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Portes JV, Rodrigues GRD, de Vasconcellos Silva JAI, de Paula Freitas A, Mercadante MEZ, Bonilha SFM, Canesin RC, Valente JDPS, Cyrillo JNDSG. Effects of inbreeding on production traits and genetic evaluations in Guzerá beef cattle raised under tropical conditions. Trop Anim Health Prod 2024; 56:132. [PMID: 38642253 DOI: 10.1007/s11250-024-03987-z] [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: 12/27/2023] [Accepted: 04/15/2024] [Indexed: 04/22/2024]
Abstract
The objectives of this study were to evaluate the influence of inbreeding on growth traits and body measurements, as well as on the estimation of genetic parameters and genetic trends in Guzerá cattle. Phenotypic records of 4,212 animals selected for postweaning weight from Guzerá Breeding Program of Advanced Beef Cattle Research Center were utilized. The pedigree file contained records from 7,213 animals born from 1928 to 2019. The traits analyzed were: birth weight (BW), weights adjusted to 210, 378 and 550 days of age (W210, W378 and W550, respectively), chest girth at 378 and 550 days of age (CG378 and CG550), scrotal circumference (SC), and hip height at 378 and 550 days of age (HH378 and H550). Linear regression was used to evaluate the effects of inbreeding on traits. Genetic parameters were obtained using models including or not the effect of inbreeding as a covariate. Inbreeding had negative effects (P ≤ 0.01) on BW (-0.09 kg), W378 (-2.86 kg), W550 (-2.95 kg), HH378 (-0.10 cm), and H550 (-0.29 cm). The lowest and highest heritability estimates were obtained for W210 (0.21 ± 0.07) and HH550 (0.57 ± 0.06), respectively. The genetic correlations were strong and positive between all traits, ranging from 0.44 ± 0.08 (SC x HH) to 0.99 ± 0.01 (W378 x W550). Spearman correlations between EBVs obtained with or without inbreeding effect ranged from 0.968 to 0.995 (P < 0.01). The results indicate loss of productive performance in inbred animals. However, the inclusion of inbreeding coefficient in genetic evaluation models did not alter the magnitude of genetic parameters or genetic trends for the traits studied.
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Affiliation(s)
- Juliana Varchaki Portes
- Department of Animal Science, Federal University of Rio Grande do Sul (UFRGS), Avenue Bento Gonçalves 7712, Porto Alegre, 91540-000, RS, Brazil
| | - Gustavo Roberto Dias Rodrigues
- School of Agricultural and Veterinarian Sciences (FCAV), São Paulo State University (UNESP), Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, 14884-900, SP, Brazil.
- Institute of Animal Science (IZ), Beef Cattle Research Center, Rodovia Carlos Tonati 94, Sertãozinho, 13380-011, SP, Brazil.
| | | | - Anielly de Paula Freitas
- Department of Genetics, University of São Paulo (USP), Avenue Bandeirantes 3900, Ribeirão Preto, 14040-905, SP, Brazil
| | - Maria Eugênia Zerlotti Mercadante
- School of Agricultural and Veterinarian Sciences (FCAV), São Paulo State University (UNESP), Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, 14884-900, SP, Brazil
- Institute of Animal Science (IZ), Beef Cattle Research Center, Rodovia Carlos Tonati 94, Sertãozinho, 13380-011, SP, Brazil
| | | | - Roberta Carrilho Canesin
- Institute of Animal Science (IZ), Beef Cattle Research Center, Rodovia Carlos Tonati 94, Sertãozinho, 13380-011, SP, Brazil
| | - Julia de Paula Soares Valente
- School of Agricultural and Veterinarian Sciences (FCAV), São Paulo State University (UNESP), Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, 14884-900, SP, Brazil
- Institute of Animal Science (IZ), Beef Cattle Research Center, Rodovia Carlos Tonati 94, Sertãozinho, 13380-011, SP, Brazil
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Carrara ER, Lopes PS, Veroneze R, Pereira RJ, Zadra LEF, Peixoto MGCD. Assessment of runs of homozygosity, heterozygosity-rich regions and genomic inbreeding estimates in a subpopulation of Guzerá (Bos indicus) dual-purpose cattle. J Anim Breed Genet 2024; 141:207-219. [PMID: 38010317 DOI: 10.1111/jbg.12836] [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: 01/24/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 11/29/2023]
Abstract
For decades, inbreeding in cattle has been evaluated using pedigree information. Nowadays, inbreeding coefficients can be obtained using genomic information such as runs of homozygosity (ROH). The aims of this study were to quantify ROH and heterozygosity-rich regions (HRR) in a subpopulation of Guzerá dual-purpose cattle, to examine ROH and HRR islands, and to compare inbreeding coefficients obtained by ROH with alternative genomic inbreeding coefficients. A subpopulation of 1733 Guzerá animals genotyped for 50k SNPs was used to obtain the ROH and HRR segments. Inbreeding coefficients by ROH (FROH ), by genomic relationship matrix based on VanRaden's method 1 using reference allele frequency in the population (FGRM ), by genomic relationship matrix based on VanRaden's method 1 using allele frequency fixed in 0.5 (FGRM_0.5 ), and by the proportion of homozygous loci (FHOM ) were calculated. A total of 15,660 ROH were identified, and the chromosome with the highest number of ROH was BTA6. A total of 4843 HRRs were identified, and the chromosome with the highest number of HRRs was BTA23. No ROH and HRR islands were identified according to established criteria, but the regions closest to the definition of an island were examined from 64 to 67 Mb of BTA6, from 36 to 37 Mb of BTA2 and from 0.50 to 1.25 Mb of BTA23. The genes identified in ROH islands have previously been associated with dairy and beef traits, while genes identified on HRR islands have previously been associated with reproductive traits and disease resistance. FROH was equal to 0.095 ± 0.084, and its Spearman correlation with FGRM was low (0.44) and moderate-high with FHOM (0.79) and with FGRM_0.5 (0.80). The inbreeding coefficients determined by ROH were higher than other cattle breeds' and higher than pedigree-based inbreeding in the Guzerá breed obtained in previous studies. It is recommended that future studies investigate the effects of inbreeding determined by ROH on the traits under selection in the subpopulation studied.
