Assessing different metrics of pedigree and genomic inbreeding and inbreeding effect on growth, fertility, and feed efficiency traits in a closed-herd Nellore cattle population.

BACKGROUND: The selection of individuals based on their predicted breeding values and mating of related individuals can increase the proportion of identical-by-descent alleles. In this context, the objectives of this study were to estimate inbreeding coefficients based on alternative metrics and data sources such as pedigree (FPED), hybrid genomic relationship matrix H (FH), and ROH of different length (FROH); and calculate Pearson correlations between the different metrics in a closed Nellore cattle population selected for body weight adjusted to 378 days of age (W378). In addition to total FROH (all classes) coefficients were also estimated based on the size class of the ROH segments: FROH1 (1-2 Mb), FROH2 (2-4 Mb), FROH3 (4-8 Mb), FROH4 (8-16 Mb), and FROH5 (> 16 Mb), and for each chromosome (FROH_CHR). Furthermore, we assessed the effect of each inbreeding metric on birth weight (BW), body weights adjusted to 210 (W210) and W378, scrotal circumference (SC), and residual feed intake (RFI). We also evaluated the chromosome-specific effects of inbreeding on growth traits. RESULTS: The correlation between FPED and FROH was 0.60 while between FH and FROH and FH and FPED were 0.69 and 0.61, respectively. The annual rate of inbreeding was 0.16% for FPED, 0.02% for FH, and 0.16% for FROH. A 1% increase in FROH5 resulted in a reduction of up to -1.327 ± 0.495 kg in W210 and W378. Four inbreeding coefficients (FPED, FH, FROH2, and FROH5) had a significant effect on W378, with reductions of up to -3.810 ± 1.753 kg per 1% increase in FROH2. There was an unfavorable effect of FPED on RFI (0.01 ± 0.0002 kg dry matter/day) and of FROH on SC (-0.056 ± 0.022 cm). The FROH_CHR coefficients calculated for BTA3, BTA5, and BTA8 significantly affected the growth traits. CONCLUSIONS: Inbreeding depression was observed for all traits evaluated. However, these effects were greater for the criterion used for selection of the animals (i.e., W378). The increase in the genomic inbreeding was associated with a higher inbreeding depression on the traits evaluated when compared to pedigree-based inbreeding. Genomic information should be used as a tool during mating to optimize control of inbreeding and, consequently, minimize inbreeding depression in Nellore cattle.

Genome-wide association study between copy number variation and feeding behavior, feed efficiency, and growth traits in Nellore cattle.

BACKGROUND: Feeding costs represent the largest expenditures in beef production. Therefore, the animal efficiency in converting feed in high-quality protein for human consumption plays a major role in the environmental impact of the beef industry and in the beef producers' profitability. In this context, breeding animals for improved feed efficiency through genomic selection has been considered as a strategic practice in modern breeding programs around the world. Copy number variation (CNV) is a less-studied source of genetic variation that can contribute to phenotypic variability in complex traits. In this context, this study aimed to: (1) identify CNV and CNV regions (CNVRs) in the genome of Nellore cattle (Bos taurus indicus); (2) assess potential associations between the identified CNVR and weaning weight (W210), body weight measured at the time of selection (WSel), average daily gain (ADG), dry matter intake (DMI), residual feed intake (RFI), time spent at the feed bunk (TF), and frequency of visits to the feed bunk (FF); and, (3) perform functional enrichment analyses of the significant CNVR identified for each of the traits evaluated. RESULTS: A total of 3,161 CNVs and 561 CNVRs ranging from 4,973 bp to 3,215,394 bp were identified. The CNVRs covered up to 99,221,894 bp (3.99%) of the Nellore autosomal genome. Seventeen CNVR were significantly associated with dry matter intake and feeding frequency (number of daily visits to the feed bunk). The functional annotation of the associated CNVRs revealed important candidate genes related to metabolism that may be associated with the phenotypic expression of the evaluated traits. Furthermore, Gene Ontology (GO) analyses revealed 19 enrichment processes associated with FF. CONCLUSIONS: A total of 3,161 CNVs and 561 CNVRs were identified and characterized in a Nellore cattle population. Various CNVRs were significantly associated with DMI and FF, indicating that CNVs play an important role in key biological pathways and in the phenotypic expression of feeding behavior and growth traits in Nellore cattle.

