Dataset Information

Genetic Basis of Blood-Based Traits and Their Relationship With Performance and Environment in Beef Cattle at Weaning.

ABSTRACT: The objectives of this study were to explore the usefulness of blood-based traits as indicators of health and performance in beef cattle at weaning and identify the genetic basis underlying the different blood parameters obtained from complete blood counts (CBCs). Disease costs represent one of the main factors determining profitability in animal production. Previous research has observed associations between blood cell counts and an animal's health status in some species. CBC were recorded from approximately 570 Angus based, crossbred beef calves at weaning born between 2015 and 2016 and raised on toxic or novel tall fescue. The calves (N = ?600) were genotyped at a density of 50k SNPs and the genotypes (N = 1160) were imputed to a density of 270k SNPs. Genetic parameters were estimated for 15 blood and 4 production. Finally, with the objective of identifying the genetic basis underlying the different blood-based traits, genome-wide association studies (GWAS) were performed for all traits. Heritability estimates ranged from 0.11 to 0.60, and generally weak phenotypic correlations and strong genetic correlations were observed among blood-based traits only. Genome-wide association study identified ninety-one 1-Mb windows that accounted for 0.5% or more of the estimated genetic variance for at least 1 trait with 21 windows overlapping across two or more traits (explaining more than 0.5% of estimated genetic variance for two or more traits). Five candidate genes have been identified in the most interesting overlapping regions related to blood-based traits. Overall, this study represents one of the first efforts represented in scientific literature to identify the genetic basis of blood cell traits in beef cattle. The results presented in this study allow us to conclude that: (1) blood-based traits have weak phenotypic correlations but strong genetic correlations among themselves. (2) Blood-based traits have moderate to high heritability. (3) There is evidence of an important overlap of genetic control among similar blood-based traits which will allow for their use in improvement programs in beef cattle.

SUBMITTER: Chinchilla-Vargas J

PROVIDER: S-EPMC7350949 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Genetic Basis of Blood-Based Traits and Their Relationship With Performance and Environment in Beef Cattle at Weaning.

Chinchilla-Vargas Josue J Kramer Luke M LM Tucker John D JD Hubbell Donald S DS Powell Jeremy G JG Lester Toby D TD Backes Elizabeth A EA Anschutz Karen K Decker Jared E JE Stalder Kenneth J KJ Rothschild Max F MF Koltes James E JE

Frontiers in genetics 20200703

The objectives of this study were to explore the usefulness of blood-based traits as indicators of health and performance in beef cattle at weaning and identify the genetic basis underlying the different blood parameters obtained from complete blood counts (CBCs). Disease costs represent one of the main factors determining profitability in animal production. Previous research has observed associations between blood cell counts and an animal's health status in some species. CBC were recorded from ...[more]

PMID: 32719722

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Project description:In beef cattle maternally influenced traits, estimates of direct-maternal genetic correlations (rdm) are usually reported to be negative. In international evaluations, rdm can differ both within countries (rdm_WC) and between countries (rdm_BC). The rdm_BC are difficult to estimate and are assumed to be zero in the current model for international beef cattle evaluations (Interbeef). Our objective was to investigate re-ranking of international estimated breeding values (IEBVs) in international beef cattle evaluations between models that either used estimated values for rdm or assumed them to be 0. Age-adjusted weaning weights and pedigree data were available for Limousin beef cattle from ten European countries. International EBVs were obtained using a multi-trait animal model with countries modeled as different traits. We compared IEBVs from a model that uses estimated rdm_BC (ranging between -0.14 and +0.14) and rdm_WC (between -0.33 and +0.40) with IEBVs obtained either from the current model that assumes rdm_BC to be 0, or from an alternative model that assumes both rdm_BC and rdm_WC to be 0. Direct and maternal IEBVs were compared across those three scenarios for different groups of animals. The ratio of population accuracies from the linear regression method was used to further investigate the impact of rdm on international evaluations, for both the whole set of animals in the evaluation and the domestic ones. Ignoring rdm_BC, i.e., replacing estimated values with 0, resulted in no (rank correlations > 0.99) or limited (between 0.98 and 0.99) re-ranking for direct and maternal IEBVs, respectively. Both rdm_BC and rdm_WC had less impact on direct IEBVs than on maternal IEBVs. Re-ranking of maternal IEBVs decreased with increasing reliability. Ignoring rdm_BC resulted in no re-ranking for sires with IEBVs that might be exchanged across countries and limited re-ranking for the top 100 sires. Using estimated rdm_BC values instead of considering them to be 0 resulted in null to limited increases in population accuracy. Ignoring both rdm_BC and rdm_WC resulted in considerable re-ranking of animals' IEBVs in all groups of animals evaluated. This study showed the limited impact of the current practice of ignoring rdm_BC in international evaluations for Limousin weaning weight, most likely because the estimated rdm_BC was close to 0. We expect that these conclusions can be extended to other traits that have reported rdm values in the range of rdm_WC values for weaning weight in Limousin.

