30 results on '"Fortes, M. R. S."'
Search Results
2. Sperm protamine deficiency correlates with sperm DNA damage in Bos indicus bulls
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Fortes, M. R. S., Satake, N., Corbet, D. H., Corbet, N. J., Burns, B. M., Moore, S. S., and Boe-Hansen, G. B.
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- 2014
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3. Evidence for pleiotropism and recent selection in the PLAG1 region in Australian Beef cattle
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Fortes, M. R. S., Kemper, K., Sasazaki, S., Reverter, A., Pryce, J. E., Barendse, W., Bunch, R., McCulloch, R., Harrison, B., Bolormaa, S., Zhang, Y. D., Hawken, R. J., Goddard, M. E., and Lehnert, S. A.
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- 2013
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4. Genome-wide association study for inhibin, luteinizing hormone, insulin-like growth factor 1, testicular size and semen traits in bovine species
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Fortes, M. R. S., Reverter, A., Kelly, M., McCulloch, R., and Lehnert, S. A.
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- 2013
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5. Genetic variants affecting meat and milk production traits appear to have effects on reproduction traits in cattle
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Collis, E., Fortes, M. R. S., Zhang, Y., Tier, B., Schutt, K., Barendse, W., and Hawken, R.
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- 2012
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6. Genomic clues of the evolutionary history of Bos indicus cattle.
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Utsunomiya, Y. T., Milanesi, M., Fortes, M. R. S., Porto‐Neto, L. R., Utsunomiya, A. T. H., Silva, M. V. G. B., Garcia, J. F., and Ajmone‐Marsan, P.
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ZEBUS ,CATTLE ,RHIPICEPHALUS ,Y chromosome ,TROPICAL climate ,MODERN civilization ,PRECISION farming - Abstract
Summary: Together with their sister subspecies Bos taurus, zebu cattle (Bos indicus) have contributed to important socioeconomic changes that have shaped modern civilizations. Zebu cattle were domesticated in the Indus Valley 8000 years before present (YBP). From the domestication site, they expanded to Africa, East Asia, southwestern Asia and Europe between 4000 and 1300 YBP, intercrossing with B. taurus to form clinal variations of zebu ancestry across the landmass of Afro‐Eurasia. In the past 150 years, zebu cattle reached the Americas and Oceania, where they have contributed to the prosperity of emerging economies. The zebu genome is characterized by two mitochondrial haplogroups (I1 and I2), one Y chromosome haplogroup (Y3) and three major autosomal ancestral groups (Indian‐Pakistani, African and Chinese). Phenotypically, zebu animals are recognized by their hump, large ears and excess skin. They are rustic, resilient to parasites and capable of bearing the hot and humid climates of the tropics. Many resources are available to study the zebu genome, including commercial arrays of SNP, reference assemblies and publicly available genotypes and whole‐genome sequences. Nevertheless, many of these resources were initially developed to support research and subsidize industrial applications in B. taurus, and therefore they can produce bias in data analysis. The combination of genomics with precision agriculture holds great promise for the identification of genetic variants affecting economically important traits such as tick resistance and heat tolerance, which were naturally selected for millennia and played a major role in the evolution of B. indicus cattle. [ABSTRACT FROM AUTHOR]
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- 2019
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7. Pre‐ and post‐puberty expression of genes and proteins in the uterus of Bos indicus heifers: the luteal phase effect post‐puberty.
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Fortes, M. R. S., Zacchi, L. F., Nguyen, L. T., Raidan, F., Weller, M. M. D. C. A., Choo, J. J. Y., Reverter, A., Rego, J. P. A., Boe‐Hansen, G. B., Porto‐Neto, L. R., Lehnert, S. A., Cánovas, A., Schulz, B. L., Islas‐Trejo, A., Medrano, J. F., Thomas, M. G., and Moore, S. S.
