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.

Meta-analysis across Nellore cattle populations identifies common metabolic mechanisms that regulate feed efficiency-related traits.

BACKGROUND: Feed efficiency (FE) related traits play a key role in the economy and sustainability of beef cattle production systems. The accurate knowledge of the physiologic background for FE-related traits can help the development of more efficient selection strategies for them. Hence, multi-trait weighted GWAS (MTwGWAS) and meta-analyze were used to find genomic regions associated with average daily gain (ADG), dry matter intake (DMI), feed conversion ratio (FCR), feed efficiency (FE), and residual feed intake (RFI). The FE-related traits and genomic information belong to two breeding programs that perform the FE test at different ages: post-weaning (1,024 animals IZ population) and post-yearling (918 animals for the QLT population). RESULTS: The meta-analyze MTwGWAS identified 14 genomic regions (-log10(p -value) > 5) regions mapped on BTA 1, 2, 3, 4, 7, 8, 11, 14, 15, 18, 21, and 29. These regions explained a large proportion of the total genetic variance for FE-related traits across-population ranging from 20% (FCR) to 36% (DMI) in the IZ population and from 22% (RFI) to 28% (ADG) in the QLT population. Relevant candidate genes within these regions (LIPE, LPL, IGF1R, IGF1, IGFBP5, IGF2, INS, INSR, LEPR, LEPROT, POMC, NPY, AGRP, TGFB1, GHSR, JAK1, LYN, MOS, PLAG1, CHCD7, LCAT, and PLA2G15) highlighted that the physiological mechanisms related to neuropeptides and the metabolic signals controlling the body's energy balance are responsible for leading to greater feed efficiency. Integrated meta-analysis results and functional pathway enrichment analysis highlighted the major effect of biological functions linked to energy, lipid metabolism, and hormone signaling that mediates the effects of peptide signals in the hypothalamus and whole-body energy homeostasis affecting the genetic control of FE-related traits in Nellore cattle. CONCLUSIONS: Genes and pathways associated with common signals for feed efficiency-related traits provide better knowledge about regions with biological relevance in physiological mechanisms associated with differences in energy metabolism and hypothalamus signaling. These pleiotropic regions would support the selection for feed efficiency-related traits, incorporating and pondering causal variations assigning prior weights in genomic selection approaches.

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.

Benchmarking machine learning and parametric methods for genomic prediction of feed efficiency-related traits in Nellore cattle.

Genomic selection (GS) offers a promising opportunity for selecting more efficient animals to use consumed energy for maintenance and growth functions, impacting profitability and environmental sustainability. Here, we compared the prediction accuracy of multi-layer neural network (MLNN) and support vector regression (SVR) against single-trait (STGBLUP), multi-trait genomic best linear unbiased prediction (MTGBLUP), and Bayesian regression (BayesA, BayesB, BayesC, BRR, and BLasso) for feed efficiency (FE) traits. FE-related traits were measured in 1156 Nellore cattle from an experimental breeding program genotyped for ~ 300 K markers after quality control. Prediction accuracy (Acc) was evaluated using a forward validation splitting the dataset based on birth year, considering the phenotypes adjusted for the fixed effects and covariates as pseudo-phenotypes. The MLNN and SVR approaches were trained by randomly splitting the training population into fivefold to select the best hyperparameters. The results show that the machine learning methods (MLNN and SVR) and MTGBLUP outperformed STGBLUP and the Bayesian regression approaches, increasing the Acc by approximately 8.9%, 14.6%, and 13.7% using MLNN, SVR, and MTGBLUP, respectively. Acc for SVR and MTGBLUP were slightly different, ranging from 0.62 to 0.69 and 0.62 to 0.68, respectively, with empirically unbiased for both models (0.97 and 1.09). Our results indicated that SVR and MTGBLUBP approaches were more accurate in predicting FE-related traits than Bayesian regression and STGBLUP and seemed competitive for GS of complex phenotypes with various degrees of inheritance.

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.

Genotype by Prenatal Environment Interaction for Postnatal Growth of Nelore Beef Cattle Raised under Tropical Grazing Conditions.

The prenatal environment is recognized as crucial for the postnatal performance in cattle. In tropical regions, pregnant beef cows commonly experience nutritional restriction during the second half of the gestation period. Thus, the present study was designed to analyze the genotype by prenatal environment interaction (G × Epn) and to identify genomic regions associated with the level and response in growth and reproduction-related traits of beef cattle to changes in the prenatal environment. A reaction norm model was applied to data from two Nelore herds using the solutions of contemporary groups for birth weight as a descriptor variable of the gestational environment quality. A better gestational environment favored weights until weaning, scrotal circumference at yearling, and days to first calving of the offspring. The G × Epn was strong enough to result in heterogeneity of variance components and genetic parameters in addition to reranking of estimated breeding values and SNPs effects. Several genomic regions associated with the level of performance and specific responses of the animals to variations in the gestational environment were revealed, which harbor QTLs and can be exploited for selection purposes. Therefore, genetic evaluation models considering G × Epn and special management and nutrition care for pregnant cows are recommended.

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.