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Ribeiro VMP, Gouveia GC, Toral FLB. Candidate genes for longitudinal traits under sequential sampling in beef cattle. J Anim Breed Genet 2024; 141:179-192. [PMID: 37917404 DOI: 10.1111/jbg.12833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 10/09/2023] [Accepted: 10/14/2023] [Indexed: 11/04/2023]
Abstract
Both the measurement age of a longitudinal trait and the common pre-sampling procedures used in beef cattle herds may affect the identification of a functional candidate gene (FCG) that is potentially associated with a trait. To identify the FCG that takes part in the genetic control of body weight at five different ages in a beef cattle population with and without sequential sampling, the animals were weighed at different measurement events, around 330, 385, 440, 495 and 550 days old. Genetic parameters were estimated for body weight at each age using a single trait (STM) and a random regression model (RRM). In addition, two different databases were used to estimate the genetic parameters: the first (DB100) was formed by all animals that were weighed in the five measurement events, and the second (DB70) has records of the same population, considering that 70% of the heaviest animals were selected after each measurement event. For DB100, genome-wide association studies (GWAS) were performed with 21,667 SNP markers to identify genomic windows that explained at least 1% of the genetic variance. Additionally, prioritization analyses were performed and FCGs were selected. We associated seven different FCGs with body weight at different ages. Among them, the gene DUSP10 was suggested as FCG in all five ages evaluated. Genetic parameters estimated for body weight using DB100 were similar when STM and RRM were applied. However, when DB70 was used as phenotypic data, there were differences between the two models. When the STM was applied, there were differences between the genetic parameters estimated for body weight when DB100 or DB70 were used as sources of phenotypes, but not for the estimates obtained with RRM. The importance of each gene for animal growth can change at different ages, and different genes may be more relevant to body weight at each different growth stage for beef cattle. Besides, sequential sampling can affect the GWAS results of a longitudinal trait. The age of the animal when a longitudinal trait is measured and pre-sampling can also contribute to inconsistencies in GWAS results for body weight in beef cattle, depending on the time when that data were collected, and consequently on the identification of FCG between studies, even when models that consider a covariance structure are used.
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Moraes MMD, Gouveia GC, Ribeiro VMP, Araújo AEMD, Toral FLB, Cardoso EP. Genetic and phenotypic parameters for sexual precocity and parasite resistance traits in Nellore cattle. J Appl Genet 2023; 64:797-807. [PMID: 37682511 DOI: 10.1007/s13353-023-00781-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 09/09/2023]
Abstract
Indicator traits of sexual precocity are widely used as selection criteria for the genetic improvement of beef cattle; however, the impact of selection for these traits on resistance to endoparasites and ectoparasites is unknown. Therefore, this study aimed to estimate the genetic and phenotypic parameters for indicator traits of sexual precocity and parasite resistance in Nellore cattle. The sexual precocity traits evaluated were probability of first calving (PFC) and scrotal circumference at 12 and 18 months of age (SC12 and SC18). The resistance-related traits included tick (TC), gastrointestinal nematode egg (NEC), and Eimeria spp. oocyst (EOC) counts. (Co)variance components were estimated by Bayesian inference using multitrait animal models. The mean heritabilities for PFC, SC12, SC18, TC, NEC, and EOC were 0.23, 0.38, 0.42, 0.14, 0.16, and 0.06, respectively, and suggest that selection will change the mean values of these traits over time. The genetic and phenotypic correlations for most pairs formed by a precocity and a resistance trait were not different from zero, suggesting that selection for sexual precocity traits will not result in changes in resistance traits. Thus, selection for indicator traits of sexual precocity does not elicit unfavorable correlated responses in resistance to endoparasites and ectoparasites, and joint selection aimed at improving these traits can be performed using multitrait selection methods, when necessary.
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Affiliation(s)
- Mariana Mamedes de Moraes
- Departamento de Zootecnia, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.
