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Asselstine V, Miglior F, Suárez-Vega A, Fonseca PAS, Mallard B, Karrow N, Islas-Trejo A, Medrano JF, Cánovas A. Genetic mechanisms regulating the host response during mastitis. J Dairy Sci 2019; 102:9043-9059. [PMID: 31421890 DOI: 10.3168/jds.2019-16504] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 06/05/2019] [Indexed: 12/21/2022]
Abstract
Mastitis is a very costly and common disease in the dairy industry. The study of the transcriptome from healthy and mastitic milk somatic cell samples using RNA-Sequencing technology can provide measurements of transcript levels associated with the immune response to the infection. The objective of this study was to characterize the Holstein milk somatic cell transcriptome from 6 cows to determine host response to intramammary infections. RNA-Sequencing was performed on 2 samples from each cow from 2 separate quarters, one classified as healthy (n = 6) and one as mastitic (n = 6). In total, 449 genes were differentially expressed between the healthy and mastitic quarters (false discovery rate <0.05, fold change >±2). Among the differentially expressed genes, the most expressed genes based on reads per kilobase per million mapped reads (RPKM) in the healthy group were associated with milk components (CSN2 and CSN3), and in the mastitic group they were associated with immunity (B2M and CD74). In silico functional analysis was performed using the list of 449 differentially expressed genes, which identified 36 significantly enriched metabolic pathways (false discovery rate <0.01), some of which were associated with the immune system, such as cytokine-cytokine interaction and cell adhesion molecules. Seven functional candidate genes were selected, based on the criteria of being highly differentially expressed between healthy and mastitic groups and significantly enriched in metabolic pathways that are relevant to the inflammatory process (GLYCAM1, B2M, CD74, BoLA-DRA, FCER1G, SDS, and NFKBIA). Last, we identified the differentially expressed genes that are located in quantitative trait locus regions previously known to be associated with mastitis, specifically clinical mastitis, somatic cell count, and somatic cell score. It was concluded that multiple genes within quantitative trait locus regions could potentially affect host response to mastitis-causing agents, making some cows more susceptible to intramammary infections. The identification of potential candidate genes with functional, statistical, biological, and positional relevance associated with host defense to infection will contribute to a better understanding of the underlying genetic architecture associated with mastitis. This in turn will improve the sustainability of agricultural practices by facilitating the selection of cows with improved host defense leading to increased resistance to mastitis.
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Affiliation(s)
- V Asselstine
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - F Miglior
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - A Suárez-Vega
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - P A S Fonseca
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - B Mallard
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - N Karrow
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - A Islas-Trejo
- Department of Animal Science, University of California-Davis, Davis 95616
| | - J F Medrano
- Department of Animal Science, University of California-Davis, Davis 95616
| | - A Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada, N1G 2W1.
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Fortes MRS, Zacchi LF, Nguyen LT, Raidan F, Weller MMDCA, Choo JJY, Reverter A, Rego JPA, Boe-Hansen GB, Porto-Neto LR, Lehnert SA, Cánovas A, Schulz BL, Islas-Trejo A, Medrano JF, Thomas MG, Moore SS. Pre- and post-puberty expression of genes and proteins in the uterus of Bos indicus heifers: the luteal phase effect post-puberty. Anim Genet 2018; 49:539-549. [PMID: 30192028 DOI: 10.1111/age.12721] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2018] [Indexed: 12/17/2022]
Abstract
Progesterone signaling and uterine function are crucial in terms of pregnancy establishment. To investigate how the uterine tissue and its secretion changes in relation to puberty, we sampled tissue and uterine fluid from six pre- and six post-pubertal Brahman heifers. Post-pubertal heifers were sampled in the luteal phase. Gene expression of the uterine tissue was investigated with RNA-sequencing, whereas the uterine fluid was used for protein profiling with mass spectrometry. A total of 4034 genes were differentially expressed (DE) at a nominal P-value of 0.05, and 26 genes were significantly DE after Bonferroni correction (P < 3.1 × 10-6 ). We also identified 79 proteins (out of 230 proteins) that were DE (P < 1 × 10-5 ) in the uterine fluid. When we compared proteomics and transcriptome results, four DE proteins were identified as being encoded by DE genes: OVGP1, GRP, CAP1 and HBA. Except for CAP1, the other three had lower expression post-puberty. The function of these four genes hypothetically related to preparation of the uterus for a potential pregnancy is discussed in the context of puberty. All DE genes and proteins were also used in pathway and ontology enrichment analyses to investigate overall function. The DE genes were enriched for terms related to ribosomal activity. Transcription factors that were deemed key regulators of DE genes are also reported. Transcription factors ZNF567, ZNF775, RELA, PIAS2, LHX4, SOX2, MEF2C, ZNF354C, HMG20A, TCF7L2, ZNF420, HIC1, GTF3A and two novel genes had the highest regulatory impact factor scores. These data can help to understand how puberty influences uterine function.