Project description:BackgroundCompared to national evaluations, international collaboration projects further improve accuracies of estimated breeding values (EBV) by building larger reference populations or performing a joint evaluation using data (or proxy of them) from different countries. Genomic selection is increasingly adopted in beef cattle, but, to date, the benefits of including genomic information in international evaluations have not been explored. Our objective was to develop an international beef cattle single-step genomic evaluation and investigate its impact on the accuracy and bias of genomic evaluations compared to current pedigree-based evaluations.MethodsWeaning weight records were available for 331,593 animals from seven European countries. The pedigree included 519,740 animals. After imputation and quality control, 17,607 genotypes at a density of 57,899 single nucleotide polymorphisms (SNPs) from four countries were available. We implemented two international scenarios where countries were modelled as different correlated traits: an international genomic single-step SNP best linear unbiased prediction (SNPBLUP) evaluation (ssSNPBLUPINT) and an international pedigree-based BLUP evaluation (PBLUPINT). Two national scenarios were implemented for pedigree and genomic evaluations using only nationally submitted phenotypes and genotypes. Accuracies, level and dispersion bias of EBV of animals born from 2014 onwards, and increases in population accuracies were estimated using the linear regression method.ResultsOn average across countries, 39 and 17% of sires and maternal-grand-sires with recorded (grand-)offspring across two countries were genotyped. ssSNPBLUPINT showed the highest accuracies of EBV and, compared to PBLUPINT, led to increases in population accuracy of 13.7% for direct EBV, and 25.8% for maternal EBV, on average across countries. Increases in population accuracies when moving from national scenarios to ssSNPBLUPINT were observed for all countries. Overall, ssSNPBLUPINT level and dispersion bias remained similar or slightly reduced compared to PBLUPINT and national scenarios.ConclusionsInternational single-step SNPBLUP evaluations are feasible and lead to higher population accuracies for both large and small countries compared to current international pedigree-based evaluations and national evaluations. These results are likely related to the larger multi-country reference population and the inclusion of phenotypes from relatives recorded in other countries via single-step international evaluations. The proposed international single-step approach can be applied to other traits and breeds.

Project description:The Montana Tropical® Composite is a recently developed beef cattle population that is rapidly expanding in Brazil and other tropical countries. This is mainly due to its improved meat quality and adaptation to tropical climate conditions compared to Zebu and Taurine cattle breeds, respectively. This study aimed to investigate the genetic architecture of ultrasound-based carcass and meat quality traits in Montana Tropical® Composite beef cattle. Therefore, we estimated variance components and genetic parameters and performed genome-wide association studies using the weighted single-step Genomic Best Linear Unbiased Prediction (GBLUP) approach. A pedigree dataset containing 28,480 animals was used, in which 1,436 were genotyped using a moderate-density Single Nucleotide Polymorphism panel (30K; 30,105 SNPs). A total of 9,358, 5,768, 7,996, and 1,972 phenotypic records for the traits Longissimus muscle area (LMA), backfat thickness (BFT), rump fat thickness (RFT), and for marbling score (MARB), respectively, were used for the analyses. Moderate to high heritability estimates were obtained and ranged from 0.16 ± 0.03 (RFT) to 0.33 ± 0.05 (MARB). A high genetic correlation was observed between BFT and RFT (0.97 ± 0.02), suggesting that a similar set of genes affects both traits. The most relevant genomic regions associated with LMA, BFT, RFT, and MARB were found on BTA10 (5.4-5.8 Mb), BTA27 (25.2-25.5 Mb), BTA18 (60.6-61.0 Mb), and BTA21 (14.8-15.4 Mb). Two overlapping genomic regions were identified for RFT and MARB (BTA13:47.9-48.1 Mb) and for BFT and RFT (BTA13:61.5-62.3 Mb). Candidate genes identified in this study, including PLAG1, LYN, WWOX, and PLAGL2, were previously reported to be associated with growth, stature, skeletal muscle growth, fat thickness, and fatty acid composition. Our results indicate that ultrasound-based carcass and meat quality traits in the Montana Tropical® Composite beef cattle are heritable, and therefore, can be improved through selective breeding. In addition, various novel and already known genomic regions related to these traits were identified, which contribute to a better understanding of the underlying genetic background of LMA, BFT, RFT, and MARB in the Montana Tropical Composite population.

Project description:Identifying causal relationships is complicated. Researchers usually overlook causality behind relationships which can generate misleading associations. Herein, we carefully examine the parametric relationship and causality between wildfire smoke exposure and animal performance and behavior metrics over a period of 2 yr in Reno, Nevada. The animals in the 2020 smoke season were grain-finished (n = 12) and grass-finished (n = 12), whereas the animals during the 2021 season were fed under the same diet but finished with either a hormonal implant (n = 9), or without (n = 9). The dataset included daily records of feed intake (FI), body weight (BW), water intake (WI), average daily gain (ADG), and WI behavior (time spent drinking [TSD]; water intake events [WIE]; no-WIE [NWIE]). Variable tree length Bayesian additive regression trees (BART) were utilized to investigate the relationships between air quality index (AQI), particulate matter 2.5 μm (PM2.5) and 10 μm (PM10), NO2, SO2, Ozone, and CO levels in the air (sensors < 1.6 km from animals) with the animal data. Additionally, linear mixed models with a 7-d lag were used to evaluate parametric relationships among the same variables. All statistical analyses were performed on R Statistical Software (R Core Team 2023). Under the linear mixed model with a 7-d lag, significant positive and negative associations were found for all parameters examined (P < 0.05). Negative associations were found between FI, WI, ADG, BW, WIE, NWIE, TSD, and PM2.5 (P < 0.05) for at least one animal group. Positive linear associations between wildfire smoke parameters and the metrics evaluated were more variable and dependent on year, treatment, and smoke parameters. When examining the credible intervals and the variable importance in the BART, relationships were more difficult to identify. However, some associations were found for Ozone, AQI, NO2, CO, and PM10 (P < 0.05). Overall, our results carefully examine the relationship between smoke parameters and cattle performance and present interesting pathways previously unexplored that could guide early culling/finishing of animals to avoid economic losses associated with performance decrease in response to wildfire smoke exposure. Though interesting associations are found under linear mixed models, causality is difficult to establish, which highlights the need for controlled exposure experiments.

Dataset Information

Genetic Basis of Blood-Based Traits and Their Relationship With Performance and Environment in Beef Cattle at Weaning.

Publications

Genetic Basis of Blood-Based Traits and Their Relationship With Performance and Environment in Beef Cattle at Weaning.

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