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Paim TDP, Hay EHA, Wilson C, Thomas MG, Kuehn LA, Paiva SR, McManus C, Blackburn HD. Dynamics of genomic architecture during composite breed development in cattle. Anim Genet 2020; 51:224-234. [PMID: 31961956 PMCID: PMC7065137 DOI: 10.1111/age.12907] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 12/16/2019] [Accepted: 12/19/2019] [Indexed: 12/31/2022]
Abstract
Some livestock breeds face the challenge of reduced genetic variation, increased inbreeding depression owing to genetic drift and selection. Hybridization can reverse these processes and increase levels of productivity and adaptation to various environmental stressors. Samples from American Brangus were used to evaluate the indicine/taurine composition through nine generations (~45 years) after the hybridization process was completed. The purpose was to determine how hybridization alters allelic combinations of a breed over time when genetic factors such as selection and drift are operating. Furthermore, we explored genomic regions with deviations from the expected composition from the progenitor breeds and related these regions to traits under selection. The Brangus composition deviated from the theoretical expectation, defined by the breed association, of 62.5% taurine, showing taurine composition to be 70.4 ± 0.6%. Taurine and indicine proportion were not consistent across chromosomes. Furthermore, these non‐uniform areas were found to be associated with traits that were probably under selection such as intermuscular fat and average daily gain. Interestingly, the sex chromosomes were predominantly taurine, which could be due to the composite being formed particularly in the final cross that resulted in progeny designated as purebred Brangus. This work demonstrated the process of new breed formation on a genomic level. It suggests that factors like genetic drift, selection and complementarity shift the genetic architecture into a uniquely different population. These findings are important to better understand how hybridization and crossbreeding systems shape the genetic architecture of composite populations.
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Affiliation(s)
- T do P Paim
- Instituto Federal de Educação, Ciência e Tecnologia Goiano, Avenida Oeste n. 350, Iporá, 76.200-000, Brazil.,Universidade de Brasília, Asa Norte, Campus Darcy Ribeiro, ICC Sul, Brasília, 70.910-900, Brazil
| | - E H A Hay
- US Department of Agriculture, Fort Keogh Livestock and Range Research Laboratory, Agricultural Research Service, 243 Fort Keogh Road, Miles City, 59301, USA
| | - C Wilson
- US Department of Agriculture, National Laboratory for Genetic Resources Preservation, Agricultural Research Service, National Animal Germplasm Program, 1111 S Mason St., Fort Collins, 80521, USA
| | - M G Thomas
- Department of Animal Sciences, Colorado State University, 350 W. Pitkin St., Fort Collins, 80523-1171, USA
| | - L A Kuehn
- US Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, 844 Rd 313, Clay Center, 68933, USA
| | - S R Paiva
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Av. W5 Norte (final) Caixa Postal 02372, Brasília, 70.770-917, Brazil
| | - C McManus
- Universidade de Brasília, Asa Norte, Campus Darcy Ribeiro, ICC Sul, Brasília, 70.910-900, Brazil
| | - H D Blackburn
- US Department of Agriculture, National Laboratory for Genetic Resources Preservation, Agricultural Research Service, National Animal Germplasm Program, 1111 S Mason St., Fort Collins, 80521, USA
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DeAtley KL, Colgrave ML, Cánovas A, Wijffels G, Ashley RL, Silver GA, Rincon G, Medrano JF, Islas-Trejo A, Fortes MRS, Reverter A, Porto-Neto L, Lehnert SA, Thomas MG. Neuropeptidome of the Hypothalamus and Pituitary Gland of Indicine × Taurine Heifers: Evidence of Differential Neuropeptide Processing in the Pituitary Gland before and after Puberty. J Proteome Res 2018; 17:1852-1865. [PMID: 29510626 DOI: 10.1021/acs.jproteome.7b00875] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Puberty in cattle is regulated by an endocrine axis, which includes a complex milieu of neuropeptides in the hypothalamus and pituitary gland. The neuropeptidome of hypothalamic-pituitary gland tissue of pre- (PRE) and postpubertal (POST) Bos indicus-influenced heifers was characterized, followed by quantitative analysis of 51 fertility-related neuropeptides in these tissues. Comparison of peptide abundances with gene expression levels allowed assessment of post-transcriptional peptide processing. On the basis of classical cleavage, 124 mature neuropeptides from 35 precursor proteins were detected in hypothalamus and pituitary gland tissues of three PRE and three POST Brangus heifers. An additional 19 peptides (cerebellins, PEN peptides) previously reported as neuropeptides that did not follow classical cleavage were also identified. In the pre-pubertal hypothalamus, a greater diversity of neuropeptides (25.8%) was identified relative to post-pubertal heifers, while in the pituitary gland, 38.6% more neuropeptides were detected in the post-pubertal heifers. Neuro-tissues of PRE and POST heifers revealed abundance differences ( p < 0.05) in peptides from protein precursors involved in packaging and processing (e.g., the granin family and ProSAAS) or neuron stimulation (PENK, CART, POMC, cerebellins). On their own, the transcriptome data of the precursor genes could not predict the neuropeptide profile in the exact same tissues in several cases. This provides further evidence of the importance of differential processing of the neuropeptide precursors in the pituitary before and after puberty.