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Affiliation(s)
- M R S Fortes
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - L F Zacchi
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - L T Nguyen
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia.,Faculty of Biotechnology, Vietnam National University of Agriculture, Gialam, Hanoi, Vietnam
| | - F Raidan
- Animal Science Department, Universidade Federal de Viçosa, Vicosa, Minas Gerais, 36570-900, Brazil
| | - M M D C A Weller
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, Brisbane, QLD 4072, Australia
| | - J J Y Choo
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - A Reverter
- Animal Science Department, Universidade Federal de Viçosa, Vicosa, Minas Gerais, 36570-900, Brazil
| | - J P A Rego
- Instituto Federal de Educação, Ciência e Tecnologia do Ceara, Fortaleza, Ceará, 62930-000, Brazil
| | - G B Boe-Hansen
- School of Veterinary Sciences, The University of Queensland, Gatton, QLD 4343, Australia
| | - L R Porto-Neto
- Animal Science Department, Universidade Federal de Viçosa, Vicosa, Minas Gerais, 36570-900, Brazil
| | - S A Lehnert
- Animal Science Department, Universidade Federal de Viçosa, Vicosa, Minas Gerais, 36570-900, Brazil
| | - A Cánovas
- Department of Animal Biosciences, Centre of Genetic Improvement for Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - B L Schulz
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - A Islas-Trejo
- Department of Animal Science, University of California Davis, Davis, CA, 95616, USA
| | - J F Medrano
- Department of Animal Science, University of California Davis, Davis, CA, 95616, USA
| | - M G Thomas
- Department of Animal Science, Colorado State University, Fort Collins, CO, 80523, USA
| | - S S Moore
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
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Nguyen LT, Reverter A, Cánovas A, Venus B, Islas-Trejo A, Porto-Neto LR, Lehnert SA, Medrano JF, Moore SS, Fortes MRS. Global differential gene expression in the pituitary gland and the ovaries of pre- and postpubertal Brahman heifers. J Anim Sci 2017; 95:599-615. [PMID: 28380590 DOI: 10.2527/jas.2016.0921] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
To understand genes, pathways, and networks related to puberty, we characterized the transcriptome of two tissues: the pituitary gland and ovaries. Samples were harvested from pre- and postpubertal Brahman heifers (same age group). Brahman heifers () are older at puberty compared with , a productivity issue. With RNA sequencing, we identified differentially expressed (DEx) genes and important transcription factors (TF) and predicted coexpression networks. The number of DEx genes detected in the pituitary gland was 284 ( < 0.05), and was the most DEx gene (fold change = 4.12, = 0.01). The gene promotes bone mineralization through transforming growth factor-β (TGFβ) signaling. Further studies of the link between bone mineralization and puberty could target . In ovaries, 3,871 genes were DEx ( < 0.05). Four highly DEx genes were noteworthy for their function: (a γ-aminobutyric acid [GABA] transporter), (), and () and its receptor . These genes had higher ovarian expression in postpubertal heifers. The GABA and its receptors and transporters were expressed in the ovaries of many mammals, suggesting a role for this pathway beyond the brain. The pathway has been known to influence the timing of puberty in rats, via modulation of GnRH. The effects of at the hypothalamus, pituitary gland, and ovaries have been documented. and its receptors are known factors in the release of GnRH, similar to and GABA, although their roles in ovarian tissue are less clear. Pathways previously related to puberty such as TGFβ signaling ( = 6.71 × 10), Wnt signaling ( = 4.1 × 10), and peroxisome proliferator-activated receptor (PPAR) signaling ( = 4.84 × 10) were enriched in our data set. Seven genes were identified as key TF in both tissues: , , , , , , and a novel gene. An ovarian subnetwork created with TF and significant ovarian DEx genes revealed five zinc fingers as regulators: , , , , and . Recent work of hypothalamic gene expression also pointed to zinc fingers as TF for bovine puberty. Although some zinc fingers may be ubiquitously expressed, the identification of DEx genes in common across tissues points to key regulators of puberty. The hypothalamus and pituitary gland had eight DEx genes in common. The hypothalamus and ovaries had 89 DEx genes in common. The pituitary gland and ovaries had 48 DEx genes in common. Our study confirmed the complexity of puberty and suggested further investigation on genes that code zinc fingers.
