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van der Nest MA, Hlongwane N, Hadebe K, Chan WY, van der Merwe NA, De Vos L, Greyling B, Kooverjee BB, Soma P, Dzomba EF, Bradfield M, Muchadeyi FC. Breed Ancestry, Divergence, Admixture, and Selection Patterns of the Simbra Crossbreed. Front Genet 2021; 11:608650. [PMID: 33584805 PMCID: PMC7876384 DOI: 10.3389/fgene.2020.608650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/18/2020] [Indexed: 12/21/2022] Open
Abstract
In this study, we evaluated an admixed South African Simbra crossbred population, as well as the Brahman (Indicine) and Simmental (Taurine) ancestor populations to understand their genetic architecture and detect genomic regions showing signatures of selection. Animals were genotyped using the Illumina BovineLD v2 BeadChip (7K). Genomic structure analysis confirmed that the South African Simbra cattle have an admixed genome, composed of 5/8 Taurine and 3/8 Indicine, ensuring that the Simbra genome maintains favorable traits from both breeds. Genomic regions that have been targeted by selection were detected using the linkage disequilibrium-based methods iHS and Rsb. These analyses identified 10 candidate regions that are potentially under strong positive selection, containing genes implicated in cattle health and production (e.g., TRIM63, KCNA10, NCAM1, SMIM5, MIER3, and SLC24A4). These adaptive alleles likely contribute to the biological and cellular functions determining phenotype in the Simbra hybrid cattle breed. Our data suggested that these alleles were introgressed from the breed's original indicine and taurine ancestors. The Simbra breed thus possesses derived parental alleles that combine the superior traits of the founder Brahman and Simmental breeds. These regions and genes might represent good targets for ad-hoc physiological studies, selection of breeding material and eventually even gene editing, for improved traits in modern cattle breeds. This study represents an important step toward developing and improving strategies for selection and population breeding to ultimately contribute meaningfully to the beef production industry.
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Affiliation(s)
| | - Nompilo Hlongwane
- Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa
| | - Khanyisile Hadebe
- Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa
| | - Wai-Yin Chan
- Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa
| | - Nicolaas A van der Merwe
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Lieschen De Vos
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Ben Greyling
- Animal Production, Agricultural Research Council, Pretoria, South Africa
| | | | - Pranisha Soma
- Animal Production, Agricultural Research Council, Pretoria, South Africa
| | - Edgar F Dzomba
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | | | - Farai C Muchadeyi
- Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa
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Slade Oliveira C, Varella Serapião R, Dos Reis Camargo AJ, de Freitas C, Tamy Iguma L, Campos Carvalho B, de Almeida Camargo LS, Zoccolaro Oliveira L, da Silva Verneque R. Oocyte origin affects the in vitro embryo production and development of Holstein (Bos taurus taurus) - Gyr (Bos taurus indicus) reciprocal cross embryos. Anim Reprod Sci 2019; 209:106165. [PMID: 31514926 DOI: 10.1016/j.anireprosci.2019.106165] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/30/2019] [Accepted: 08/08/2019] [Indexed: 11/27/2022]
Abstract
A reciprocal crossbred embryo production approach was used to assess effects of maternal breed on embryo development in tropical conditions (average temperature 22.0 °C and 77.9% relative humidity). Oocytes were recovered by ovum pick-up (OPU) from Gyr and Holstein donors (n = 90 Holstein and 83 Gyr OPUs). Female F1 embryos were produced by fertilization with sperm bearing X-chromosomes from Holstein semen (n = 615 Gyr oocytes) or Gyr semen (n = 255 Holstein oocytes). Blastocysts were transferred to recipients 168 h post-insemination (h.p.i.) (n = 70-144) and there were assessments of pregnancies until birth. Oocyte number per OPU (Gyr 10.0 ± 0.7 compared with Holstein 6.3 ± 0.4) and percentage viable oocytes (Gyr 78.8 ± 1.9% compared with Holstein 71.2 ± 2.2%) were less for Holstein donor animals. There was a 2.8 fold fewer total number of F1 blastocysts when Holstein donors were used (Gyr: 260, Holstein: 91). Pregnancy assessment during the different stages of gestation indicated the percentage pregnancy was less when embryos were produced from Holstein oocytes (Gyr and Holstein respectively: early pregnancy, 47.9% compared with 38.6%; mid-pregnancy, 44.4% compared with 31.4%; late pregnancy, 41.0% compared with 22.9%). Pregnancy length was also affected by maternal breed (Gyr: 280.8 ± 0.6, Holstein: 286.3 ± 0.7). It is concluded that in a tropical environment the maternal breed affects crossbred embryo development with pregnancy rates during the latter stages of gestation being greater when Gyr oocytes are used for production of embryos.