Effect of high temperature on physiological parameters of Nelore (Bos taurus indicus) and Caracu (Bos taurus taurus) cattle breeds.

The climate-related problems that affect animal production in tropical countries have encouraged seeking solutions to increase herd productivity and one alternative is the use of breeds adapted to high-temperature environments. The objective of this study was to evaluate the effect of temperature on 77 Caracu and Nelore males submitted to three different environments: morning period (8:00 to 10:00 AM), afternoon in the sun, and afternoon in a shaded environment (11:00 AM to 1:00 PM). The following physiological parameters were measured in each treatment: heart and respiration rates, rectal and dorsal surface temperatures, and cortisol level. The data were analyzed with the MIXED procedure (SAS) and the model included the fixed effects of treatment (morning, sun, and shade), breed (Nelore and Caracu), month of measurement (December and February), and the interaction between effects. A higher dorsal surface temperature was observed in animals of both breeds in the sun treatment compared with the shade treatment. Caracu animals had a higher dorsal surface temperature than Nelore animals, which probably caused the higher rectal temperature observed in the sun treatment compared with the shade treatment in both breeds over the 2 months of the study. All physiological parameters measured in this study were efficient to detect the thermal stress in both breeds. Despite the variations in rectal temperature observed during the treatments, the animals of the two breeds exhibited no significant changes in heart rate, respiration rate, and cortisol level for the maintenance of thermal homeostasis. In conclusion, both breeds were considered tolerant to sun exposure, demonstrating adaptation of these animals to high-temperature environments, without evidence of harm to its health and welfare.

Differentially expressed mRNAs, proteins and miRNAs associated to energy metabolism in skeletal muscle of beef cattle identified for low and high residual feed intake.

BACKGROUND: Feed efficiency is one of the most important parameters that affect beef production costs. The energy metabolism of skeletal muscle greatly contributes to variations in feed efficiency. However, information regarding differences in proteins involved in the energy metabolism of the skeletal muscle in beef cattle divergently identified for feed efficiency is scarce. In this study, we aimed to investigate energy metabolism of skeletal muscle of Nellore beef cattle, identified for low and high residual feed intake using a proteomics approach. We further assessed the expression of candidate microRNAs as a one of the possible mechanisms controlling the biosynthesis of the proteins involved in energy metabolism that were differentially abundant between high and low residual feed intake animals. RESULTS: A greater abundance of 14-3-3 protein epsilon (P = 0.01) was observed in skeletal muscle of residual feed intake (RFI) high animals (RFI-High). Conversely, a greater abundance of Heat Shock Protein Beta 1 (P < 0.01) was observed in the skeletal muscle of RFI-Low cattle. A greater mRNA expression of YWHAE, which encodes the 14-3-3 protein epsilon, was also observed in the skeletal muscle of RFI-High animals (P = 0.01). A lower mRNA expression of HSPB1, which encodes the Heat Shock Protein Beta 1, was observed in the skeletal muscle of RFI-High animals (P = 0.01). The miR-665 was identified as a potential regulator of the 14-3-3 protein epsilon, and its expression was greater in RFI-Low animals (P < .001). A greater expression of miR-34a (P = 0.01) and miR-2899 (P < .001) was observed in the skeletal muscle of RFI-High animals, as both miRNAs were identified as potential regulators of HSPB1 expression. CONCLUSION: Our results show that Nellore cattle divergently identified for feed efficiency by RFI present changes in the abundance of proteins involved in energy expenditure in skeletal muscle. Moreover, our data point towards that miR-665, miR34a and miR-2899 are likely involved in controlling both 14-3-3 epsilon and HSPB1 proteins identified as differentially abundant in the skeletal muscle of RFI-High and RFI-Low Nellore cattle.

Detection and characterization of copy number variation in three differentially-selected Nellore cattle populations.