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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] [What about the content of this article? (0)] [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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Dias MM, Cánovas A, Mantilla-Rojas C, Riley DG, Luna-Nevarez P, Coleman SJ, Speidel SE, Enns RM, Islas-Trejo A, Medrano JF, Moore SS, Fortes MRS, Nguyen LT, Venus B, Diaz ISDP, Souza FRP, Fonseca LFS, Baldi F, Albuquerque LG, Thomas MG, Oliveira HN. SNP detection using RNA-sequences of candidate genes associated with puberty in cattle. Genet Mol Res 2017; 16:gmr-16-01-gmr.16019522. [PMID: 28340271 DOI: 10.4238/gmr16019522] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Fertility traits, such as heifer pregnancy, are economically important in cattle production systems, and are therefore, used in genetic selection programs. The aim of this study was to identify single nucleotide polymorphisms (SNPs) using RNA-sequencing (RNA-Seq) data from ovary, uterus, endometrium, pituitary gland, hypothalamus, liver, longissimus dorsi muscle, and adipose tissue in 62 candidate genes associated with heifer puberty in cattle. RNA-Seq reads were assembled to the bovine reference genome (UMD 3.1.1) and analyzed in five cattle breeds; Brangus, Brahman, Nellore, Angus, and Holstein. Two approaches used the Brangus data for SNP discovery 1) pooling all samples, and 2) within each individual sample. These approaches revealed 1157 SNPs. These were compared with those identified in the pooled samples of the other breeds. Overall, 172 SNPs within 13 genes (CPNE5, FAM19A4, FOXN4, KLF1, LOC777593, MGC157266, NEBL, NRXN3, PEPT-1, PPP3CA, SCG5, TSG101, and TSHR) were concordant in the five breeds. Using Ensembl's Variant Effector Predictor, we determined that 12% of SNPs were in exons (71% synonymous, 29% nonsynonymous), 1% were in untranslated regions (UTRs), 86% were in introns, and 1% were in intergenic regions. Since these SNPs were discovered in RNA, the variants were predicted to be within exons or UTRs. Overall, 160 novel transcripts in 42 candidate genes and five novel genes overlapping five candidate genes were observed. In conclusion, 1157 SNPs were identified in 62 candidate genes associated with puberty in Brangus cattle, of which, 172 were concordant in the five cattle breeds. Novel transcripts and genes were also identified.
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Affiliation(s)
- M M Dias
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil
| | - A Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Bioscience, University of Guelph, Guelph, ON, Canada
| | - C Mantilla-Rojas
- Department of Animal Science, Texas A&M University, College Station, TX, USA
| | - D G Riley
- Department of Animal Science, Texas A&M University, College Station, TX, USA
| | - P Luna-Nevarez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, SON, México
| | - S J Coleman
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - S E Speidel
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - R M Enns
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - A Islas-Trejo
- Department of Animal Science, University of California, Davis, CA, USA
| | - J F Medrano
- Department of Animal Science, University of California, Davis, CA, USA
| | - S S Moore
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
| | - M R S Fortes
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, St Lucia, Australia
| | - L T Nguyen
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, St Lucia, Australia.,Faculty of Biotechnology, Vietnam National University of Agriculture, Vietnam
| | - B Venus
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
| | - I S D P Diaz
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil
| | - F R P Souza
- Departamento de Ecologia, Zoologia e Genética, Universidade Federal de Pelotas, Pelotas, RS, Brasil
| | - L F S Fonseca
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil
| | - F Baldi
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil