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Affiliation(s)
- E R Carrara
- Department of Animal Science, Federal University of Viçosa, Viçosa, Minas Gerais, Brazil
| | - P S Lopes
- Department of Animal Science, Federal University of Viçosa, Viçosa, Minas Gerais, Brazil
| | - R Veroneze
- Department of Animal Science, Federal University of Viçosa, Viçosa, Minas Gerais, Brazil
| | - R J Pereira
- Mato Grosso Animal Breeding Group, Institute of Agrarian and Technological Sciences, Federal University of Rondonópolis, Rondonópolis, Mato Grosso, Brazil
| | - L E F Zadra
- Brazilian Center for the Genetic Improvement of Guzerá, Belo Horizonte, Minas Gerais, Brazil
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da Silva Morales D, Silva DO, Ayres DR, Junior MLS, Bignardi AB, Ventura RV, de Oliveira Menezes GR, Carvalheiro R, Piccoli ML, Roso VM, Pereira RJ. Genetic associations between stayability to consecutive calvings and traits of economic interest in taurine and zebu breeds. J Anim Breed Genet 2024; 141:83-95. [PMID: 37789663 DOI: 10.1111/jbg.12827] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 09/18/2023] [Accepted: 09/20/2023] [Indexed: 10/05/2023]
Abstract
Stayability (STAY) is a way to evaluate the productive longevity of females. Measuring the STAY at each cow calving allows earlier indicators of longevity to be obtained. Our objective with this study was to verify the association between STAY and consecutive calvings and traits potentially used as selection criteria in beef cattle, such as age at first calving (AFC), days to calving (DC), weaning weight (WW), and yearling weight (YW). Data from the Nelore, Angus/Brangus, and Hereford/Braford breeds were used. The estimation of variance components and subsequent prediction of breeding values were performed for all traits. The estimated breeding values (EBV) were used to analyse the association between STAY and the other traits. The Pearson's correlation estimated between the EBV for the intercept coefficient for STAY to consecutive calvings and those of AFC, DC, WW (direct and maternal effects), and YW was favourable and of low magnitude (<0.25) depending on the breed studied. The influence of the genetic merit of AFC on the chance of selection for STAY was favourable and relevant regardless of the intensity of selection and breed. DC and WW (maternal effect) traits were favourably influenced by the chance of selection for STAY, irrespective of breed. The WW (direct effect) did not affect the chance of selection for STAY for the Nelore and Hereford/Braford breeds and negatively influenced, but to a small extent, the Angus/Brangus breed. For YW, an increase in genetic merit affected the chances of selection for STAY, depending on the breed and selection intensity evaluated. The influence of the genetic merit for AFC, DC, and WW (maternal effect) on the chance of selection for STAY to consecutive calvings was favourable and relevant regardless of the selection intensity scenario evaluated. The WW (direct effect) did not influence the chance of selection for STAY. For the scenario with high selection intensity, the selection for YW favourably influenced the chance of selection for STAY in Angus/Brangus and Hereford/Braford breeds but not in Nelore.
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Affiliation(s)
- Débora da Silva Morales
- Grupo de Melhoramento Animal de Mato Grosso (GMAT), Universidade Federal de Rondonopolis, Rondonópolis, Brazil
| | - Diogo Osmar Silva
- Grupo de Melhoramento Animal de Mato Grosso (GMAT), Universidade Federal de Rondonopolis, Rondonópolis, Brazil
| | - Denise Rocha Ayres
- Grupo de Melhoramento Animal de Mato Grosso (GMAT), Universidade Federal de Rondonopolis, Rondonópolis, Brazil
| | - Mário Luiz Santana Junior
- Grupo de Melhoramento Animal de Mato Grosso (GMAT), Universidade Federal de Rondonopolis, Rondonópolis, Brazil
| | - Annaiza Braga Bignardi
- Grupo de Melhoramento Animal de Mato Grosso (GMAT), Universidade Federal de Rondonopolis, Rondonópolis, Brazil
| | - Ricardo Vieira Ventura
- Universidade de São Paulo (USP)-Faculdade de Medicina Veterinário e Zootecnia (FMVZ), Pirassununga, Brazil
| | | | - Roberto Carvalheiro
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, Brazil
| | | | | | - Rodrigo Junqueira Pereira
- Grupo de Melhoramento Animal de Mato Grosso (GMAT), Universidade Federal de Rondonopolis, Rondonópolis, Brazil
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Ugnivenko A, Kos N, Nosevych D, Mushtruk M, Slobodyanyuk N, Zasukha Y, Otchenashko V, Chumachenko I, Gryshchenko S, Snizhko O. The yield of adipose tissue and by-products in the course of the slaughter of inbred and outbred bulls of the Ukrainian beef breed. POTRAVINARSTVO 2022. [DOI: 10.5219/1758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The research focuses on analysing and generalising the distribution of internal adipose tissue and organs that are not part of the carcasses of inbred and outbred bulls of the Ukrainian beef breed. Animal stock inbreeding was determined based on five breeding records according to Wright’s method modified by Kyslovskyi. Two experimental groups of 5 bulls were formed. The average inbreeding coefficient for inbred bulls was 3.43%. Animals were bred up to 18 months of age. Following slaughter, the mass and the yield of the head, liver, lungs, heart, kidneys, and brain were determined, and 4 types of fat were separated and weighed: perirenal, from the stomach, intestines, and pericardial. Inbred animals are more prone to the accretion of internal adipose tissue. Inbred bulls have 1.8 points more of it. Fat is more intensely accumulated around inbred bulls' multichambered stomachs and kidneys. Intensive fat accumulation was observed around the hearts and intestines of outbred bulls. Adipose tissue around the heart and intestines is more variable in inbred and outbred animals – from the forestomach and kidneys. The weight of inbred bulls’ liver is less by 22.4%, kidneys – by 62.5%, heart – by 11.1%, and head – by 23.8% compared to outbred ones. The weight of their lungs is more by 10.5%. At the same time, inbred bulls tend to have brain weight gain of 12.5% and testicles – by 8.3%. Thus, inbreeding application in Ukrainian beef breeds with a small population size affects the growth of internal organs and the intensity of accumulation and distribution of interior fat. Due to more intensive accumulation of internal adipose tissue, inbred bulls have increased expenditure of forage energy for its formation. They are characterized by an increased yield of low-value raw fat, making them less efficient than outbred bulls for beef production.
