existence of a moderate correlation between larger ROH indicates that FROH can be used as an alternative to inbreeding estimates in the absence of pedigree records.

Whole genome sequencing of Gir cattle for identifying polymorphisms and loci under selection

Abstract: Genetic variation in Gir cattle (Bos indicus) has so far not been well characterized. In this study, we used whole genome sequencing of three Gir bulls and a pooled sample from another 11 bulls to ...

History, structure, and genetic diversity of Brazilian Gir cattle

Abstract: The Gir cattle breed (Bos indicus) is an important genetic resource for milk production throughout the tropics. The small number of Gir animals introduced in Brazil, rapid dissemination of this breed recently, and the intensification of selection practices could contribute to increase of inbreeding level and reduce genetic diversity in this population. The population was analyzed in terms of pedigree completeness level, inbreeding coefficient, coancestry, generation interval, effective population size, effective number of founders and ancestors, among others. Despite the low mean inbreeding (around 2%), minor problems were identified in the population structure of the Brazilian Gir cattle, e.g., trend of narrower bottlenecks in the pedigree in recent years. The effective population sizes based on inbreeding (94) or coancestry (165.9) as well as the effective number of ancestors (76) and founders (143) were relativity high. The major subdivision of the Gir breed was observed between 1993 and 2002 (dairy and dual-purpose herds, wide use of within-herd matings). In this period the level of inbreeding remained at a higher level, there was a small increase in coancestry and the number of equivalent subpopulations was approximately 6. After 2002, there was genetic exchange between subpopulations, reduction in the average inbreeding, pronounced increase in the average coancestry, and the number of equivalent subpopulations was about 2. Furthermore, it was found that the mean generation interval of the population tended to increase in recent years (around 9 years). About 2.3% of genetic diversity has been lost since the first generation of founders. Based on the effective population size, number of equivalent subpopulations, inbreeding, coancestry, and loss of genetic diversity, the Gir population is still highly structured, but there is ample room for artificial selection. The results regarding the effective number of founders and ancestors in the present population demonstrate the existence of bottlenecks in the pedigree and indicate the need for population structure monitoring. Nevertheless, the Brazilian Gir breed can perfectly face a breeding program with high selection intensity.

Structure and genetic diversity of Brazilian Zebu cattle breeds assessed by pedigree analysis

Abstract: The monitoring of population structure, inbreeding and other related parameters has great potential to prevent major losses of genetic diversity in populations of Zebu cattle in Brazil. Therefore, the objective of the present study was to investigate the structure and genetic diversity of Brazilian Zebu cattle breeds by pedigree analysis. The national pedigree file of the seven Brazilian Zebu breeds was used, which included all registered animals (12,290,243) born between 1938 and 2012: Brahman, Gir, Guzera, Indubrasil, Nelore, Sindi, and Tabapua. Almost all breeds studied undergo expansion in their census which, however, is not accompanied by the maintenance of genetic diversity. Problems were encountered in all breeds, but most of them can currently be considered less important. Using the calculation method considered as the most accurate for pedigree analysis when some population substructure exists, all breeds, except Sindi, had effective population size greater than 100. The most common problems were the presence of tight bottlenecks in the pedigree, which were mainly due to the intensive use of few animals as parents and the high degree of population subdivision. The use of a wider range of sires is therefore recommended. However, most Zebu breeds can deal with breeding programs using high selection intensities. Greater care should be taken in the case of the Indubrasil breed since its census was reduced drastically over the last few years, a fact favoring the occurrence of serious problems related to inbreeding. Although Sindi presents problems due to subdivision and possesses a relatively small census compared to other Zebu breeds, this population would have a promising future if its breeding policy were revised.