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Affiliation(s)
- Kasey L DeAtley
- Department of Animal and Range Sciences , New Mexico State University , Las Cruces , New Mexico 88003 , United States
| | - Michelle L Colgrave
- CSIRO, Agriculture and Food , 306 Carmody Road , St. Lucia , Queensland 4067 , Australia
| | - Angela Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences , University of Guelph , Guelph , Ontario N1G 2W1 , Canada
| | - Gene Wijffels
- CSIRO, Agriculture and Food , 306 Carmody Road , St. Lucia , Queensland 4067 , Australia
| | - Ryan L Ashley
- Department of Animal and Range Sciences , New Mexico State University , Las Cruces , New Mexico 88003 , United States
| | - Gail A Silver
- Department of Animal and Range Sciences , New Mexico State University , Las Cruces , New Mexico 88003 , United States
| | - Gonzalo Rincon
- Zoetis Animal Health , Kalamazoo , Michigan 49007 , United States
| | - Juan F Medrano
- Department of Animal Science , University of California , Davis , California 95616 , United States
| | - Alma Islas-Trejo
- Department of Animal Science , University of California , Davis , California 95616 , United States
| | - Marina R S Fortes
- School of Chemistry and Molecular Biosciences , University of Queensland , St. Lucia , Queensland 4042 , Australia
- Queensland Alliance for Agriculture and Food Innovation, St. Lucia , Queensland 4072 , Australia
| | - Antonio Reverter
- CSIRO, Agriculture and Food , 306 Carmody Road , St. Lucia , Queensland 4067 , Australia
| | - Laercio Porto-Neto
- CSIRO, Agriculture and Food , 306 Carmody Road , St. Lucia , Queensland 4067 , Australia
| | - Sigrid A Lehnert
- CSIRO, Agriculture and Food , 306 Carmody Road , St. Lucia , Queensland 4067 , Australia
| | - Milton G Thomas
- Department of Animal Sciences , Colorado State University , Fort Collins , Colorado 80523 , United States
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Fortes MRS, Nguyen LT, Weller MMDCA, Cánovas A, Islas-Trejo A, Porto-Neto LR, Reverter A, Lehnert SA, Boe-Hansen GB, Thomas MG, Medrano JF, Moore SS. Transcriptome analyses identify five transcription factors differentially expressed in the hypothalamus of post- versus prepubertal Brahman heifers. J Anim Sci 2017; 94:3693-3702. [PMID: 27898892 DOI: 10.2527/jas.2016-0471] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Puberty onset is a developmental process influenced by genetic determinants, environment, and nutrition. Mutations and regulatory gene networks constitute the molecular basis for the genetic determinants of puberty onset. The emerging knowledge of these genetic determinants presents opportunities for innovation in the breeding of early pubertal cattle. This paper presents new data on hypothalamic gene expression related to puberty in (Brahman) in age- and weight-matched heifers. Six postpubertal heifers were compared with 6 prepubertal heifers using whole-genome RNA sequencing methodology for quantification of global gene expression in the hypothalamus. Five transcription factors (TF) with potential regulatory roles in the hypothalamus were identified in this experiment: , , , , and . These TF genes were significantly differentially expressed in the hypothalamus of postpubertal versus prepubertal heifers and were also identified as significant according to the applied regulatory impact factor metric ( < 0.05). Two of these 5 TF, and , were zinc fingers, belonging to a gene family previously reported to have a central regulatory role in mammalian puberty. The gene belongs to the family of homologues of Drosophila sine oculis () genes implicated in transcriptional regulation of gonadotrope gene expression. Tumor-related genes such as and are known to affect basic cellular processes that are relevant in both cancer and developmental processes. Mutations in were associated with puberty in humans. Mutations in these TF, together with other genetic determinants previously discovered, could be used in genomic selection to predict the genetic merit of cattle (i.e., the likelihood of the offspring presenting earlier than average puberty for Brahman). Knowledge of key mutations involved in genetic traits is an advantage for genomic prediction because it can increase its accuracy.