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Affiliation(s)
- Clara Slade Oliveira
- Animal Reproduction Laboratory, Santa Monica Experimental Station, Embrapa Dairy Cattle, Fazenda Santa Monica Road, Barao de Juparana, Valença, RJ, Brazil.
| | - Raquel Varella Serapião
- Animal Biology Laboratory, Agriculture Research Company of the Rio de Janeiro State (PESAGRO RIO), Sao Boa Ventura Ave, 770, Niterói, RJ, Brazil
| | - Agostinho Jorge Dos Reis Camargo
- Animal Biology Laboratory, Agriculture Research Company of the Rio de Janeiro State (PESAGRO RIO), Sao Boa Ventura Ave, 770, Niterói, RJ, Brazil
| | - Celio de Freitas
- Animal Reproduction Laboratory, Santa Monica Experimental Station, Embrapa Dairy Cattle, Fazenda Santa Monica Road, Barao de Juparana, Valença, RJ, Brazil
| | - Lilian Tamy Iguma
- Animal Reproduction Laboratory, Embrapa Dairy Cattle, Juiz de Fora, MG, Brazil
| | | | | | - Letícia Zoccolaro Oliveira
- Department of Veterinary Clinic and Surgery, Veterinary School, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
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Xiang R, Ghanipoor-Samami M, Johns WH, Eindorf T, Rutley DL, Kruk ZA, Fitzsimmons CJ, Thomsen DA, Roberts CT, Burns BM, Anderson GI, Greenwood PL, Hiendleder S. Maternal and paternal genomes differentially affect myofibre characteristics and muscle weights of bovine fetuses at midgestation. PLoS One 2013; 8:e53402. [PMID: 23341941 PMCID: PMC3544898 DOI: 10.1371/journal.pone.0053402] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 11/30/2012] [Indexed: 12/19/2022] Open
Abstract
Postnatal myofibre characteristics and muscle mass are largely determined during fetal development and may be significantly affected by epigenetic parent-of-origin effects. However, data on such effects in prenatal muscle development that could help understand unexplained variation in postnatal muscle traits are lacking. In a bovine model we studied effects of distinct maternal and paternal genomes, fetal sex, and non-genetic maternal effects on fetal myofibre characteristics and muscle mass. Data from 73 fetuses (Day153, 54% term) of four genetic groups with purebred and reciprocal cross Angus and Brahman genetics were analyzed using general linear models. Parental genomes explained the greatest proportion of variation in myofibre size of Musculus semitendinosus (80–96%) and in absolute and relative weights of M. supraspinatus, M. longissimus dorsi, M. quadriceps femoris and M. semimembranosus (82–89% and 56–93%, respectively). Paternal genome in interaction with maternal genome (P<0.05) explained most genetic variation in cross sectional area (CSA) of fast myotubes (68%), while maternal genome alone explained most genetic variation in CSA of fast myofibres (93%, P<0.01). Furthermore, maternal genome independently (M. semimembranosus, 88%, P<0.0001) or in combination (M. supraspinatus, 82%; M. longissimus dorsi, 93%; M. quadriceps femoris, 86%) with nested maternal weight effect (5–6%, P<0.05), was the predominant source of variation for absolute muscle weights. Effects of paternal genome on muscle mass decreased from thoracic to pelvic limb and accounted for all (M. supraspinatus, 97%, P<0.0001) or most (M. longissimus dorsi, 69%, P<0.0001; M. quadriceps femoris, 54%, P<0.001) genetic variation in relative weights. An interaction between maternal and paternal genomes (P<0.01) and effects of maternal weight (P<0.05) on expression of H19, a master regulator of an imprinted gene network, and negative correlations between H19 expression and fetal muscle mass (P<0.001), suggested imprinted genes and miRNA interference as mechanisms for differential effects of maternal and paternal genomes on fetal muscle.