| | - Gabriela Canabrava Gouveia
- Departamento de Zootecnia, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Andresa Eva Melo de Araújo
- Departamento de Zootecnia, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Fabio Luiz Buranelo Toral
- Departamento de Zootecnia, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
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Gouveia GC, Ribeiro VMP, Fortes MRS, Raidan FSS, Reverter A, Porto-Neto LR, Moraes MMD, Gonçalves DR, Silva MVGBD, Toral FLB. Unravelling the genetic variability of host resilience to endo- and ectoparasites in Nellore commercial herds. Genet Sel Evol 2023; 55:81. [PMID: 37990289 PMCID: PMC10664541 DOI: 10.1186/s12711-023-00844-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 09/19/2023] [Indexed: 11/23/2023] Open
Abstract
BACKGROUND Host resilience (HR) to parasites can affect the performance of animals. Therefore, the aim of this study was to present a detailed investigation of the genetic mechanisms of HR to ticks (TICK), gastrointestinal nematodes (GIN), and Eimeria spp. (EIM) in Nellore cattle that were raised under natural infestation and a prophylactic parasite control strategy. In our study, HR was defined as the slope coefficient of body weight (BW) when TICK, GIN, and EIM burdens were used as environmental gradients in random regression models. In total, 1712 animals were evaluated at five measurement events (ME) at an average age of 331, 385, 443, 498, and 555 days, which generated 7307 body weight (BW) records. Of the 1712 animals, 1075 genotyped animals were used in genome-wide association studies to identify genomic regions associated with HR. RESULTS Posterior means of the heritability estimates for BW ranged from 0.09 to 0.54 across parasites and ME. The single nucleotide polymorphism (SNP)-derived heritability for BW at each ME ranged from a low (0.09 at ME.331) to a moderate value (0.23 at ME.555). Those estimates show that genetic progress can be achieved for BW through selection. Both genetic and genomic associations between BW and HR to TICK, GIN, and EIM confirmed that parasite infestation impacted the performance of animals. Selection for BW under an environment with a controlled parasite burden is an alternative to improve both, BW and HR. There was no impact of age of measurement on the estimates of genetic variance for HR. Five quantitative trait loci (QTL) were associated with HR to EIM but none with HR to TICK and to GIN. These QTL contain genes that were previously shown to be associated with the production of antibody modulators and chemokines that are released in the intestinal epithelium. CONCLUSIONS Selection for BW under natural infestation and controlled parasite burden, via prophylactic parasite control, contributes to the identification of animals that are resilient to nematodes and Eimeria ssp. Although we verified that sufficient genetic variation existed for HR, we did not find any genes associated with mechanisms that could justify the expression of HR to TICK and GIN.
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Affiliation(s)
- Gabriela Canabrava Gouveia
- Departamento de Zootecnia, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Marina Rufino Salinas Fortes
- School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Fernanda Santos Silva Raidan
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization (CSIRO), Brisbane, QLD, Australia
- Swine Business Unit, Hendrix Genetics, 5831 CK, Boxmeer, The Netherlands
| | - Antonio Reverter
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization (CSIRO), Brisbane, QLD, Australia
| | - Laercio Ribeiro Porto-Neto
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization (CSIRO), Brisbane, QLD, Australia
| | - Mariana Mamedes de Moraes
- Departamento de Zootecnia, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | - Fabio Luiz Buranelo Toral
- Departamento de Zootecnia, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
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Hu G, Do DN, Davoudi P, Manafiazar G, Kelvin AA, Plastow G, Wang Z, Sargolzaei M, Miar Y. Genetic and phenotypic correlations between Aleutian disease tests with body weight, growth, and feed efficiency traits in mink. J Anim Sci 2022; 100:skac346. [PMID: 36250683 PMCID: PMC9733502 DOI: 10.1093/jas/skac346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/15/2022] [Indexed: 12/15/2022] Open
Abstract
The ineffectiveness of vaccination, medicine, and culling strategy leads mink farmers to control Aleutian disease (AD) by selecting AD-resilient mink based on AD tests. However, the genetic background of AD tests and their correlations with economically important or AD-resilient traits are limited. This study estimated the genetic and phenotypic correlations between four AD tests and seven body weight (BW) traits, six growth parameters from the Richards growth model, and eight feed-related traits. Univariate models were used to test the significance (P < 0.05) of fixed effects (sex, color type, AD test year, birth year, and row-by-year), random effects (additive genetic, maternal genetic, and permanent environmental), and a covariate of age using ASReml 4.1. Likewise, pairwise bivariate analyses were conducted to estimate the phenotypic and genetic correlations among the studied traits. Both antigen- and virus capsid protein-based enzyme-linked immunosorbent assay tests (ELISA-G and ELISA-P) showed significant (P < 0.05) moderate positive genetic correlations (±SE) with maturation rate (from 0.36 ± 0.18 to 0.38 ± 0.19). ELISA-G showed a significant negative genetic correlation (±SE) with average daily gain (ADG, -0.37 ± 0.16). ELISA-P showed a significant positive moderate genetic correlation (±SE) with off-feed days (DOF, 0.42 ± 0.17). These findings indicated that selection for low ELISA scores would reduce the maturation rate, increase ADG (by ELISA-G), and minimize DOF (by ELISA-P). The iodine agglutination test (IAT) showed significant genetic correlations with DOF (0.73 ± 0.16), BW at 16 weeks of age (BW16, 0.45 ± 0.23), and BW at harvest (HW, -0.47 ± 0.20), indicating that selection for lower IAT scores would lead to lower DOF and BW16, and higher HW. These estimated genetic correlations suggested that the selection of AD tests would not cause adverse effects on the growth, feed efficiency, and feed intake of mink. The estimates from this study might strengthen the previous finding that ELISA-G could be applied as a reliable and practical indicator trait in the genetic selection of AD-resilient mink in AD-positive farms.