Introduction: Nellore cattle (Bos taurus indicus) is the main beef cattle breed raised in Brazil. This breed is well adapted to tropical conditions and, more recently, has experienced intensive genetic selection for multiple performance traits. Over the past 43 years, an experimental breeding program has been developed in the Institute of Animal Science (IZ, Sertaozinho, SP, Brazil), which resulted in three differentially-selected lines known as Nellore Control (NeC), Nellore Selection (NeS), and Nellore Traditional (NeT). The primary goal of this selection experiment was to determine the response to selection for yearling weight (YW) and residual feed intake (RFI) on Nellore cattle. The main objectives of this study were to: 1) identify copy number variation (CNVs) in Nellore cattle from three selection lines; 2) identify and characterize CNV regions (CNVR) on these three lines; and 3) perform functional enrichment analyses of the CNVR identified. Results: A total of 14,914 unique CNVs and 1,884 CNVRs were identified when considering all lines as a single population. The CNVRs were non-uniformly distributed across the chromosomes of the three selection lines included in the study. The NeT line had the highest number of CNVRs (n = 1,493), followed by the NeS (n = 823) and NeC (n = 482) lines. The CNVRs covered 23,449,890 bp (0.94%), 40,175,556 bp (1.61%), and 63,212,273 bp (2.54%) of the genome of the NeC, NeS, and NeT lines, respectively. Two CNVRs were commonly identified between the three lines, and six, two, and four exclusive regions were identified for NeC, NeS, and NeT, respectively. All the exclusive regions overlap with important genes, such as SMARCD3, SLC15A1, and MAPK1. Key biological processes associated with the candidate genes were identified, including pathways related to growth and metabolism. Conclusion: This study revealed large variability in CNVs and CNVRs across three Nellore lines differentially selected for YW and RFI. Gene annotation and gene ontology analyses of the exclusive CNVRs to each line revealed specific genes and biological processes involved in the expression of growth and feed efficiency traits. These findings contribute to the understanding of the genetic mechanisms underlying the phenotypic differences among the three Nellore selection lines.

Evidence of negative relationship between female fertility and feed efficiency in Nellore cattle.

The objective of this study was to evaluate phenotypic and genetic relationships between fertility traits and feed efficiency in male and female Nellore cattle. Data from 320 females born between 2004 and 2011 were used for phenotypic evaluation. These animals were evaluated for postweaning residual feed intake (RFI) and classified as negative (RFI < 0, mean = -0.294 ± 0.017 kg DM/d) or positive RFI (RFI > 0, mean = 0.305 ± 0.0189 kg DM/d). Of these, 118 prepuberal heifers were submitted to ultrasonography of the uterus and ovaries for monitoring the presence (or absence) of a corpus luteum and for the measurement of endometrial thickness. The following fertility traits were evaluated in all females: age at first calving, days to calving, first calving interval, calving success, stayability, and longevity. The variance components were estimated by the average information restricted maximum likelihood method under an animal model in 5-trait analysis of backfat and rump fat thickness, scrotal circumference, days to calving, and RFI. The total number of animals with records was 6,718, including 927 males with records of scrotal circumference and RFI and 264 females with records of days to calving and RFI. Negative RFI females consumed 12.5% less DM daily than positive RFI females and had a lower rump fat thickness when evaluated postweaning. Among the fertility traits studied, only first calving interval differed (P = 0.0858) between RFI classes, with the interval of negative RFI females being 45 d shorter than that of positive RFI animals. The heritability estimates were 0.29, 0.34, 0.50, 0.12, and 0.16 for backfat and rump fat thickness, scrotal circumference, days to calving, and RFI, respectively. The genetic correlations between RFI and the other traits studied were unfavorable for selection and were of moderate magnitude with backfat thickness, rump fat thickness, and days to calving (0.53, 0.37, and -0.49, respectively) and close to zero with scrotal circumference (0.07). Scrotal circumference (0.17 and 0.15) and days to calving (-0.10 and -0.22) were weakly and favorably correlated with backfat and rump fat thickness. There is evidence of moderate genetic antagonism between female fertility and feed efficiency, but with no evidence of a genetic correlation between male fertility and feed efficiency. There is also evidence of low genetic synergism between fat thickness and fertility.