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ZEBUS , *PUBERTY , *RNA sequencing , *GENE expression , *TRANSCRIPTOMES , *CATTLE - Abstract
Summary: 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. [ABSTRACT FROM AUTHOR]
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- 2018
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8. A marker-derived gene network reveals the regulatory role of PPARGC1A, HNF4G, and FOXP3 in intramuscular fat deposition of beef cattle
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RAMAYO CALDAS, Yuliaxis, Fortes, M. R. S., Hudson, N. J., Porto-Neto, L. R., Bolormaa, S., Barendse, W., Kelly, M., Moore, S. S., Goddard, M. E., Lehnert, S. A., Reverter, A., Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Food Futures Flagship - Animal Food and Health Sciences, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Facultat de Veterinària, Departament de Ciencia Animal i dels Aliments, Universitat Autònoma de Barcelona [Barcelona] (UAB), Queensland Alliance for Agriculture and Food Innovation, Center for Animal Science, University of Queensland [Brisbane], Victorian Department of Environment and Primary Industries, Univ Melbourne, Sch Land & Environm, Parkville, Vic 3010, Australia, Université Paris Diderot - Paris 7 (UPD7), Victorian Dept Environm & Primary Ind, Bundoora, Vic 3083, Australia, Spanish Ministerio de Educacion [AP2008-01450], European Union [267196], European Project: 267196, Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and Universitat Autònoma de Barcelona (UAB)
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[SDV]Life Sciences [q-bio] ,association weight matrix ,fat deposition ,beef quality ,genomewide association study ,marbling - Abstract
High intramuscular fat (IMF) awards price premiums to beef producers and is associated with meat quality and flavor. Studying gene interactions and pathways that affect IMF might unveil causative physiological mechanisms and inform genomic selection, leading to increased accuracy of predictions of breeding value. To study gene interactions and pathways, a gene network was derived from genetic markers associated with direct measures of IMF, other fat phenotypes, feedlot performance, and a number of meat quality traits relating to body conformation, development, and metabolism that might be plausibly expected to interact with IMF biology. Marker associations were inferred from genomewide association studies (GWAS) based on high density genotypes and 29 traits measured on 10,181 beef cattle animals from 3 breed types. For the network inference, SNP pairs were assessed according to the strength of the correlation between their additive association effects across the 29 traits. The co-association inferred network was formed by 2,434 genes connected by 28,283 edges. Topological network parameters suggested a highly cohesive network, in which the genes are strongly functionally interconnected. Pathway and network analyses pointed towards a trio of transcription factors (TF) as key regulators of carcass IMF: PPARG-C1A, HNF4G, and FOXP3. Importantly, none of these genes would have been deemed as significantly associated with IMF from the GWAS. Instead, a total of 313 network genes show significant co-association with the 3 TF. These genes belong to a wide variety of biological functions, canonical pathways, and genetic networks linked to IMF-related phenotypes. In summary, our GWAS and network predictions are supported by the current literature and suggest a cooperative role for the 3 TF and other interacting genes including CAPN6, STC2, MAP2K4, EYA1, COPS5, XKR4, NR2E1, TOX, ATF1, ASPH, TGS1, and TTPA as modulators of carcass and meat quality traits in beef cattle.
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- 2014
9. Morphological defects, sperm DNA integrity, and protamination of bovine spermatozoa.
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Boe‐Hansen, G. B., Fortes, M. R. S., and Satake, N.
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SPERMATOZOA , *DNA , *CHROMATIN , *EMBRYOS , *GERM cells - Abstract
Summary: The association between sperm morphology characteristics and DNA conformation and integrity is still controversial. In bulls, major morphological sperm abnormalities have been associated with reduced fertility, and morphological assessment is used to provide an indication of potential fertility of the individual. Sperm DNA fragmentation and damage has a negative effect on embryo development and subsequently fertility, with bull spermatozoa generally displaying low levels of DNA damage and tight chromatin. However, sensitive methods for detecting chromatin damage may reveal associations with morphological defects. The objective was to determine whether morphological sperm abnormalities and variables expressing sperm DNA integrity and protamination are correlated in bulls, using the sperm chromatin structure assay (SCSA) and the sperm protamine deficiency assay (SPDA). Electroejaculated samples (n = 1009) from two‐year‐old tropically adapted bulls were split and fixed and submitted to microscopic sperm morphology assessment, and snap‐frozen for sperm nuclear integrity assessments by SPDA and SCSA. For SPDA, the variables were defective (MCB) and deprotaminated (HCB), and for SCSA, the variables were DNA fragmentation index (DFI) and high DNA stainability (HDS). HCB correlated with DFI; τKen2 = 0.317 and HDS; 0.098, and MCB correlated with DFI; 0.183 (p < 0.001). The percentage of morphological normal spermatozoa was correlated negatively to DFI; τKen2 = −0.168, MCB; −0.116 and HCB; −0.137 (p < 0.001). HCB and DFI were both positively correlated to head defects, proximal droplets, and spermatogenic immaturity, but not to distal droplets, vacuoles, or diadems. Sperm DNA integrity and protamination, using the SCSA and SPDA, respectively, in bulls show associations with morphological parameters, particularly with head shape abnormalities and indicators of spermatogenic immaturity, including proximal droplets. The vacuoles and diadem defects were not correlated with sperm nuclear integrity, and hence, these are likely physiological features that may not directly affect sperm chromatin configuration. [ABSTRACT FROM AUTHOR]
- Published
- 2018
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10. Adipose tissue proteomic analyses to study puberty in Brahman heifers.