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Affiliation(s)
- Guoyu Hu
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, B2N 5E3, Canada
| | - Duy Ngoc Do
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, B2N 5E3, Canada
| | - Pourya Davoudi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, B2N 5E3, Canada
| | - Ghader Manafiazar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, B2N 5E3, Canada
| | - Alyson A Kelvin
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, S7N 5E3, Canada
| | - Graham Plastow
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Zhiquan Wang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Mehdi Sargolzaei
- Department of Pathobiology, University of Guelph, Guelph, ON, N1G 2W1, Canada
- Select Sires Inc., Plain City, OH 43064, USA
| | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, B2N 5E3, Canada
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Use of a graph neural network to the weighted gene co-expression network analysis of Korean native cattle. Sci Rep 2022; 12:9854. [PMID: 35701465 PMCID: PMC9197844 DOI: 10.1038/s41598-022-13796-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 05/27/2022] [Indexed: 11/25/2022] Open
Abstract
In the general framework of the weighted gene co-expression network analysis (WGCNA), a hierarchical clustering algorithm is commonly used to module definition. However, hierarchical clustering depends strongly on the topological overlap measure. In other words, this algorithm may assign two genes with low topological overlap to different modules even though their expression patterns are similar. Here, a novel gene module clustering algorithm for WGCNA is proposed. We develop a gene module clustering network (gmcNet), which simultaneously addresses single-level expression and topological overlap measure. The proposed gmcNet includes a “co-expression pattern recognizer” (CEPR) and “module classifier”. The CEPR incorporates expression features of single genes into the topological features of co-expressed ones. Given this CEPR-embedded feature, the module classifier computes module assignment probabilities. We validated gmcNet performance using 4,976 genes from 20 native Korean cattle. We observed that the CEPR generates more robust features than single-level expression or topological overlap measure. Given the CEPR-embedded feature, gmcNet achieved the best performance in terms of modularity (0.261) and the differentially expressed signal (27.739) compared with other clustering methods tested. Furthermore, gmcNet detected some interesting biological functionalities for carcass weight, backfat thickness, intramuscular fat, and beef tenderness of Korean native cattle. Therefore, gmcNet is a useful framework for WGCNA module clustering.
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Naserkheil M, Mehrban H, Lee D, Park MN. Genome-wide Association Study for Carcass Primal Cut Yields Using Single-step Bayesian Approach in Hanwoo Cattle. Front Genet 2021; 12:752424. [PMID: 34899840 PMCID: PMC8662546 DOI: 10.3389/fgene.2021.752424] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/02/2021] [Indexed: 12/30/2022] Open
Abstract
The importance of meat and carcass quality is growing in beef cattle production to meet both producer and consumer demands. Primal cut yields, which reflect the body compositions of carcass, could determine the carcass grade and, consequently, command premium prices. Despite its importance, there have been few genome-wide association studies on these traits. This study aimed to identify genomic regions and putative candidate genes related to 10 primal cut traits, including tenderloin, sirloin, striploin, chuck, brisket, top round, bottom round, shank, flank, and rib in Hanwoo cattle using a single-step Bayesian regression (ssBR) approach. After genomic data quality control, 43,987 SNPs from 3,745 genotyped animals were available, of which 3,467 had phenotypic records for the analyzed traits. A total of 16 significant genomic regions (1-Mb window) were identified, of which five large-effect quantitative trait loci (QTLs) located on chromosomes 6 at 38–39 Mb, 11 at 21–22 Mb, 14 at 6–7 Mb and 26–27 Mb, and 19 at 26–27 Mb were associated with more than one trait, while the remaining 11 QTLs were trait-specific. These significant regions were harbored by 154 genes, among which TOX, FAM184B, SPP1, IBSP, PKD2, SDCBP, PIGY, LCORL, NCAPG, and ABCG2 were noteworthy. Enrichment analysis revealed biological processes and functional terms involved in growth and lipid metabolism, such as growth (GO:0040007), muscle structure development (GO:0061061), skeletal system development (GO:0001501), animal organ development (GO:0048513), lipid metabolic process (GO:0006629), response to lipid (GO:0033993), metabolic pathways (bta01100), focal adhesion (bta04510), ECM–receptor interaction (bta04512), fat digestion and absorption (bta04975), and Rap1 signaling pathway (bta04015) being the most significant for the carcass primal cut traits. Thus, identification of quantitative trait loci regions and plausible candidate genes will aid in a better understanding of the genetic and biological mechanisms regulating carcass primal cut yields.
