scholarly journals The search for genetic functional variants of feed efficiency in Nelore cattle

2021 ◽  
Author(s):  
Gabriela Ribeiro
Keyword(s):  
Feed Efficiency ◽  
Functional Variants ◽  
Nelore Cattle

scholarly journals PSIV-B-28 Late-Breaking: Performance and carcass quality of Nelore bull’s progenies with contrasting traits for precocity, growth and muscularity

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 319-321
Author(s):  
Taiane S Martins ◽  
Juliana Silva ◽  
Lenise Mueller ◽  
Tamyres Amorim ◽  
Annelise Aila G Lobo ◽  
...  
Keyword(s):  
Feed Efficiency ◽  
Average Daily Gain ◽  
Backfat Thickness ◽  
Longissimus Muscle ◽  
Muscle Area ◽  
Final Body Weight ◽  
Fat Thickness ◽  
Nelore Cattle ◽  
Daily Gain

Abstract The goal of this study was to evaluate the performance and the carcass traits of Nelore cattle progenies from bulls selected by contrasting traits for precocity, growth and muscularity, through the Expected Progeny Difference (EPD). One hundred and five Nelore bulls (initial weight of 350kg±15kg) and 20 months of age were confined and fed with same diet (73% of concentrate). Thirty-two animals were selected to create the contrasting groups for precocity, growth and muscularity (16 animals assigned as a low EPD group - LEPD and 16 animals assigned as a high EPD group - HEPD), based on the EPD of their parents. The ribeye area and backfat thickness were performed by ultrasonography of 12–13th rib fat thickness and longissimus muscle area (LMA), as well as rump fat thickness (RF) measurements. Animals were harvested after 100 days and during the deboning, meat cuts were weight for cutting yield. The animals selected for the HEPD group had greater average daily gain (P = 0.006), which can be explained by the higher feed intake (P = 0.006). However, there are no difference between groups for the final body weight (P = 0.254) and feed efficiency (P = 0.715). The LEPD group presented higher dressing percentage (P = 0.028). Although the groups evaluated did not presented difference in LMA (P = 0.329) and weight of longissimus muscle (P = 0.480), the weight of rump displayed heaviest in the HEPD (P = 0.037). There was no difference between groups for RF (P = 0.086). Nevertheless, backfat thickness was higher in HEPD group (P = 0.006). The present study indicates that Nelore cattle progenies, with parents displaying higher potential for precocity, growth, and muscularity, show greater backfat thickness and weightiest of rump than the other genetic backgrounds. Thanks to FAPESP for the scholarship (Grant # 2017/02349–1).

scholarly journals Identification of genomic regions associated with feed efficiency in Nelore cattle

BMC Genetics ◽  
2014 ◽  
Vol 15 (1) ◽  
Author(s):  
Priscila SN de Oliveira ◽  
Aline SM Cesar ◽  
Michele L do Nascimento ◽  
Amália S Chaves ◽  
Polyana C Tizioto ◽  
...  
Keyword(s):  
Feed Efficiency ◽  
Genomic Regions ◽  
Nelore Cattle

scholarly journals Gene networks for three feed efficiency criteria reveal shared and specific biological processes

2020 ◽  
Vol 52 (1) ◽  
Author(s):  
Sébastien Taussat ◽  
Mekki Boussaha ◽  
Yuliaxis Ramayo-Caldas ◽  
Pauline Martin ◽  
Eric Venot ◽  
...  
Keyword(s):  
Feed Intake ◽  
Feed Efficiency ◽  
Gene Networks ◽  
Average Daily Gain ◽  
Snp Array ◽  
Genetic Determinism ◽  
Biological Processes ◽  
Continuous Increase ◽  
Functional Variants ◽  
A Genome