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Affiliation(s)
- Ruidong Xiang
- J.S. Davies Non-Mendelian Genetics Group, School of Animal and Veterinary Sciences, Roseworthy Campus, The University of Adelaide, South Australia, Australia
- Robinson Institute, The University of Adelaide, South Australia, Australia
| | - Mani Ghanipoor-Samami
- J.S. Davies Non-Mendelian Genetics Group, School of Animal and Veterinary Sciences, Roseworthy Campus, The University of Adelaide, South Australia, Australia
- Robinson Institute, The University of Adelaide, South Australia, Australia
| | - William H. Johns
- NSW Department of Primary Industries, Beef Industry Centre, Trevenna Rd, University of New England, Armidale, New South Wales, Australia
| | - Tanja Eindorf
- J.S. Davies Non-Mendelian Genetics Group, School of Animal and Veterinary Sciences, Roseworthy Campus, The University of Adelaide, South Australia, Australia
| | - David L. Rutley
- J.S. Davies Non-Mendelian Genetics Group, School of Animal and Veterinary Sciences, Roseworthy Campus, The University of Adelaide, South Australia, Australia
| | - Zbigniew A. Kruk
- J.S. Davies Non-Mendelian Genetics Group, School of Animal and Veterinary Sciences, Roseworthy Campus, The University of Adelaide, South Australia, Australia
| | - Carolyn J. Fitzsimmons
- J.S. Davies Non-Mendelian Genetics Group, School of Animal and Veterinary Sciences, Roseworthy Campus, The University of Adelaide, South Australia, Australia
| | - Dana A. Thomsen
- J.S. Davies Non-Mendelian Genetics Group, School of Animal and Veterinary Sciences, Roseworthy Campus, The University of Adelaide, South Australia, Australia
- Robinson Institute, The University of Adelaide, South Australia, Australia
| | - Claire T. Roberts
- Robinson Institute, The University of Adelaide, South Australia, Australia
- School of Paediatrics and Reproductive Health, The University of Adelaide, South Australia, Australia
| | - Brian M. Burns
- The University of Queensland, Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, Rockhampton, Queensland, Australia
| | - Gail I. Anderson
- J.S. Davies Non-Mendelian Genetics Group, School of Animal and Veterinary Sciences, Roseworthy Campus, The University of Adelaide, South Australia, Australia
| | - Paul L. Greenwood
- NSW Department of Primary Industries, Beef Industry Centre, Trevenna Rd, University of New England, Armidale, New South Wales, Australia
| | - Stefan Hiendleder
- J.S. Davies Non-Mendelian Genetics Group, School of Animal and Veterinary Sciences, Roseworthy Campus, The University of Adelaide, South Australia, Australia
- Robinson Institute, The University of Adelaide, South Australia, Australia
- * E-mail:
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Pacheco RDL, Millen DD, DiLorenzo N, Martins CL, Marino C, Fossa MV, Beier SL, DiCostanzo A, Rodrigues PHM, Arrigoni MDB. Effects of feeding a multivalent polyclonal antibody preparation on feedlot performance, carcass characteristics, rumenitis, and blood gas profile in Bos indicus biotype yearling bulls1. J Anim Sci 2012; 90:1898-909. [DOI: 10.2527/jas.2010-3521] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- R. D. L. Pacheco