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Forneris NS, Garcia-Baccino CA, Cantet RJC, Vitezica ZG. Estimating inbreeding depression for growth and reproductive traits using pedigree and genomic methods in Argentinean Brangus cattle. J Anim Sci 2021; 99:6396951. [PMID: 34648628 DOI: 10.1093/jas/skab289] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 10/13/2021] [Indexed: 12/20/2022] Open
Abstract
Inbreeding depression reduces the mean phenotypic value of important traits in livestock populations. The goal of this work was to estimate the level of inbreeding and inbreeding depression for growth and reproductive traits in Argentinean Brangus cattle, in order to obtain a diagnosis and monitor breed management. Data comprised 359,257 (from which 1,990 were genotyped for 40,678 single nucleotide polymorphisms [SNPs]) animals with phenotypic records for at least one of three growth traits: birth weight (BW), weaning weight (WW), and finishing weight (FW). For scrotal circumference (SC), 52,399 phenotypic records (of which 256 had genotype) were available. There were 530,938 animals in pedigree. Three methods to estimate inbreeding coefficients were used. Pedigree-based inbreeding coefficients were estimated accounting for missing parents. Inbreeding coefficients combining genotyped and nongenotyped animal information were also computed from matrix H of the single-step approach. Genomic inbreeding coefficients were estimated using homozygous segments obtained from a Hidden Markov model (HMM) approach. Inbreeding depression was estimated from the regression of the phenotype on inbreeding coefficients in a multiple-trait mixed model framework, either for the whole dataset or for the dataset of genotyped animals. All traits were unfavorably affected by inbreeding depression. A 10% increase in pedigree-based or combined inbreeding would result in a reduction of 0.34 to 0.39 kg in BW, 2.77 to 3.28 kg in WW, and 0.23 cm in SC. For FW, a 10% increase in pedigree-based, genomic, or combined inbreeding would result in a decrease of 8.05 to 11.57 kg. Genomic inbreeding based on the HMM was able to capture inbreeding depression, even in such a compressed genotyped dataset.
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Affiliation(s)
- Natalia S Forneris
- Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, C1417DSQ Buenos Aires, Argentina.,CONICET-Universidad de Buenos Aires, Instituto de Investigaciones en Producción Animal (INPA), C1427CWO Buenos Aires, Argentina
| | - Carolina A Garcia-Baccino
- Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, C1417DSQ Buenos Aires, Argentina
| | - Rodolfo J C Cantet
- Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, C1417DSQ Buenos Aires, Argentina.,CONICET-Universidad de Buenos Aires, Instituto de Investigaciones en Producción Animal (INPA), C1427CWO Buenos Aires, Argentina
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Bessa AFDO, Duarte INH, Rola LD, Bernardes PA, Gonzaga Neto S, Lôbo RB, Munari DP, Buzanskas ME. Genetic evaluation for reproductive and productive traits in Brahman cattle. Theriogenology 2021; 173:261-268. [PMID: 34403971 DOI: 10.1016/j.theriogenology.2021.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/22/2021] [Accepted: 08/05/2021] [Indexed: 10/20/2022]
Abstract
Our objectives were to estimate genetic parameters for male and female reproductive traits and their genetic correlations with body weight and carcass traits, evaluate the genetic trends over the years, and verify the effect of inbreeding on the phenotypes of Brahman cattle. The traits evaluated were body weights at 120, 210, 365, and 450 days of age (W120, W210, W365, and W450); scrotal circumference at 365 and 450 days of age (SC365 and SC450), age at first calving (AFC), gestation length (GL), stayability (STAY), ribeye area (REA), backfat thickness (BFT), and rump fat thickness (RFT). Direct heritability estimates ranged from 0.10 ± 0.03 (AFC) to 0.43 ± 0.06 (GL). Maternal heritability estimates for body weights, scrotal circumferences, and GL ranged from 0.07 ± 0.02 to 0.15 ± 0.03. The proportion of the maternal permanent environment for W120 and W210 was equal to 0.11 ± 0.02. Genetic correlations varied between -0.60 ± 0.25 (STAY and BFT) to 0.97 ± 0.01 (W365 and W450). Except for AFC, all genetic trends were significant (p < 0.05) and presented favorable annual genetic gains. Unfavorable effects due to the increase of inbreeding coefficients were observed for body weights and AFC, suggesting greater attention be paid to the applied mating systems to control inbreeding. Reproductive traits, such as AFC and STAY, could be assisted indirectly by scrotal circumference selection. The emphasis applied to body weight selection, especially at W210, may assist REA. The BFT and RFT traits presented genetic variability and have responded to selection, although not included in the Brahman selection index.
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Affiliation(s)
| | | | - Luciana Diniz Rola
- Universidade Federal da Paraíba, Departamento de Zootecnia, 58397-000, Areia, Paraíba, Brazil
| | - Priscila Arrigucci Bernardes
- Universidade Federal de Santa Catarina, Departamento de Zootecnia e Desenvolvimento Rural, 88040-900, Florianópolis, Santa Catarina, Brazil
| | - Severino Gonzaga Neto
- Universidade Federal da Paraíba, Departamento de Zootecnia, 58397-000, Areia, Paraíba, Brazil
| | - Raysildo Barbosa Lôbo
- Nacional Association of Breeders and Researchers (ANCP), 14020-230, Ribeirão Preto, São Paulo, Brazil
| | - Danísio Prado Munari
- Universidade Estadual Paulista, Departamento de Engenharia e Ciências Exatas, 14884-900, Jaboticabal, São Paulo, Brazil
| | - Marcos Eli Buzanskas
- Universidade Federal da Paraíba, Departamento de Zootecnia, 58397-000, Areia, Paraíba, Brazil.
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How Depressing Is Inbreeding? A Meta-Analysis of 30 Years of Research on the Effects of Inbreeding in Livestock. Genes (Basel) 2021; 12:genes12060926. [PMID: 34207101 PMCID: PMC8234567 DOI: 10.3390/genes12060926] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/12/2021] [Accepted: 06/15/2021] [Indexed: 11/17/2022] Open
Abstract
Inbreeding depression has been widely documented for livestock and other animal and plant populations. Inbreeding is generally expected to have a stronger unfavorable effect on fitness traits than on other traits. Traditionally, the degree of inbreeding depression in livestock has been estimated as the slope of the linear regression of phenotypic values on pedigree-based inbreeding coefficients. With the increasing availability of SNP-data, pedigree inbreeding can now be replaced by SNP-based measures. We performed a meta-analysis of 154 studies, published from 1990 to 2020 on seven livestock species, and compared the degree of inbreeding depression (1) across different trait groups, and (2) across different pedigree-based and SNP-based measures of inbreeding. Across all studies and traits, a 1% increase in pedigree inbreeding was associated with a median decrease in phenotypic value of 0.13% of a trait’s mean, or 0.59% of a trait’s standard deviation. Inbreeding had an unfavorable effect on all sorts of traits and there was no evidence for a stronger effect on primary fitness traits (e.g., reproduction/survival traits) than on other traits (e.g., production traits or morphological traits). p-values of inbreeding depression estimates were smaller for SNP-based inbreeding measures than for pedigree inbreeding, suggesting more power for SNP-based measures. There were no consistent differences in p-values for percentage of homozygous SNPs, inbreeding based on runs of homozygosity (ROH) or inbreeding based on a genomic relationship matrix. The number of studies that directly compares these different measures, however, is limited and comparisons are furthermore complicated by differences in scale and arbitrary definitions of particularly ROH-based inbreeding. To facilitate comparisons across studies in future, we provide the dataset with inbreeding depression estimates of 154 studies and stress the importance of always reporting detailed information (on traits, inbreeding coefficients, and models used) along with inbreeding depression estimates.