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Nguyen, L T, Zacchi, L F, Schulz, B L, Moore, S S, and Fortes, M R S
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ADIPOSE tissues ,PROTEOMICS ,HEIFERS ,PUBERTY ,ENDOCRINE glands ,ESTROGEN ,ZEBUS ,CATTLE - Abstract
The adipose tissue has been recognized as an active endocrine organ which can modulate numerous physiological processes such as metabolism, appetite, immunity, and reproduction. The aim of this study was to look for differentially abundant proteins and their biological functions in the abdominal adipose tissue between pre- and postpubertal Brahman heifers. Twelve Brahman heifers were divided into 2 groups and paired on slaughter day. Prepubertal heifers had never ovulated and postpubertal heifers were slaughtered on the luteal phase of their second estrous cycle. After ensuring the occurrence of puberty in postpubertal heifers, abdominal adipose tissue samples were collected. Mass spectrometry proteomic analysis identified 646 proteins and revealed that 171 proteins showed differential abundance in adipose tissue between the pre- and postpuberty groups (adjusted
P -value < 0.05). Data are available via ProteomeXchange with identifier PXD009452. Using a list of 51 highly differentially abundant proteins as the target (adjustedP -value < 10−5 ), we found 14 enriched pathways. The results indicated that gluconeogenesis was enhanced when puberty approached. The metabolism of glucose, lipids, and AA in the adipose tissue mainly participated in oxidation and energy supply for heifers when puberty occurred. Our study also revealed the differentially abundant proteins were enriched for estrogen signaling and PI3K-Akt signaling pathways, which are known integrators of metabolism and reproduction. These results suggest new candidate proteins that may contribute to a better understanding of the signaling mechanisms that relate adipose tissue function to puberty. Protein–protein interaction network analysis identified 4 hub proteins that had the highest degrees of connection: PGK1, ALDH5A1, EEF2, and LDHB. Highly connected proteins are likely to influence the functions of all differentially abundant proteins identified, directly or indirectly. [ABSTRACT FROM AUTHOR]- Published
- 2018
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11. Genomic inbreeding depression for climatic adaptation of tropical beef cattle.
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Reverter, A., Porto-Neto, L. R., Fortes, M. R. S., Kasarapu, P., de Cara, M. A. R., Burrow, H. M., and Lehnert, S. A.