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Oberbauer A, Belanger J, Rincon G, Cánovas A, Islas-Trejo A, Gularte-Mérida R, Thomas M, Medrano J. Bovine and murine tissue expression of insulin like growth factor-I. Gene 2014; 535:101-5. [DOI: 10.1016/j.gene.2013.11.089] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 11/30/2013] [Indexed: 11/25/2022]
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Fortes MRS, Snelling WM, Reverter A, Nagaraj SH, Lehnert SA, Hawken RJ, DeAtley KL, Peters SO, Silver GA, Rincon G, Medrano JF, Islas-Trejo A, Thomas MG. Gene network analyses of first service conception in Brangus heifers: use of genome and trait associations, hypothalamic-transcriptome information, and transcription factors. J Anim Sci 2012; 90:2894-906. [PMID: 22739780 DOI: 10.2527/jas.2011-4601] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Measures of heifer fertility are economically relevant traits for beef production systems and knowledge of candidate genes could be incorporated into future genomic selection strategies. Ten traits related to growth and fertility were measured in 890 Brangus heifers (3/8 Brahman × 5/8 Angus, from 67 sires). These traits were: BW and hip height adjusted to 205 and 365 d of age, postweaning ADG, yearling assessment of carcass traits (i.e., back fat thickness, intramuscular fat, and LM area), as well as heifer pregnancy and first service conception (FSC). These fertility traits were collected from controlled breeding seasons initiated with estrous synchronization and AI targeting heifers to calve by 24 mo of age. The BovineSNP50 BeadChip was used to ascertain 53,692 SNP genotypes for ∼802 heifers. Associations of genotypes and phenotypes were performed and SNP effects were estimated for each trait. Minimally associated SNP (P < 0.05) and their effects across the 10 traits formed the basis for an association weight matrix and its derived gene network related to FSC (57.3% success and heritability = 0.06 ± 0.05). These analyses yielded 1,555 important SNP, which inferred genes linked by 113,873 correlations within a network. Specifically, 1,386 SNP were nodes and the 5,132 strongest correlations (|r| ≥ 0.90) were edges. The network was filtered with genes queried from a transcriptome resource created from deep sequencing of RNA (i.e., RNA-Seq) from the hypothalamus of a prepubertal and a postpubertal Brangus heifer. The remaining hypothalamic-influenced network contained 978 genes connected by 2,560 edges or predicted gene interactions. This hypothalamic gene network was enriched with genes involved in axon guidance, which is a pathway known to influence pulsatile release of LHRH. There were 5 transcription factors with 21 or more connections: ZMAT3, STAT6, RFX4, PLAGL1, and NR6A1 for FSC. The SNP that identified these genes were intragenic and were on chromosomes 1, 5, 9, and 11. Chromosome 5 harbored both STAT6 and RFX4. The large number of interactions and genes observed with network analyses of multiple sources of genomic data (i.e., GWAS and RNA-Seq) support the concept of FSC being a polygenic trait.
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Affiliation(s)
- M R S Fortes
- School of Veterinary Science, The University of Queensland, Gatton Campus, QLD 4343, Australia
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Expected Versus Realized Progeny Differences for Various Beef Cattle Traits11Published with approval of the director of the Kentucky Agricultural Experiment Station as Journal Article 06-07-094. ACTA ACUST UNITED AC 2006. [DOI: 10.15232/s1080-7446(15)31141-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Metabolic Hormone Profiles and Evaluation of Associations of Metabolic Hormones with Body Fat and Reproductive Characteristics of Angus, Brangus, and Brahman Heifers1. ACTA ACUST UNITED AC 2006. [DOI: 10.15232/s1080-7446(15)31104-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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