| | - L G Albuquerque
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil
| | - M G Thomas
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - H N Oliveira
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil
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Nguyen LT, Reverter A, Cánovas A, Venus B, Islas-Trejo A, Porto-Neto LR, Lehnert SA, Medrano JF, Moore SS, Fortes MRS. Global differential gene expression in the pituitary gland and the ovaries of pre- and postpubertal Brahman heifers. J Anim Sci 2017. [DOI: 10.2527/jas2016.0921] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Cánovas A, Cockrum R, Brown D, Riddle S, Neary JM, Holt TN, Medrano JF, Islas-Trejo A, Enns RM, Speidel SE, Cammack K, Stenmark KR, Thomas MG. 0260 Functional SNP in a polygenic disease induced by high-altitude in fattening Angus steers using systems biology approach. J Anim Sci 2016. [DOI: 10.2527/jam2016-0260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Welly BT, Miller MR, Stott JL, Blanchard MT, Islas-Trejo A, O’Rourke SM, Young AE, Medrano JF, Van Eenennaam AL. P6032 Identification and characterization of a novel pathogen causing bovine abortion. J Anim Sci 2016. [DOI: 10.2527/jas2016.94supplement4164a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Canovas A, Cockrum R, Brown D, Riddle S, Neary JM, Holt TN, Medrano JF, Islas-Trejo A, Enns RM, Speidel SE, Cammack K, Stenmark KR, Thomas MG. P3050 Functional genomics of high altitude disease in angus cattle: Leveraging-OMICS and systems biology to better understanding of the function and role of key contributing genes. J Anim Sci 2016. [DOI: 10.2527/jas2016.94supplement478x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 11/30/2013] [Indexed: 11/25/2022]
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Cánovas A, Rincón G, Islas-Trejo A, Jimenez-Flores R, Laubscher A, Medrano JF. RNA sequencing to study gene expression and single nucleotide polymorphism variation associated with citrate content in cow milk. J Dairy Sci 2013; 96:2637-2648. [PMID: 23403202 DOI: 10.3168/jds.2012-6213] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 12/11/2012] [Indexed: 11/19/2022]
Abstract
The technological properties of milk have significant importance for the dairy industry. Citrate, a normal constituent of milk, forms one of the main buffer systems that regulate the equilibrium between Ca(2+) and H(+) ions. Higher-than-normal citrate content is associated with poor coagulation properties of milk. To identify the genes responsible for the variation of citrate content in milk in dairy cattle, the metabolic steps involved in citrate and fatty acid synthesis pathways in ruminant mammary tissue using RNA sequencing were studied. Genetic markers that could influence milk citrate content in Holstein cows were used in a marker-trait association study to establish the relationship between 74 single nucleotide polymorphisms (SNP) in 20 candidate genes and citrate content in 250 Holstein cows. This analysis revealed 6 SNP in key metabolic pathway genes [isocitrate dehydrogenase 1 (NADP+), soluble (IDH1); pyruvate dehydrogenase (lipoamide) β (PDHB); pyruvate kinase (PKM2); and solute carrier family 25 (mitochondrial carrier; citrate transporter), member 1 (SLC25A1)] significantly associated with increased milk citrate content. The amount of the phenotypic variation explained by the 6 SNP ranged from 10.1 to 13.7%. Also, genotype-combination analysis revealed the highest phenotypic variation was explained combining IDH1_23211, PDHB_5562, and SLC25A1_4446 genotypes. This specific genotype combination explained 21.3% of the phenotypic variation. The largest citrate associated effect was in the 3' untranslated region of the SLC25A1 gene, which is responsible for the transport of citrate across the mitochondrial inner membrane. This study provides an approach using RNA sequencing, metabolic pathway analysis, and association studies to identify genetic variation in functional target genes determining complex trait phenotypes.