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INBREEDING ,ANIMAL adaptation ,BEEF cattle ,CATTLE genetics ,SINGLE nucleotide polymorphisms - Abstract
Inbreeding has the potential to negatively impact animal performance. Strategies to monitor and mitigate inbreeding depression require that it can be accurately estimated. Here, we used genomewide SNP data to explore 3 alternative measures of genomic inbreeding: the diagonal elements of the genomic relationship matrix (FGRM), the proportion of homozygous SNP (FHOM), and the proportion of the genome covered by runs of homozygosity (FROH). We used 2,111 Brahman (BR) and 2,550 Tropical Composite (TC) cattle with phenotypes recorded for 10 traits of relevance to tropical adaptation. We further explored 3 marker densities ranging from a highdensity chip (729,068 SNP), a medium-density chip (71,726 SNP) specifically designed for Bos indicus cattle, and a low-density chip (18,860 SNP) associated with the measures of inbreeding. Measures of FGRM were highly correlated across the 3 SNP densities and negatively correlated with FHOM and FROH in the BR population. In both populations, there was a strong positive correlation for each measure of inbreeding across the 3 SNP panels. We found significant (P < 0.01) inbreeding depression for various traits, particularly when using the highest-density SNP chip in the BR population, where inbreeding was negatively associated with coat color and coat type such that inbred animals presented shorter, slicker, and lighter coats. Based on FGRM using the medium-density chip, we found that a 1% increase in inbreeding in the BR and TC populations was associated with a decrease of 0.514 and 0.579 kg BW, respectively, in yearlings. In the TC population, a 1% increase in FHOM was associated with a decrease in BCS of -0.636% (P < 0.001). The low-density chip, comprising SNP associated with inbreeding, captured genes, and regions with pleiotropic effects (P < 0.001). However, it did not improve our ability to identify inbreeding depression, relative to the use of higher-density panels. We conclude that where heterogeneous populations are present, such as in tropical environments where composite animals abound, measures of inbreeding that do not depend on allele frequencies, such as FHOM and FROH, are preferable for estimating genomic inbreeding. Finally, the sustainable intensification of livestock systems in tropical regions will rely on genetic safeguards to ensure that productivity is improved while also adapting animals to cope with climate change. The results of this study are a step toward achieving that goal. [ABSTRACT FROM AUTHOR]
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- 2017
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12. Multiple-trait genomewide mapping and gene network analysis for scrotal circumference growth curves in Brahman cattle.
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Soares, A. C. C., Guimarães, S. E. F., Kelly, M. J., Fortes, M. R. S., e Silva, F. F., Verardo, L. L., Mota, R. R., and Moore, S.
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GENE mapping ,ANIMAL genetics ,ANIMAL genetic engineering ,GENE regulatory networks ,ZEBUS - Abstract
Fertility traits are economically important in cattle breeding programs. Scrotal circumference (SC) measures are repeatable, easily obtained, highly heritable, and positively correlated with female fertility traits and sperm quality traits in males. A useful approach to summarize SC measures over time is using nonlinear models, which summarize specific measures of SC in a few parameters with biological interpretation. This approach facilitates the selection of bulls with larger SC and maturity index (K), that is, early maturing animals. Because SC is a sex-limited trait, identifying the underlying genomics of growth curve parameters will allow selection across both males and females. We reported the first multitrait genomewide association study (GWAS) of estimated growth curve parameters for SC data in Brahman cattle. Five widely used nonlinear models were tested to fit a total of 3,612 SC records, measured at 6, 12, 18, and 24 mo of age. The von Bertalanffy model, individually fitted for each animal, best fit this SC data. Parameter estimates SC at maturity (A) and K as well as SC at all ages were jointly analyzed in a GWAS to identify 1-Mb regions most strongly associated with each trait. Heritabilities were 0.25 for K and 0.32 for A and ranged from 0.51 to 0.72 for SC at 6 (SC6), 12 (SC12), 18 (SC18), and 24 mo of age (SC24). An overlapping window on chromosome 14 explaining around 0.8% of genetic variance for K, SC12, SC18, and SC24 was observed. The major positional candidate genes within 1 Mb upstream and downstream of this overlapping window were LYN, CHD7, RAB2A, and ARFGEF1. Windows of 1 Mb explaining more than 0.4% of each trait on chromosomes 1, 3, 6, 7, 14, 17, 18, 24, 25, and 26 were identified. Pathways and net-work analyses were indicated through transcription factors playing a role on fertility traits: SOX9, BRCA1, STAT3, NFE2L2, EGR1, PPARG, and NFKB1. Further validation studies on larger populations or other breeds are required to validate these findings and to improve our understanding of the biology and complex genetic architecture of traits associated with scrotal growth and male fertility in cattle. [ABSTRACT FROM AUTHOR]
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- 2017
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13. Global differential gene expression in the pituitary gland and the ovaries of pre- and postpubertal Brahman heifers.