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Affiliation(s)
- Masoumeh Naserkheil
- Animal Breeding and Genetics Division, National Institute of Animal Science, Cheonan-si, South Korea
| | - Hossein Mehrban
- Department of Animal Science, Shahrekord University, Shahrekord, Iran
| | - Deukmin Lee
- Department of Animal Life and Environment Sciences, Hankyong National University, Anseong-si, South Korea
| | - Mi Na Park
- Animal Breeding and Genetics Division, National Institute of Animal Science, Cheonan-si, South Korea
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Martinez-Castillero M, Then C, Altarriba J, Srihi H, López-Carbonell D, Díaz C, Martinez P, Hermida M, Varona L. Detection of Genomic Regions with Pleiotropic Effects for Growth and Carcass Quality Traits in the Rubia Gallega Cattle Breed. Animals (Basel) 2021; 11:ani11061682. [PMID: 34200089 PMCID: PMC8227173 DOI: 10.3390/ani11061682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/25/2021] [Accepted: 06/02/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The breeding scheme in the Rubia Gallega cattle population is based upon traits measured in farms and slaughterhouses. We have developed a ssGWAS by backsolving the SNP effects after implementing a ssGBLUP. The results showed an apparent heterogeneity of the additive genetic variance across the genome. Some of the genomic regions explaining the most of this additive variance were shared across traits, indicating the presence of pleiotropic effects, which were reflected in their genetic correlations. Abstract The breeding scheme in the Rubia Gallega cattle population is based upon traits measured in farms and slaughterhouses. In recent years, genomic evaluation has been implemented by using a ssGBLUP (single-step Genomic Best Linear Unbiased Prediction). This procedure can reparameterized to perform ssGWAS (single-step Genome Wide Association Studies) by backsolving the SNP (single nucleotide polymorphisms) effects. Therefore, the objective of this study was to identify genomic regions associated with the genetic variability in growth and carcass quality traits. We implemented a ssGBLUP by using a database that included records for Birth Weight (BW-327,350 records-), Weaning Weight (WW-83,818-), Cold Carcass Weight (CCW-91,621-), Fatness (FAT-91,475-) and Conformation (CON-91,609-). The pedigree included 464,373 individuals, 2449 of which were genotyped. After a process of filtering, we ended up using 43,211 SNP markers. We used the GBLUP and SNPBLUP model equivalences to obtain the effects of the SNPs and then calculated the percentage of variance explained by the regions of the genome between 1 Mb. We identified 7 regions of the genome for CCW; 8 regions for BW, WW, FAT and 9 regions for CON, which explained the percentage of variance above 0.5%. Furthermore, a number of the genome regions had pleiotropic effects, located at: BTA1 (131–132 Mb), BTA2 (1–11 Mb), BTA3 (32–33 Mb), BTA6 (36–38 Mb), BTA16 (24–26 Mb), and BTA 21 (56–57 Mb). These regions contain, amongst others, the following candidate genes: NCK1, MSTN, KCNA3, LCORL, NCAPG, and RIN3.
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Affiliation(s)
- Maria Martinez-Castillero
- Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, 50013 Zaragoza, Spain; (C.T.); (J.A.); (H.S.); (D.L.-C.); (L.V.)
- Correspondence:
| | - Carlos Then
- Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, 50013 Zaragoza, Spain; (C.T.); (J.A.); (H.S.); (D.L.-C.); (L.V.)
| | - Juan Altarriba
- Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, 50013 Zaragoza, Spain; (C.T.); (J.A.); (H.S.); (D.L.-C.); (L.V.)
| | - Houssemeddine Srihi
- Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, 50013 Zaragoza, Spain; (C.T.); (J.A.); (H.S.); (D.L.-C.); (L.V.)
| | - David López-Carbonell
- Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, 50013 Zaragoza, Spain; (C.T.); (J.A.); (H.S.); (D.L.-C.); (L.V.)
| | - Clara Díaz
- Instituto Nacional de Investigación y Tecnología Agraria (INIA), 28040 Madrid, Spain;
| | - Paulino Martinez
- Facultad de Veterinaria, Universidad de Santiago de Compostela, 27002 Lugo, Spain; (P.M.); (M.H.)
| | - Miguel Hermida
- Facultad de Veterinaria, Universidad de Santiago de Compostela, 27002 Lugo, Spain; (P.M.); (M.H.)
| | - Luis Varona
- Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, 50013 Zaragoza, Spain; (C.T.); (J.A.); (H.S.); (D.L.-C.); (L.V.)
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