Abstract Background French beef producers suffer from the decrease in profitability of their farms mainly because of the continuous increase in feed costs. Selection for feed efficiency in beef cattle represents a relevant solution to face this problem. However, feed efficiency is a complex trait that can be assessed by three major criteria: residual feed intake (RFI), residual gain (RG) and feed efficiency ratio (FE), which involve different genetic determinisms. An analysis that combines phenotype and whole-genome sequence data provides a unique framework for genomic studies. The aim of our study was to identify the gene networks and the biological processes that are responsible for the genetic determinism that is shared between these three feed efficiency criteria. Results A population of 1477 French Charolais young bulls was phenotyped for feed intake (FI), average daily gain (ADG) and final weight (FW) to estimate RFI, RG and FE. A subset of 789 young bulls was genotyped on the BovineSNP50 single nucleotide polymorphism (SNP) array and imputed at the sequence level using RUN6 of the 1000 Bull Genomes Project. We conducted a genome-wide association study (GWAS) to estimate the individual effect of 8.5 million SNPs and applied an association weight matrix (AWM) approach to analyse the results, one for each feed efficiency criterion. The results highlighted co-association networks including 626 genes for RFI, 426 for RG and 564 for FE. Enrichment assessment revealed the biological processes that show the strongest association with RFI, RG and FE, i.e. digestive tract (salivary, gastric and mucin secretion) and metabolic processes (cellular and cardiovascular). Energetic functions were more associated with RFI and FE and cardio-vascular and cellular processes with RG. Several hormones such as apelin, glucagon, insulin, aldosterone, the gonadotrophin releasing hormone and the thyroid hormone were also identified, and these should be tested in future studies as candidate biomarkers for feed efficiency. Conclusions The combination of network and pathway analyses at the sequence level led to the identification of both common and specific mechanisms that are involved in RFI, RG and FE, and to a better understanding of the genetic determinism underlying these three criteria. The effects of the genes involved in each of the identified processes need to be tested in genomic evaluations to confirm the potential gain in reliability of using functional variants to select animals for feed efficiency.

Accuracies of genomic prediction of feed efficiency traits using different prediction and validation methods in an experimental Nelore cattle population1

2016 ◽  
Vol 94 (9) ◽  
pp. 3613-3623 ◽  
Author(s):  
R. M. O. Silva ◽  
B. O. Fragomeni ◽  
D. A. L. Lourenco ◽  
A. F. B. Magalhães ◽  
N. Irano ◽  
...  
Keyword(s):  
Genomic Prediction ◽  
Feed Efficiency ◽  
Validation Methods ◽  
Nelore Cattle

scholarly journals PSVIII-41 Study of functional variants in homozygous islands in Nelore cattle

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 260-261
Author(s):  
Ana Fabricia Braga Magalhães ◽  
Maria Eugênia Zerlotti Mercadante ◽  
Danielly Beraldo dos Santos Silva ◽  
Gerardo Alves Fernandes Júnior ◽  
Ana Cristina Herrera Rios ◽  
...  
Keyword(s):  
Bovine Genome ◽  
Untranslated Regions ◽  
Causative Mutation ◽  
Runs Of Homozygosity ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Missense Variants ◽  
Functional Variants ◽  
Nellore Cattle ◽  
Nelore Cattle

Abstract The aim of this study was to identify functional variants within runs of homozygosity (ROH) islands present in the genome of Nellore cattle. Genotypic information of 3,492 animals and 755,319 single nucleotide polymorphism (SNPs), were used. ROH segments were detected using PLINK software. Only ROH segments shared by more than 50% of the population individuals were used for identifying homozygosity islands. The islands functional variants were classified using the VEP tool (predictor of variant effect) from ENSEMBL software. If the variant SIFT score was less than 0.05 it was considered to be “deleterious,” otherwise it was “tolerant.” We found five islands of homozygosity, located in chromosome 5, 7, 12, 21 and 26. Within the islands, a total of 1,181 variants were processed by VEP and all of them were recognized as existing variants. In total, 51 overlapped genes and 69 overlapped transcripts were found. Most of the variants were SNPs located in the intronic regions (55%), followed by intergenic spaces (14%), upstream (13%) and downstream gene variants (12%). The intronic variants can be related to specific QTLs, either because they are associated with regions affecting gene expression or in linkage disequilibrium with the causative mutation or even because they have an unknown function. Only a small portion of the variants is in synonymous regions (4%), splice regions (1%), untranslated regions (UTRs) (1%) or are missense variants (1%). We have found 11 missense variants, being three considered deleterious and eight tolerant. The deleterious variants were annotated: INHBC, SMIM33 e FBXW4 genes. The knowledge of functional variants distribution is important for improving annotation of the bovine genome. This study was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES) - Finance Code 001 and by São Paulo Research Foundation FAPESP (grants 2018/04313-7 and 2017/10630–2).