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Affiliation(s)
- A Cánovas
- Department of Animal Science, University of California-Davis, One Shields Ave., Davis 95616
| | - G Rincón
- Department of Animal Science, University of California-Davis, One Shields Ave., Davis 95616
| | - A Islas-Trejo
- Department of Animal Science, University of California-Davis, One Shields Ave., Davis 95616
| | - R Jimenez-Flores
- Dairy Products Technology Center, Department of Agriculture, California Polytechnic State University, San Luis Obispo 93407
| | - A Laubscher
- Dairy Products Technology Center, Department of Agriculture, California Polytechnic State University, San Luis Obispo 93407
| | - J F Medrano
- Department of Animal Science, University of California-Davis, One Shields Ave., Davis 95616.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Luna-Nevarez P, Rincon G, Medrano JF, Riley DG, Chase CC, Coleman SW, VanLeeuwen DM, DeAtley KL, Islas-Trejo A, Silver GA, Thomas MG. Single nucleotide polymorphisms in the growth hormone–insulin-like growth factor axis in straightbred and crossbred Angus, Brahman, and Romosinuano heifers: Population genetic analyses and association of genotypes with reproductive phenotypes1. J Anim Sci 2011; 89:926-34. [DOI: 10.2527/jas.2010-3483] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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14
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Rincón G, Islas-Trejo A, Casellas J, Ronin Y, Soller M, Lipkin E, Medrano JF. Fine mapping and association analysis of a quantitative trait locus for milk production traits on Bos taurus autosome 4. J Dairy Sci 2009; 92:758-64. [PMID: 19164688 DOI: 10.3168/jds.2008-1395] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
To fine map a quantitative trait locus (QTL) affecting milk production traits previously associated with microsatellite RM188, we implemented an interval mapping analysis by using microsatellite markers in a large Israeli Holstein half-sib sire family, and linkage disequilibrium (LD) mapping in a large set of US Holstein bulls. Interval mapping located the target QTL to the near vicinity of RM188. For the LD mapping, we identified 42 single nucleotide polymorphisms (SNP) in 15 genes in a 12-Mb region on bovine chromosome 4. A total of 24 tag SNP were genotyped in 882 bulls belonging to the University of California Davis archival collection of Holstein bull DNA samples with predicted transmitted ability phenotypes. Marker-to-marker LD analysis revealed 2 LD blocks, with intrablock r(2) values of 0.10 and 0.46, respectively; outside the blocks, r(2) values ranged from 0.002 to 0.23. A standard additive/dominance model using the generalized linear model procedure of SAS and the regression module of HelixTree software were used to test marker-trait associations. Single nucleotide polymorphism 9 on ARL4A, SNP10 on XR_027435.1, SNP12 on ETV1, SNP21 on SNX13, and SNP24 were significantly associated with milk production traits. We propose the interval encompassing ARL4A and SNX13 genes as a candidate region in bovine chromosome 4 for a concordant QTL related to milk protein traits in dairy cattle. Functional studies are needed to confirm this result.
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Affiliation(s)
- G Rincón
- Department of Animal Science, University of California, Davis 95616, USA
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Islas-Trejo A, Land M, Tcherepanova I, Freedman JH, Rubin CS. Structure and expression of the Caenorhabditis elegans protein kinase C2 gene. Origins and regulated expression of a family of Ca2+-activated protein kinase C isoforms. J Biol Chem 1997; 272:6629-40. [PMID: 9045693 DOI: 10.1074/jbc.272.10.6629] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The molecular and cellular basis for concerted Ca2+/lipid signaling in Caenorhabditis elegans was investigated. A unique gene (pkc-2) and cognate cDNAs that encode six Ca2+/diacylglycerol-stimulated PKC2 isoenzymes were characterized. PKC2 polypeptides (680-717 amino acid residues) share identical catalytic, Ca2+-binding, diacylglycerol-activation and pseudosubstrate domains. However, sequences of the N- and C-terminal regions of the kinases diverge. PKC2 diversity is partly due to differential activation of transcription by distinct promoters. Each promoter precedes an adjacent exon that encodes 5'-untranslated RNA, an initiator AUG codon and a unique open reading frame. PKC2 mRNAs also incorporate one of two 3'-terminal exons via alternative splicing. Cells that are capable of receiving and propagating signals carried by Ca2+/diacylglycerol were identified by assessing activities of pkc-2 gene promoters in transgenic C. elegans and visualizing the distribution of PKC2 polypeptides via immunofluorescence. Highly-selective expression of certain PKC2 isoforms was observed in distinct subsets of neurons, intestinal and muscle cells. A low level of PKC2 isoforms is observed in embryos. When L1 larvae hatch and interact with the external environment PKC2 content increases 10-fold. Although 77- and 78-kDa PKC2 isoforms are evident throughout post-embryonic development, an 81-kDa isoform appears to be adapted for function in L1 and L2 larvae.