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Lozada-Soto EA, Maltecca C, Lu D, Miller S, Cole JB, Tiezzi F. Trends in genetic diversity and the effect of inbreeding in American Angus cattle under genomic selection. Genet Sel Evol 2021; 53:50. [PMID: 34134619 PMCID: PMC8207663 DOI: 10.1186/s12711-021-00644-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 06/07/2021] [Indexed: 11/10/2022] Open
Abstract
Background While the adoption of genomic evaluations in livestock has increased genetic gain rates, its effects on genetic diversity and accumulation of inbreeding have raised concerns in cattle populations. Increased inbreeding may affect fitness and decrease the mean performance for economically important traits, such as fertility and growth in beef cattle, with the age of inbreeding having a possible effect on the magnitude of inbreeding depression. The purpose of this study was to determine changes in genetic diversity as a result of the implementation of genomic selection in Angus cattle and quantify potential inbreeding depression effects of total pedigree and genomic inbreeding, and also to investigate the impact of recent and ancient inbreeding. Results We found that the yearly rate of inbreeding accumulation remained similar in sires and decreased significantly in dams since the implementation of genomic selection. Other measures such as effective population size and the effective number of chromosome segments show little evidence of a detrimental effect of using genomic selection strategies on the genetic diversity of beef cattle. We also quantified pedigree and genomic inbreeding depression for fertility and growth. While inbreeding did not affect fertility, an increase in pedigree or genomic inbreeding was associated with decreased birth weight, weaning weight, and post-weaning gain in both sexes. We also measured the impact of the age of inbreeding and found that recent inbreeding had a larger depressive effect on growth than ancient inbreeding. Conclusions In this study, we sought to quantify and understand the possible consequences of genomic selection on the genetic diversity of American Angus cattle. In both sires and dams, we found that, generally, genomic selection resulted in decreased rates of pedigree and genomic inbreeding accumulation and increased or sustained effective population sizes and number of independently segregating chromosome segments. We also found significant depressive effects of inbreeding accumulation on economically important growth traits, particularly with genomic and recent inbreeding. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00644-z.
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Affiliation(s)
| | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, NC, 27607, USA
| | - Duc Lu
- Angus Genetics Inc, St. Joseph, MO, 64506, USA
| | | | - John B Cole
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Service, USDA, Beltsville, MD, 20705, USA
| | - Francesco Tiezzi
- Department of Animal Science, North Carolina State University, Raleigh, NC, 27607, USA
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Randhawa IAS, McGowan MR, Porto-Neto LR, Hayes BJ, Lyons RE. Comparison of Genetic Merit for Weight and Meat Traits between the Polled and Horned Cattle in Multiple Beef Breeds. Animals (Basel) 2021; 11:870. [PMID: 33803763 PMCID: PMC8003249 DOI: 10.3390/ani11030870] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 12/16/2022] Open
Abstract
Breeding for polled animals is deemed the most practical solution to eradicate horns naturally and circumvent management costs and risks on health and welfare. However, there has been a historical reluctance by some farmers to select polled animals due to perceived lower productivity of their calves. This study has compared estimated breeding values (EBVs) between horned and polled animals (N = 2,466,785) for 12 production and carcass traits to assess historical (before 2000) and recent (2000-2018) genetic implications of poll breeding. Older generations of the polled animals in most breeds had significantly lower (Bonferroni-corrected p = 0.05) genetic merits for live (birth to maturity) and carcass weights, milk, meat quality, and fat content traits. Substantial gains of genetic potential were achieved during 2000 to 2018 in each breed, such that polled animals have significantly improved for the majority of traits studied. Generally, polled cohorts showed advantageous EBVs for live and carcass weights irrespective of the lower birth weights in some breeds. While Polled Brahman showed inferior production parameters, the poll genetics' effect size (d) and correlation (r) were very small on recent birth weight (d = -0.30, r = -0.08), 200 days (-0.19, -0.05), 400 days (-0.06, -0.02), 600 days (-0.05, -0.01), mature cow live weight (-0.08, -0.02), and carcass weight (-0.19, -0.05). In conclusion, although there is some evidence that historical selection for polled breeding animals may have reduced productivity, there is strong evidence that more recent selection for polled genotypes in the breeds studied has not resulted in any adverse effects on genetic merit.
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Affiliation(s)
- Imtiaz A. S. Randhawa
- School of Veterinary Science, University of Queensland, Gatton, QLD 4343, Australia; (M.R.M.); (R.E.L.)
| | - Michael R. McGowan
- School of Veterinary Science, University of Queensland, Gatton, QLD 4343, Australia; (M.R.M.); (R.E.L.)
| | | | - Ben J. Hayes
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD 4072, Australia;
| | - Russell E. Lyons
- School of Veterinary Science, University of Queensland, Gatton, QLD 4343, Australia; (M.R.M.); (R.E.L.)