scholarly journals Potential Biomarkers for Feed Efficiency-Related Traits in Nelore Cattle Identified by Co-expression Network and Integrative Genomics Analyses

2020 ◽  
Vol 11 ◽  
Author(s):  
Andressa O. de Lima ◽  
James E. Koltes ◽  
Wellison J. S. Diniz ◽  
Priscila S. N. de Oliveira ◽  
Aline S. M. Cesar ◽  
...  
Keyword(s):  
Feed Efficiency ◽  
Integrative Genomics ◽  
Nelore Cattle ◽  
Potential Biomarkers

scholarly journals Potential Functional Variants in Innate Immune Response Genes Associated with Feed Efficiency in Beef Cattle

2020 ◽  
Author(s):  
Gabriela Ribeiro ◽  
Aline Silva Mello Cesar ◽  
Pâmela Almeida Alexandre ◽  
José Bento Sterman Ferraz ◽  
Heidge Fukumasu
Keyword(s):  
Immune Response ◽  
Beef Cattle ◽  
Innate Immune Response ◽  
Feed Efficiency ◽  
Factor H ◽  
Innate Immune ◽  
Functional Enrichment ◽  
Rna Seq ◽  
Immune Response Genes ◽  
Functional Variants

Abstract Background: Identifying and selecting animals for feed efficiency (FE) is extremely important for the beef production chain. Currently, the most common parameter to access the FE animals is residual feed intake (RFI), which is the residual of the linear regression that estimates DMI based on average daily gain and mid-test metabolic body weight. However, it relies on costly and time-consuming data collection, creating a growing demand for alternative approaches to identify genetically superior animals for FE. This study aimed to detect potential liver-specific functional variants from RNA-seq data of 16 Nellore bulls divergently selected for FE. Results: The variant call analysis detected 247 missense SNPs and nine insertion-deletions (INDELs) that alter the protein functions. These variants were found within 190 genes differentially found (P < 0.05) in liver tissue between high FE (HFE) and low FE (LFE) animals. To better understand the role of these variants in biological pathways, we performed a functional enrichment analysis, which highlighted six genes involved in complement cascade and cascade complement regulation pathways, and 20 genes involved in the regulation of the innate immune system. They had four different significant variants in the complement factor H (CFH) family genes, and all were homozygous in HFE animals rather than some degree of heterozygous in LFE animals. Conclusion: We developed a pipeline to detect potential liver-specific functional variants from RNA-seq data from animals divergently selected for feed efficiency. With this approach, we found potential functional variants in innate immune response genes associated with feed efficiency in beef cattle.

Fine Structural Alterations in Thyroid Follicular Cells (FC) and Changes in Serum Thyroxine Produced by Feeding Polychlorinated Biphenyl (PCB) to Rats

1977 ◽  
Vol 35 ◽  
pp. 498-499
Author(s):  
W.T. Collins ◽  
Charles C. Capen ◽  
Louis Kasza
Keyword(s):  
Feed Efficiency ◽  
Polychlorinated Biphenyl ◽  
Serum Proteins ◽  
Skin Lesions ◽  
Hepatic Necrosis ◽  
Ultrastructural Changes ◽  
Lymphoid Tissues ◽  
Heat Transfer Fluids ◽  
Thyroid Follicular Cells ◽  
Peripheral Metabolism

The widespread contamination of the environment with PCB, a compound used extensively by industry in hydraulic and heat transfer fluids as well as plasticizers and solvents in adhesives and sealants, has resulted in detectable tissue levels in a large portion of the human population, domestic animals, and wildlife. Intoxication with PCB produces severe hepatic necrosis, degeneration of lymphoid tissues and kidney, skin lesions, decreased reproductive performance, reduced feed efficiency, and decreased weight gain. PCB also has been reported to reduce the binding of thyroid hormone to serum proteins and enhance the peripheral metabolism of thyroxine with increased excretion of thyroxine-glucuronide in the bile (Bastomsky, Endocrinology 95: 1150-1155, 1974).The objectives of this investigation were (1) to investigate the histopathologic, histochemical, and ultrastructural changes in thyroid FC produced by the acute (4 week) and chronic (12 week) administration of low (50 ppm) and high (500 ppm) doses of PCB to rats, (2) to correlate these alterations to changes in serum immunoreactive thyroxine concentration, and (3) to investigate the persistence of the effects of PCB on the thyroid gland.

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