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Affiliation(s)
- A Islas-Trejo
- Department of Molecular Pharmacology, Atran Laboratories, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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Land M, Islas-Trejo A, Rubin CS. Origin, properties, and regulated expression of multiple mRNAs encoded by the protein kinase C1 gene of Caenorhabditis elegans. J Biol Chem 1994; 269:14820-7. [PMID: 8182089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Recently, we cloned and characterized cDNA encoding a novel, protein kinase C (designated PKC1B) from Caenorhabditis elegans. PKC1B (707 amino acid residues) is a developmentally regulated, calcium-independent kinase that is expressed exclusively in sensory neurons and related interneurons. We have now discovered a mechanism by which a second, distinct mRNA (PKC1A mRNA) with increased protein coding potential is generated from the C. elegans PKC1 gene. PKC1A mRNA is produced in a process that involves the utilization of an alternative, distal promoter, the incorporation of two unique exons into the mRNA, and alternative cis/trans splicing. Diversity among PKC1 gene transcripts is increased substantially by trans-splicing. The 5' end of PKC1A mRNA contains an acceptor site that is modified by the addition of either a classical spliced leader sequence 2 or one of four novel spliced leaders. PKC1A mRNA encodes a predicted kinase that contains the entire sequence of PKC1B as well as an N-terminal extension of 56 residues. The extension contains a preponderance of basic amino acids. The levels of transcripts arising from the distal (1A) and proximal (1B) promoters for the PKC1 gene are differentially regulated during C. elegans development. The ratio of 1B mRNA:1A mRNA varies from 40:1 to unity as the nematodes progress from early larval stages to mature adults. The novel exons in the PKC1A structural gene are not contiguous with the PKC1A promoter but are instead positioned downstream from a second gene, kinase upstream gene-1, in the context of a multicystronic operon. PKC1A and kinase upstream gene-1 mRNAs are coordinately expressed in a fixed ratio throughout C. elegans post-embryonic development, suggesting that a shared upstream promoter regulates transcription of both genes. Finally, PKC1A and PKC1B mRNA levels are differentially regulated by phorbol esters in a process that may involve the participation of another PKC isoform that is analogous to mammalian PKC delta.
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Affiliation(s)
- M Land
- Department of Molecular Pharmacology, Atran Laboratories, Albert Einstein College of Medicine, Bronx, New York 10461
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Land M, Islas-Trejo A, Rubin C. Origin, properties, and regulated expression of multiple mRNAs encoded by the protein kinase C1 gene of Caenorhabditis elegans. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)36698-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Land M, Islas-Trejo A, Freedman JH, Rubin CS. Structure and expression of a novel, neuronal protein kinase C (PKC1B) from Caenorhabditis elegans. PKC1B is expressed selectively in neurons that receive, transmit, and process environmental signals. J Biol Chem 1994; 269:9234-44. [PMID: 8132661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The nematode Caenorhabditis elegans provides an advantageous system for investigating the regulation, expression, and functions of protein kinase C (PKC) isoforms. We cloned and characterized cDNAs encoding a novel C. elegans PKC designated PKC1B. The predicted PKC1B polypeptide contains features characteristic of the nPKC subfamily of PKC isoforms. The levels of PKC1B and its cognate mRNA vary over a 7-fold range during C. elegans postembryonic development. PKC1B protein and mRNA are abundant at the earliest larval stage, but their relative concentrations decrease coordinately in late larvae. Embryos, which are enriched in PKC1B mRNA, contain little PKC1B protein. Thus, PKC1B expression is regulated at a translational or post-translational level during early development. Cells engaged in PKC1B gene transcription were identified in transgenic C. elegans that carry the lacZ gene under the regulation of the PKC1B promoter. Staining for beta-galactosidase revealed PKC1B promoter activity exclusively in sensory neurons and interneurons. Immunofluorescence microscopy disclosed that the PKC1B polypeptide is located in the processes (axons and dendrites) and perinuclear regions of approximately 75 neurons that constitute the sensory circuitry of the nematode. The intracellular localization of PKC1B and the enzyme's differential solubility in ionic and nonionic detergents suggest that the kinase is associated with membranes and the cytoskeleton.
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Affiliation(s)
- M Land
- Department of Molecular Pharmacology, Atran Laboratories, Albert Einstein College of Medicine, Bronx, New York 10461
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