- Agri-Genetics Consulting, Brisbane, QLD 4074, Australia
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Freitas PHF, Wang Y, Yan P, Oliveira HR, Schenkel FS, Zhang Y, Xu Q, Brito LF. Genetic Diversity and Signatures of Selection for Thermal Stress in Cattle and Other Two Bos Species Adapted to Divergent Climatic Conditions. Front Genet 2021; 12:604823. [PMID: 33613634 PMCID: PMC7887320 DOI: 10.3389/fgene.2021.604823] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/15/2021] [Indexed: 12/21/2022] Open
Abstract
Understanding the biological mechanisms of climatic adaptation is of paramount importance for the optimization of breeding programs and conservation of genetic resources. The aim of this study was to investigate genetic diversity and unravel genomic regions potentially under selection for heat and/or cold tolerance in thirty-two worldwide cattle breeds, with a focus on Chinese local cattle breeds adapted to divergent climatic conditions, Datong yak (Bos grunniens; YAK), and Bali (Bos javanicus) based on dense SNP data. In general, moderate genetic diversity levels were observed in most cattle populations. The proportion of polymorphic SNP ranged from 0.197 (YAK) to 0.992 (Mongolian cattle). Observed and expected heterozygosity ranged from 0.023 (YAK) to 0.366 (Sanhe cattle; SH), and from 0.021 (YAK) to 0.358 (SH), respectively. The overall average inbreeding (±SD) was: 0.118 ± 0.028, 0.228 ± 0.059, 0.194 ± 0.041, and 0.021 ± 0.004 based on the observed versus expected number of homozygous genotypes, excess of homozygosity, correlation between uniting gametes, and runs of homozygosity (ROH), respectively. Signatures of selection based on multiple scenarios and methods (F ST, HapFLK, and ROH) revealed important genomic regions and candidate genes. The candidate genes identified are related to various biological processes and pathways such as heat-shock proteins, oxygen transport, anatomical traits, mitochondrial DNA maintenance, metabolic activity, feed intake, carcass conformation, fertility, and reproduction. This highlights the large number of biological processes involved in thermal tolerance and thus, the polygenic nature of climatic resilience. A comprehensive description of genetic diversity measures in Chinese cattle and YAK was carried out and compared to 24 worldwide cattle breeds to avoid potential biases. Numerous genomic regions under positive selection were detected using three signature of selection methods and candidate genes potentially under positive selection were identified. Enriched function analyses pinpointed important biological pathways, molecular function and cellular components, which contribute to a better understanding of the biological mechanisms underlying thermal tolerance in cattle. Based on the large number of genomic regions identified, thermal tolerance has a complex polygenic inheritance nature, which was expected considering the various mechanisms involved in thermal stress response.
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Affiliation(s)
- Pedro H. F. Freitas
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Yachun Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA – National Engineering Laboratory for Animal Breeding – College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ping Yan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Hinayah R. Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Flavio S. Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Yi Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA – National Engineering Laboratory for Animal Breeding – College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qing Xu
- College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, China
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
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12
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Oliveira HR, McEwan JC, Jakobsen J, Blichfeldt T, Meuwissen T, Pickering N, Clarke SM, Brito LF. Genetic Connectedness Between Norwegian White Sheep and New Zealand Composite Sheep Populations With Similar Development History. Front Genet 2020; 11:371. [PMID: 32391056 PMCID: PMC7194024 DOI: 10.3389/fgene.2020.00371] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 03/26/2020] [Indexed: 11/25/2022] Open
Abstract
The Norwegian White sheep (NWS) and New Zealand Terminal Sire Composite (NZC) sheep breeds have been developed based on crossing of multiple breeds, mainly of Northern European origin. A close genetic relationship between these populations could enable across-country genomic evaluations. The main objectives of this study were to assess the genetic connectedness between Norwegian and New Zealand sheep populations and estimate numerous genetic diversity metrics for these two populations. A total of 792 NWS and 16,912 NZC animals were genotyped using a high-density Illumina SNP chip panel (∼606K SNPs). The NZC animals were grouped based on their breed composition as: Finn, Lamb Supreme, Primera, Texel, “Other Dual Purpose”, and “Other Terminal Sire”. The average level of linkage disequilibrium ranged from 0.156 (for Primera) to 0.231 (for Finn). The lowest consistency of gametic phase was estimated between NWS and Finn (0.397), and between NWS and Texel (0.443), respectively. Similar consistency of gametic phase was estimated between NWS and the other NZC populations (∼ 0.52). For all composite sheep populations analyzed in this study, the majority of runs of homozygosity (ROH) segments identified had short length (<2,500 kb), indicating ancient (instead of recent) inbreeding. The variation in the number of ROH segments observed in the NWS was similar to the variation observed in Primera and Lamb Supreme. There was no clear discrimination between NWS and NZC based on the first few principal components. In addition, based on admixture analyses, there seems to be a significant overlap of the ancestral populations that contributed to the development of both NWS and NZC. There were no evident signatures of selection in these populations, which might be due to recent crossbreeding. In conclusion, the NWS composite breed was shown to be moderately related to NZC populations, especially Primera and Lamb Supreme. The findings reported here indicate a promising opportunity for collaborative genomic analyses involving NWS and NZC sheep populations.
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Affiliation(s)
- Hinayah Rojas Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States.,Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - John Colin McEwan
- AgResearch Limited, Invermay Agricultural Centre, Mosgiel, New Zealand
| | - Jette Jakobsen
- The Norwegian Association of Sheep and Goat Breeders, Ås, Norway
| | - Thor Blichfeldt
- The Norwegian Association of Sheep and Goat Breeders, Ås, Norway
| | - Theodorus Meuwissen
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway
| | | | | | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
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13
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Martikainen K, Koivula M, Uimari P. Identification of runs of homozygosity affecting female fertility and milk production traits in Finnish Ayrshire cattle. Sci Rep 2020; 10:3804. [PMID: 32123255 PMCID: PMC7052207 DOI: 10.1038/s41598-020-60830-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 02/17/2020] [Indexed: 11/09/2022] Open
Abstract
Inbreeding gives rise to continuous lengths of homozygous genotypes called runs of homozygosity (ROH) that occur when identical haplotypes are inherited from both parents. ROHs are enriched for deleterious recessive alleles and can therefore be linked to inbreeding depression, defined as decreased phenotypic performance of the animals. However, not all ROHs within a region are expected to have harmful effects on the trait of interest. We aimed to identify ROHs that unfavourably affect female fertility and milk production traits in the Finnish Ayrshire population. The estimated effect of ROHs with the highest statistical significance varied between parities from 9 to 17 days longer intervals from calving to first insemination, from 13 to 38 days longer intervals from first to last insemination and from 0.3 to 1.0 more insemination per conception. Similarly, for milk production traits ROHs were associated with a reduction of 208 kg for milk yield, 7 kg for protein yield and 16 kg for fat yield. We also found regions where ROHs displayed unfavourable effects across multiple traits. Our findings can be exploited for more efficient control of inbreeding depression, for example by minimizing the occurrence of unfavourable haplotypes as homozygous state in breeding programmes.