- Departament of Breeding and Animal Nutrition, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil 18618-000
| | - D. D. Millen
- Departament of Breeding and Animal Nutrition, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil 18618-000
| | - N. DiLorenzo
- North Florida Research and Education Center, University of Florida, Marianna 32446
| | - C. L. Martins
- Departament of Breeding and Animal Nutrition, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil 18618-000
| | - C.T. Marino
- Departament of Animal Nutrition and Production, University of São Paulo, Pirassununga, São Paulo, Brazil 13635-900
| | - M. V. Fossa
- Departament of Breeding and Animal Nutrition, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil 18618-000
| | - S. L. Beier
- Department of Veterinary Medicine, Santa Catarina State University, Lages, Santa Catarina, Brazil 88520-000
| | - A. DiCostanzo
- Department of Animal Science, University of Minnesota, Saint Paul 55108
| | - P. H. M. Rodrigues
- Departament of Animal Nutrition and Production, University of São Paulo, Pirassununga, São Paulo, Brazil 13635-900
| | - M. D. B. Arrigoni
- Departament of Breeding and Animal Nutrition, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil 18618-000
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Imumorin IG, Kim EH, Lee YM, De Koning DJ, van Arendonk JA, De Donato M, Taylor JF, Kim JJ. Genome Scan for Parent-of-Origin QTL Effects on Bovine Growth and Carcass Traits. Front Genet 2011; 2:44. [PMID: 22303340 PMCID: PMC3268597 DOI: 10.3389/fgene.2011.00044] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Accepted: 06/25/2011] [Indexed: 11/13/2022] Open
Abstract
Parent-of-origin effects (POE) such as genomic imprinting influence growth and body composition in livestock, rodents, and humans. Here, we report the results of a genome scan to detect quantitative trait loci (QTL) with POE on growth and carcass traits in Angus × Brahman cattle crossbreds. We identified 24 POE–QTL on 15 Bos taurus autosomes (BTAs) of which six were significant at 5% genome-wide (GW) level and 18 at the 5% chromosome-wide (CW) significance level. Six QTL were paternally expressed while 15 were maternally expressed. Three QTL influencing post-weaning growth map to the proximal end of BTA2 (linkage region of 0–9 cM; genomic region of 5.0–10.8 Mb), for which only one imprinted ortholog is known so far in the human and mouse genomes, and therefore may potentially represent a novel imprinted region. The detected QTL individually explained 1.4 ∼ 5.1% of each trait’s phenotypic variance. Comparative in silico analysis of bovine genomic locations show that 32 out of 1,442 known mammalian imprinted genes from human and mouse homologs map to the identified QTL regions. Although several of the 32 genes have been associated with quantitative traits in cattle, only two (GNAS and PEG3) have experimental proof of being imprinted in cattle. These results lend additional support to recent reports that POE on quantitative traits in mammals may be more common than previously thought, and strengthen the need to identify and experimentally validate cattle orthologs of imprinted genes so as to investigate their effects on quantitative traits.