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Nguyen, L. T., Reverter, A., Cánovas, A., Venus, B., Islas-Trejo, A., Porto-Neto, L. R., Lehnert, S. A., Medrano, J. F., Moore, S. S., and Fortes, M. R. S.
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OVARIAN diseases ,GENE expression ,PITUITARY gland ,HEIFERS ,AGE groups ,ZEBUS ,RNA sequencing - 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 (Bos indicus) are older at puberty compared with Bos taurus, 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 (P < 0.05), and VWC2L was the most DEx gene (fold change = 4.12, P = 0.01). The gene VWC2L promotes bone mineralization through transforming growth factor-β (TGFβ) signaling. Further studies of the link between bone mineralization and puberty could target VWC2L. In ovaries, 3,871 genes were DEx (P < 0.05). Four highly DEx genes were noteworthy for their function: SLC6A13 (a γ-aminobutyric acid [GABA] transporter), OXT (oxytocin), and NPY (neuropeptide Y) and its receptor NPY2R. 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 OXT pathway has been known to influence the timing of puberty in rats, via modulation of GnRH. The effects of NPY at the hypothalamus, pituitary gland, and ovaries have been documented. Neuropeptide Y and its receptors are known factors in the release of GnRH, similar to OXT and GABA, although their roles in ovarian tissue are less clear. Pathways previously related to puberty such as TGFβ signaling (P = 6.71 × 10
-5 ), Wnt signaling (P = 4.1 × 10-2 ), and peroxisome proliferator-activated receptor (PPAR) signaling (P = 4.84 × 10-2 ) were enriched in our data set. Seven genes were identified as key TF in both tissues: HIC2, ZIC4, ZNF219, ZSCAN26, LHX1, OLIG1, and a novel gene. An ovarian subnetwork created with TF and significant ovarian DEx genes revealed five zinc fingers as regulators: ZNF507, ZNF12, ZNF512, ZNF184, and ZNF432. 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. [ABSTRACT FROM AUTHOR]- Published
- 2017
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14. Genomic analyses of tropical beef cattle fertility based on genotyping pools of Brahman cows with unknown pedigree.
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Reverter, A., Porto-Neto, L. R., Fortes, M. R. S., McCulloch, R., Lyons, R. E., Moore, S., Nicol, D., Henshall, J., and Lehnert, S. A.
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BEEF cattle ,GENOMICS ,ANIMAL herds ,CATTLE ,HERDING behavior in animals - Abstract
We introduce an innovative approach to lowering the overall cost of obtaining genomic EBV (GEBV) and encourage their use in commercial extensive herds of Brahman beef cattle. In our approach, the DNA genotyping of cow herds from 2 independent properties was performed using a highdensity bovine SNP chip on DNA from pooled blood samples, grouped according to the result of a pregnancy test following their first and second joining opportunities. For the DNA pooling strategy, 15 to 28 blood samples from the same phenotype and contemporary group were allocated to pools. Across the 2 properties, a total of 183 pools were created representing 4,164 cows. In addition, blood samples from 309 bulls from the same properties were also taken. After genotyping and quality control, 74,584 remaining SNP were used for analyses. Pools and individual DNA samples were related by means of a "hybrid" genomic relationship matrix. The pooled genotyping analysis of 2 large and independent commercial populations of tropical beef cattle was able to recover significant and plausible associations between SNP and pregnancy test outcome. We discuss 24 SNP with significant association (P < 1.0 x 10
-5 ) and mapped within 40 kb of an annotated gene. We have established a method to estimate the GEBV in young herd bulls for a trait that is currently unable to be predicted at all. In summary, our novel approach allowed us to conduct genomic analyses of fertility in 2 large commercial Brahman herds managed under extensive pastoral conditions. [ABSTRACT FROM AUTHOR]- Published
- 2016
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15. Transcriptome analyses identify five transcription factors differentially expressed in the hypothalamus of post- versus prepubertal Brahman heifers.
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Fortes, M. R. S., Nguyen, L. T., Weller, M. M. D. C. A., Cánovas, A., Islas-Trejo, A., Porto-Neto, L. R., Reverter, A., Lehnert, S. A., Boe-Hansen, G. B., Thomas, M. G., Medrano, J. F., and Moore, S. S.