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Affiliation(s)
- K Martikainen
- Department of Agricultural Sciences, University of Helsinki, P.O. Box 28, FI-00014, Helsinki, Finland.
| | - M Koivula
- Natural Resources Institute Finland (Luke), Green Technology, FI-31600, Jokioinen, Finland
| | - P Uimari
- Department of Agricultural Sciences, University of Helsinki, P.O. Box 28, FI-00014, Helsinki, Finland
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14
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Varona L, Altarriba J, Moreno C, Martínez-Castillero M, Casellas J. A multivariate analysis with direct additive and inbreeding depression load effects. Genet Sel Evol 2019; 51:78. [PMID: 31878872 PMCID: PMC6933709 DOI: 10.1186/s12711-019-0521-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 12/17/2019] [Indexed: 11/16/2022] Open
Abstract
Background Inbreeding is caused by mating between related individuals and its most common consequence is inbreeding depression. Several studies have detected heterogeneity in inbreeding depression among founder individuals, and recently a procedure for predicting hidden inbreeding depression loads associated with founders and the Mendelian sampling of non-founders has been developed. The objectives of our study were to expand this model to predict the inbreeding loads for all individuals in the pedigree and to estimate the covariance between the inbreeding loads and the additive genetic effects for the trait of interest. We tested the proposed approach with simulated data and with two datasets of records on weaning weight from the Spanish Pirenaica and Rubia Gallega beef cattle breeds. Results The posterior estimates of the variance components with the simulated datasets did not differ significantly from the simulation parameters. In addition, the correlation between the predicted and simulated inbreeding loads were always positive and ranged from 0.27 to 0.82. The beef cattle datasets comprised 35,126 and 75,194 records on weights between 170 and 250 days of age, and pedigrees of 308,836 and 384,434 individual-sire-dam entries for the Pirenaica and Rubia Gallega breeds, respectively. The posterior mean estimates of the variance of inbreeding depression loads were 29,967.8 and 28,222.4 for the Pirenaica and Rubia Gallega breeds, respectively. They were larger than those of the additive variance (695.0 and 439.8 for Pirenaica and Rubia Gallega, respectively), because they should be understood as the variance of the inbreeding depression achieved by a fully inbred (100%) descendant. Therefore, the inbreeding loads have to be rescaled for smaller inbreeding coefficients. In addition, a strong negative correlation (− 0.43 ± 0.10) between additive effects and inbreeding loads was detected in the Pirenaica, but not in the Rubia Gallega breed. Conclusions The results of the simulation study confirmed the ability of the proposed procedure to predict inbreeding depression loads for all individuals in the populations. Furthermore, the results obtained from the two real datasets confirmed the variability in the inbreeding depression loads in both breeds and suggested a negative correlation of the inbreeding loads with the additive genetic effects in the Pirenaica breed.
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Affiliation(s)
- Luis Varona
- Departamento de Anatomía Embriología y Genética Animal, Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, 50013, Saragossa, Spain.
| | - Juan Altarriba
- Departamento de Anatomía Embriología y Genética Animal, Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, 50013, Saragossa, Spain
| | - Carlos Moreno
- Departamento de Anatomía Embriología y Genética Animal, Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, 50013, Saragossa, Spain
| | - María Martínez-Castillero
- Dipartimento di Agronomia Animali, Alimenti Risorce Naturali e Ambiente, Università degli Studi di Padova, 35122, Padua, Italy
| | - Joaquim Casellas
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
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15
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Population Structure and Genetic Diversity of Italian Beef Breeds as a Tool for Planning Conservation and Selection Strategies. Animals (Basel) 2019; 9:ani9110880. [PMID: 31671823 PMCID: PMC6912484 DOI: 10.3390/ani9110880] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/18/2019] [Accepted: 10/22/2019] [Indexed: 02/01/2023] Open
Abstract
The aim was to investigate the population structure of eight beef breeds: three local Tuscan breeds under extinction, Calvana (CAL), Mucca Pisana (MUP), and Pontremolese (PON); three local unselected breeds reared in Sardinia, Sarda (SAR), Sardo Bruna (SAB), and Sardo Modicana (SAM); and two cosmopolitan breeds, Charolais (CHA) and Limousine (LIM), reared in the same regions. An effective population size ranges between 14.62 (PON) to 39.79 (SAM) in local breeds, 90.29 for CHA, and 135.65 for LIM. The average inbreeding coefficients were higher in Tuscan breeds (7.25%, 5.10%, and 3.64% for MUP, CAL, and PON, respectively) compared to the Sardinian breeds (1.23%, 1.66%, and 1.90% in SAB, SAM, and SAR, respectively), while for CHA and LIM they were <1%. The highest rates of mating between half-siblings were observed for CAL and MUP (~9% and 6.5%, respectively), while the highest rate of parent-offspring mating was ~8% for MUP. Our findings describe the urgent situation of the three Tuscan breeds and support the application of conservation measures and/or the development of breeding programs. Development of breeding strategies is suggested for the Sardinian breeds.
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16
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da Silveira DD, De Vargas L, Pereira RJ, Campos GS, Vaz RZ, Lôbo RB, de Souza FRP, Boligon AA. Quantitative study of genetic gain for growth, carcass, and morphological traits of Nelore cattle. CANADIAN JOURNAL OF ANIMAL SCIENCE 2019. [DOI: 10.1139/cjas-2018-0078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The aim of this study was to evaluate the genetic variability, genetic and phenotypic associations, and genetic gains of birth (BW), weaning (WW), and yearling (YW) weights, loin muscle area (LMA), backfat thickness (BF), rump fat thickness (RF), scores of body structure (BS), finishing precocity (FS), and muscling (MS) in Nelore cattle. Genetic parameters were obtained through Bayesian inference using BLUPF90 programs. All studied traits showed genetic variability, with heritability ranging from 0.29 to 0.47. In all studied ages, weights presented positive genetic correlations with LMA (ranging from 0.13 to 0.53), being generally stronger in comparison with the other carcass traits analyzed (BF and RF). Similarly, weights were higher genetic associated with BS (0.47–0.92) than with FS (0.18–0.62) and MS (0.22–0.65), respectively. The BF and RF showed positive and moderate genetic associations with FS and MS (0.31–0.36). Genetic trends were significant (P < 0.05) and favorable for WW, YW, and visual scores. Selection for increasing BW, WW, YW, and LMA will result in modest or no change in BF and RF (correlated response ranging from −0.04 to 0.07 mm per generation). In this population, carcass traits must be included in the selection indexes to obtain genetic gains in carcass quality, if desired.