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Bonilla CA, Rubio MS, Sifuentes AM, Parra-Bracamonte GM, Arellano VW, Méndez MRD, Berruecos JM, Ortiz R. Association of CAPN1 316, CAPN1 4751 and TG5 markers with bovine meat quality traits in Mexico. GENETICS AND MOLECULAR RESEARCH 2010; 9:2395-405. [PMID: 21161888 DOI: 10.4238/vol9-4gmr959] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
We examined allele and genotype frequencies for the molecular markers CAPN1 316, CAPN1 4751 and TG5, and determined whether they are associated with beef quality traits in Mexican cattle. One hundred and twenty-four longissimus dorsi muscle samples were collected from cattle from north, central and southern Mexico. CAPN1 316 and CAPN1 4751 frequencies were determined using the allelic discrimination assay and the TG5 marker was typed by PCR-RFLP. Meat quality traits included intramuscular fat content (IMF) and tenderness determined by Warner-Bratzler shear force (WBSF) at 24 h postmortem. The association test was made using a mixed model, including genotypes, genetic group, and sampling location as fixed effects. Least squares means and significant interactions were compared using least significant differences based on the mixed procedure. CAPN1 316 CC was found at a low frequency (0.03) and has been reported as a favorable genotype associated with tenderness meat. Genotype frequencies for CAPN1 4751 were similar in favorable (CC) and unfavorable (TT) genotypes (0.26 and 0.28, respectively). The TG5 CC genotype had a frequency of 0.73, while the TT genotype frequency was 0.01. The means for WBSF and IMF were 4.08 ± 1.35 kg and 5.23 ± 2.14%, respectively. Sampling site and the CAPN1 316 genotypes significantly affected WBSF (P < 0.05). Samples collected from Hermosillo, Sonora, had the lowest WBSF (P < 0.05), while those collected in Veracruz were toughest (WBSF = 5.267 kg). The effect of GG and TG5 genotypes on IMF was significant (P < 0.05). CAPN1 316 and TG5 markers were found to be significantly associated with beef quality traits and thus will be useful for Mexican beef characterization.
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Affiliation(s)
- C A Bonilla
- Laboratorio de Ciencia de la Carne, Secretaría de Producción Animal, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad Universitaria, México
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Review: Preweaning, Postweaning, and Carcass Trait Comparisons for Progeny Sired by Subtropically Adapted Beef Sire Breeds at Various US Locations123. ACTA ACUST UNITED AC 2010. [DOI: 10.15232/s1080-7446(15)30633-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Growth performances of F1 angus plus calves grazing on pasture in Hawaii’s tropical climate. Trop Anim Health Prod 2008; 41:593-8. [DOI: 10.1007/s11250-008-9229-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2008] [Accepted: 08/21/2008] [Indexed: 10/21/2022]
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Bonilha SFM, Tedeschi LO, Packer IU, Razook AG, Alleoni GF, Nardon RF, Resende FD. Evaluation of carcass characteristics of Bos indicus and tropically adapted Bos taurus breeds selected for postweaning weight. J Anim Sci 2008; 86:1770-80. [PMID: 18407987 DOI: 10.2527/jas.2007-0507] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Data from 9 studies were compiled to evaluate the effects of 20 yr of selection for postweaning weight (PWW) on carcass characteristics and meat quality in experimental herds of control Nellore (NeC) and selected Nellore (NeS), Caracu (CaS), Guzerah (GuS), and Gir (GiS) breeds. These studies were conducted with animals from a genetic selection program at the Experimental Station of Sertãozinho, São Paulo State, Brazil. After the performance test (168 d postweaning), bulls (n = 490) from the calf crops born between 1992 and 2000 were finished and slaughtered to evaluate carcass traits and meat quality. Treatments were different across studies. A meta-analysis was conducted with a random coefficients model in which herd was considered a fixed effect and treatments within year and year were considered as random effects. Either calculated maturity degree or initial BW was used interchangeably as the covariate, and least squares means were used in the multiple-comparison analysis. The CaS and NeS had heavier (P = 0.002) carcasses than the NeC and GiS; GuS were intermediate. The CaS had the longest carcass (P < 0.001) and heaviest spare ribs (P < 0.001), striploin (P < 0.001), and beef plate (P = 0.013). Although the body, carcass, and quarter weights of NeS were similar to those of CaS, NeS had more edible meat in the leg region than did CaS bulls. Selection for PWW increased rib-eye area in Nellore bulls. Selected Caracu had the lowest (most favorable) shear force values compared with the NeS (P = 0.003), NeC (P = 0.005), GuS (P = 0.003), and GiS (P = 0.008). Selection for PWW increased body, carcass, and meat retail weights in the Nellore without altering dressing percentage and body fat percentage.
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Affiliation(s)
- S F M Bonilha
- Department of Animal Science, Texas A&M University, College Station 77843-2471, USA
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