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CATTLE breeding , *TRANSCRIPTION factors , *HYPOTHALAMUS , *PUBERTY , *ANIMAL mutation , *GENE expression , *RNA sequencing , *ZEBUS , *CATTLE - 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 Bos indicus (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: E2F8, NFAT5, SIX5, ZBTB38, and ZNF605. 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 (P < 0.05). Two of these 5 TF, ZBTB38 and ZNF605, were zinc fingers, belonging to a gene family previously reported to have a central regulatory role in mammalian puberty. The SIX5 gene belongs to the family of homologues of Drosophila sine oculis (SIX) genes implicated in transcriptional regulation of gonadotrope gene expression. Tumor-related genes such as E2F8 and NFAT5 are known to affect basic cellular processes that are relevant in both cancer and developmental processes. Mutations in NFAT5 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. [ABSTRACT FROM AUTHOR]
- Published
- 2016
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16. Effect of maternal nutrition and days of gestation on pituitary gland and gonadal gene expression in cattle.
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Weller, M. M. D. C. A., Fortes, M. R. S., Marcondes, M. I., Rotta, P. P., Gionbeli, T. R. S., Valadares Filho, S. C., Campos, M. M., Silva, F. F., Silva, W., Moore, S., and Guimarães, S. E. F.
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MATERNAL nutrition , *FETAL development , *GENE expression , *PREGNANCY in animals , *PITUITARY gland , *PHYSIOLOGY , *CATTLE - Abstract
This study investigated effects of maternal overnutrition on gonadal development and pituitary-gonadal gene expression in cattle fetuses at mid- and late-gestation. Twenty-seven multiparous dry cows were fed either high (ad libitum, H) or moderate (M) intake of the same diet. Twelve cows from H (n = 6) and M (n = 6) intake carrying females fetuses were euthanized at 199 and 268 d of gestation (DG; n = 3 for H or M on each DG). Fifteen cows from H (n = 6) and M intake (n = 9) carrying male fetuses were euthanized at 139, 199, and 241 DG (n = 2 for H and n = 3 for M on each DG). Fetal gonads and pituitary gland were sampled for gene expression and histological analyses. Sex-specific responses to maternal intake were observed. Primordial and total follicle numbers were lower in fetal ovaries from H than in M intake cows. These results were the reverse for preantral and antral follicles. Volumetric proportion and diameter of seminiferous cord were lower in fetal testis of H than M intake cows. The expression level of FSHB was greater in pituitary gland of the female fetus from H compared with M intake cows, irrespective of DG, whereas LHB gene expression did not differ. In males, FSHB and LHB gene expression levels were similar between maternal intake groups. Fetal ovarian expression of P450 aromatase, StAR, BMPR2, TGFBR1, GDF9, FSHR, Bax, and CASP3 genes were higher in H than in M intake cows, irrespective of DG. Fetal testicular expression of StAR, HSD17B3, IGF1, IGF2, and IGF1R genes was higher in M than in H intake cows. The differences in gene expression for steroidogenesis, folliculogenesis, and apoptosis may explain the distinct pattern of follicular growth between offspring of M and H intake cows. By contrast, the lower volumetric proportion, diameter, and length of seminiferous cord may relate to decreased gene expression in fetal testis from H intake cows. In conclusion, maternal H intake seems to affect fetal ovarian follicular growth and number of follicles, which may affect the size of ovarian reserve in their offspring. In male fetus, maternal H intake seems to disturb testicular development and may have implications on sperm production. The underlying mechanism of differential gene expression and the effect on offspring reproductive potential should be the focus of further research, especially considering larger sample size, reducing the chance for type I errors. [ABSTRACT FROM AUTHOR]
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- 2016
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17. Genome-wide association for the outcome of fixed-time artificial insemination of Brahman heifers in northern Australia.
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Porto-Neto, L. R., Edwards, S., Fortes, M. R. S., Lehnert, S. A., Reverter, A., and McGowan, M.