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Affiliation(s)
| | - Lucas De Vargas
- Departamento de Zootecnia, Universidade Federal de Pelotas, Pelotas, RS CEP 96160-000, Brazil
| | - Rodrigo Junqueira Pereira
- Grupo de Melhoramento Animal de Mato Grosso (GMAT), Instituto de Ciências Agrárias e Tecnológicas, Universidade Federal de Mato Grosso, MT-270, Km 06, Campus Rondonópolis, MT CEP 78735-00, Brazil
| | - Gabriel Soares Campos
- Departamento de Zootecnia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS CEP 91540-000, Brazil
| | - Ricardo Zambarda Vaz
- Departamento de Zootecnia, Universidade Federal de Pelotas, Pelotas, RS CEP 96160-000, Brazil
| | - Raysildo Barbosa Lôbo
- Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP CEP 14049-900, Brazil
| | | | - Arione Augusti Boligon
- Departamento de Zootecnia, Universidade Federal de Pelotas, Pelotas, RS CEP 96160-000, Brazil
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17
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Inbreeding depression causes reduced fecundity in Golden Retrievers. Mamm Genome 2019; 30:166-172. [PMID: 31115595 PMCID: PMC6606663 DOI: 10.1007/s00335-019-09805-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 05/15/2019] [Indexed: 01/09/2023]
Abstract
Inbreeding depression has been demonstrated to impact vital rates, productivity, and performance in human populations, wild and endangered species, and in recent years, the domestic species. In all cases, standardized, high-quality phenotype data on all individuals are invaluable for longitudinal analyses such as those required to evaluate vital rates of a study cohort. Further, many investigators agree upon the preference for and utility of genomic measures of inbreeding in lieu of pedigree-based estimates of inbreeding. We evaluated the association of measures of reproductive fitness in 93 Golden Retrievers enrolled in the Golden Retriever Lifetime Study with a genomic measurement of inbreeding, FROH. We demonstrate a statistically significant negative correlation between fecundity and FROH. This work sets the stage for larger scale analyses to investigate genomic regions associated with fecundity and other measures of fitness.
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18
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Sumreddee P, Toghiani S, Hay EH, Roberts A, Agrrey SE, Rekaya R. Inbreeding depression in line 1 Hereford cattle population using pedigree and genomic information. J Anim Sci 2019; 97:1-18. [PMID: 30304409 DOI: 10.1093/jas/sky385] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/04/2018] [Indexed: 11/14/2022] Open
Abstract
This study aimed at assessing inbreeding and its effect on growth and fertility traits using the longtime closed line 1 Hereford cattle population. Inbreeding was estimated based on pedigree (FPED) and genomic information. For the latter, three estimates were derived based on the diagonal elements of the genomic relationship matrix using estimated (FGRM) or fixed (FGRM0.5) minor allele frequencies or runs of homozygosity (ROH) (FROH). A pedigree containing 10,186 animals was used to calculate FPED. Genomic inbreeding was evaluated using 785 animals genotyped for 30,810 SNP. Traits analyzed were birth weight (BWT), weaning weight (WWT), yearling weight (YWT), ADG, and age at first calving (AFC). The number of ROH per animal ranged between 6 and 119 segments with an average of 83. The shortest and longest segments were 1.36 and 64.86 Mb long, respectively, reflecting both ancient and recent inbreeding occurring in the last 30 to 40 generations. The average inbreeding was 29.2%, 16.1%, 30.2%, and 22.9% for FPED, FGRM, FGRM0.5, and FROH, respectively. FROH provided the highest correlations with FPED (r = 0.66). Across paternal half-sib families, with minimal variation in FPED, there were substantial variations in their genomic inbreeding. Inbreeding depression analyses showed that a 1% increase in an animal's FPED resulted in a decrease of 1.20 kg, 2.03 kg, and 0.004 kg/d in WWT, YWT, and ADG, respectively. Maternal inbreeding showed significantly negative effects on progeny growth performance. AFC increased by 1.4 and 0.8 d for each 1% increase in FPED of the cow and her dam, respectively. Using genomic inbreeding, similar impact on growth traits was observed although the magnitude of the effect varied between methods. Across all genomic measures, WWT, YWT, and ADG decreased by 0.21 to 0.53 kg, 0.46 to 1.13 kg, and 0.002 to 0.006 kg/d for each 1% increase in genomic inbreeding, respectively. Four chromosomes (9, 12, 17, and 27) were identified to have a significant association between their homozygosity (FROH-CHR) and growth traits. Variability in genomic inbreeding could be useful when deciding between full and half-sib selection candidates. Despite the high level of inbreeding in this study, its negative impact on growth performance was not as severe as expected, which may be attributed to the purging of the deleterious alleles due to natural or artificial selection over time.
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Affiliation(s)
| | - Sajjad Toghiani
- Department of Animal and Dairy Science, The University of Georgia, Athens, GA
| | - El Hamidi Hay
- USDA Agricultural Research Service, Fort Keogh Livestock and Range Research Laboratory, Miles City, MT
| | - Andrew Roberts
- USDA Agricultural Research Service, Fort Keogh Livestock and Range Research Laboratory, Miles City, MT
| | - Samuel E Agrrey
- Department of Poultry Science, The University of Georgia, Athens, GA.,Institute of Bioinformatics, The University of Georgia, Athens, GA
| | - Romdhane Rekaya
- Department of Animal and Dairy Science, The University of Georgia, Athens, GA.,Institute of Bioinformatics, The University of Georgia, Athens, GA.,Department of Statistics, The University of Georgia, Athens, GA
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19
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Perez B, Balieiro J, Oliveira Junior G, Andrietta L, Vizoná R, Ventura R, Bruneli F, Peixoto M. State of inbreeding and genetic trends for estimated breeding values in IVF embryos and oocyte donors in the Brazilian Guzerá cattle. Theriogenology 2019; 125:71-78. [DOI: 10.1016/j.theriogenology.2018.10.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 10/23/2018] [Accepted: 10/27/2018] [Indexed: 01/02/2023]
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20
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Stachowicz K, Brito LF, Oliveira HR, Miller SP, Schenkel FS. Assessing genetic diversity of various Canadian sheep breeds through pedigree analyses. CANADIAN JOURNAL OF ANIMAL SCIENCE 2018. [DOI: 10.1139/cjas-2017-0187] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The loss of genetic variability in a population will drastically affect the success of a breeding program by reducing selection response and fitness and, consequently, affecting reproduction, resilience, and production efficiency. The objective of this study was to perform an in-depth analysis of the pedigree of the Canadian sheep breeds to assess the levels of inbreeding, effective population size, and other metrics of genetic diversity, which included the five most important sheep breeds in Canada: Dorset, Polypay (PO), Rideau-Arcott, Romanov (RV), and Suffolk, using a large dataset (1 336 926 animals). As measures of genetic diversity, effective population size, inbreeding coefficient, effective number of founders, effective number of founder genomes, effective number of nonfounders, and effective number of ancestors were estimated. The completeness and depth of the Canadian sheep pedigree datasets were reasonably high, with <20% parental information missing. More attention should be given to PO breed, which was found to have the smallest effective population size (55), and RV breed, which had the highest average level of inbreeding (4.8%). Techniques such as optimum contribution selection and minimum coancestry mating could be used to minimize the inbreeding of future generations, while maintaining genetic progress at a desirable level.
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Affiliation(s)
- Katarzyna Stachowicz
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Luiz F. Brito
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Hinayah R. Oliveira
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
- Department of Animal Science, Universidade Federal de Viçosa, Av. Peter Henry Rolfs, Viçosa, Minas Gerais 36570-000, Brazil
| | - Stephen P. Miller
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
- Angus Genetics Inc., St. Joseph, MO 64506, USA
| | - Flávio S. Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
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21
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Peripolli E, Metzger J, de Lemos MVA, Stafuzza NB, Kluska S, Olivieri BF, Feitosa FLB, Berton MP, Lopes FB, Munari DP, Lôbo RB, Magnabosco CDU, Di Croce F, Osterstock J, Denise S, Pereira ASC, Baldi F. Autozygosity islands and ROH patterns in Nellore lineages: evidence of selection for functionally important traits. BMC Genomics 2018; 19:680. [PMID: 30223795 PMCID: PMC6142381 DOI: 10.1186/s12864-018-5060-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 09/07/2018] [Indexed: 12/20/2022] Open
Abstract
Background The aim of this study was to assess genome-wide autozygosity in a Nellore cattle population and to characterize ROH patterns and autozygosity islands that may have occurred due to selection within its lineages. It attempts also to compare estimates of inbreeding calculated from ROH (FROH), genomic relationship matrix (FGRM), and pedigree-based coefficient (FPED). Results The average number of ROH per animal was 55.15 ± 13.01 with an average size of 3.24 Mb. The Nellore genome is composed mostly by a high number of shorter segments accounting for 78% of all ROH, although the proportion of the genome covered by them was relatively small. The genome autozygosity proportion indicates moderate to high inbreeding levels for classical standards, with an average value of 7.15% (178.70 Mb). The average of FPED and FROH, and their correlations (− 0.05 to 0.26) were low. Estimates of correlation between FGRM-FPED was zero, while the correlation (− 0.01 to − 0.07) between FGRM-FROH decreased as a function of ROH length, except for FROH > 8Mb (− 0.03). Overall, inbreeding coefficients were not high for the genotyped animals. Autozygosity islands were evident across the genome (n = 62) and their genomic location did not largely differ within lineages. Enriched terms (p < 0.01) associated with defense response to bacteria (GO:0042742), immune complex reaction (GO:0045647), pregnancy-associated glycoproteins genes (GO:0030163), and organism growth (GO:0040014) were described within the autozygotic islands. Conclusions Low FPED-FROH correlation estimates indicate that FPED is not the most suitable method for capturing ancient inbreeding when the pedigree does not extend back many generations and FROH should be used instead. Enriched terms (p < 0.01) suggest a strong selection for immune response. Non-overlapping islands within the lineages greatly explain the mechanism underlying selection for functionally important traits in Nellore cattle. Electronic supplementary material The online version of this article (10.1186/s12864-018-5060-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elisa Peripolli
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil.
| | - Julia Metzger
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, 30559, Hannover, Germany
| | - Marcos Vinícius Antunes de Lemos
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Nedenia Bonvino Stafuzza
- Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Sabrina Kluska
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Bianca Ferreira Olivieri
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Fabieli Louise Braga Feitosa
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Mariana Piatto Berton
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Fernando Brito Lopes
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Danísio Prado Munari
- Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Raysildo Barbosa Lôbo
- Associação Nacional de Criadores e Pesquisadores (ANCP), Ribeirão Preto, 14020-230, Brazil
| | | | | | | | | | | | - Fernando Baldi
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
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Reverter A, Porto-Neto LR, Fortes MRS, Kasarapu P, de Cara MAR, Burrow HM, Lehnert SA. Genomic inbreeding depression for climatic adaptation of tropical beef cattle1. J Anim Sci 2017. [DOI: 10.2527/jas.2017.1643] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
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Martikainen K, Tyrisevä AM, Matilainen K, Pösö J, Uimari P. Estimation of inbreeding depression on female fertility in the Finnish Ayrshire population. J Anim Breed Genet 2017; 134:383-392. [PMID: 28748554 DOI: 10.1111/jbg.12285] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 06/14/2017] [Indexed: 01/01/2023]
Abstract
Single nucleotide polymorphism (SNP) data enable the estimation of inbreeding at the genome level. In this study, we estimated inbreeding levels for 19,075 Finnish Ayrshire cows genotyped with a low-density SNP panel (8K). The genotypes were imputed to 50K density, and after quality control, 39,144 SNPs remained for the analysis. Inbreeding coefficients were estimated for each animal based on the percentage of homozygous SNPs (FPH ), runs of homozygosity (FROH ) and pedigree (FPED ). Phenotypic records were available for 13,712 animals including non-return rate (NRR), number of inseminations (AIS) and interval from first to last insemination (IFL) for heifers and up to three parities for cows, as well as interval from calving to first insemination (ICF) for cows. Average FPED was 0.02, FROH 0.06 and FPH 0.63. A correlation of 0.71 was found between FPED and FROH , 0.66 between FPED and FPH and 0.94 between FROH and FPH . Pedigree-based inbreeding coefficients did not show inbreeding depression in any of the traits. However, when FROH or FPH was used as a covariate, significant inbreeding depression was observed; a 10% increase in FROH was associated with 5 days longer IFL0 and IFL1, 2 weeks longer IFL3 and 3 days longer ICF2 compared to non-inbred cows.
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Affiliation(s)
- K Martikainen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - A M Tyrisevä
- Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - K Matilainen
- Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - J Pösö
- Finnish Animal Breeding Association, Vantaa, Finland
| | - P Uimari
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
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