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ARTIFICIAL insemination of cattle ,VETERINARY genetics ,CATTLE breeds ,GENETIC markers ,OVULATION ,CATTLE - Abstract
Fixed-time AI (FTAI) is a powerful tool for genetic improvement of extensively managed beef cattle. A genomewide association study (GWAS) was conducted to investigate genes and genetic markers associated with the outcome (pregnant or not pregnant) of FTAI in 614 commercial Brahman heifers genotyped for 18,895 SNP and imputed to 51,588 SNP. The likelihood of Brahman heifers becoming pregnant after hormonal treatment to synchronize ovulation followed by FTAI was influenced by the Bos indicus content of their genomes, as determined by a principal component analysis. The principal component analysis involved comparisons between the studied heifers and populations of known Bos taurus and B. indicus ancestry. The heritability of FTAI outcome was h² = 0.18, which is higher than for most other reproductive outcome traits. The number of SNP associated with FTAI outcome was 101 (P < 0.001, false discovery rate = 0.53). Compared with all SNP tested, associated SNP had a tendency for highly divergent allelic frequencies between B. indicus and B. taurus. Associated SNP were located in nearly all chromosomes, a result that shows a complex genetic architecture that is typical of highly complex traits with low heritability. Considering this and previous GWAS that examined Brahman heifer puberty and postpartum anestrus interval, 3 genomic regions emerge as important for overall Brahman heifer fertility, which mapped to chromosomes 1, 7, and 9. Further analyses, including improved genome annotation, are required to elucidate the link between these regions and heifer fertility. Additional studies are needed to confirm SNP and gene associations reported herein and further elucidate the genetics of FTAI outcome. Future GWAS should target other Braham populations and additional cattle breeds with FTAI records, including breeds with higher B. taurus ancestry. [ABSTRACT FROM AUTHOR]
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- 2015
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18. Prospecting major genes in dairy buffaloes.
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de Camargo, G. M. F., Aspilcueta-Borquis, R. R., Fortes, M. R. S., Porto-Neto, R., Cardoso, D. F., Santos, D. J. A., Lehnert, S. A., Reverter, A., Moore, S. S., and Tonhati, H.
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WATER buffalo ,GENE expression ,ANIMAL diversity ,GENOMES ,WATER buffalo milk yield - Abstract
Background: Asian buffaloes (Bubalus bubalis) have an important socio-economic role. The majority of the population is situated in developing countries. Due to the scarce resources in these countries, very few species-specific biotechnology tools exist and a lot of cattle-derived technologies are applied to buffaloes. However, the application of cattle genomic tools to buffaloes is not straightforward and, as results suggested, despite genome sequences similarity the genetic polymorphisms are different. Results: The first SNP chip genotyping platform designed specifically for buffaloes has recently become available. Herein, a genome-wide association study (GWAS) and gene network analysis carried out in buffaloes is presented. Target phenotypes were six milk production and four reproductive traits. GWAS identified SNP with significant associations and suggested candidate genes that were specific to each trait and also genes with pleiotropic effect, associated to multiple traits. Conclusions: Network predictions of interactions between these candidate genes may guide further molecular analyses in search of disruptive mutations, help select genes for functional experiments and evidence metabolism differences in comparison to cattle. The cattle SNP chip does not offer an optimal coverage of buffalo genome, thereafter the development of new buffalo-specific genetic technologies is warranted. An annotated reference genome would greatly facilitate genetic research, with potential impact to buffalo-based dairy production. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
- View/download PDF
19. Comparison of metabolic, hematological, and peripheral blood leukocyte cytokine profiles of dairy cows and heifers during the periparturient period.
- Author
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Jonsson, N. N., Fortes, M. R. S., Piper, E. K., Vankan, D. M., De Cisneros, J. Prada J., and Wittek, T.
- Subjects
- *
DAIRY cattle , *COWS , *CATTLE parturition , *CATTLE reproduction , *CYTOKINES , *HYPOCALCEMIA , *HEIFERS - Abstract
The periparturient period presents major physiological challenges for the dairy cow. It is a period that is affected by metabolic stressors, major changes in endocrine status, and altered immune function, which together result in an increased risk of disease. Immunological, hematological, and metabolic profiles from the periparturient period of heifers (primipara) were compared with those of cows (pluripara) to test the hypothesis that at the time of calving they have qualitatively different peripheral blood profiles. Blood samples were collected from 22 Holstein-Friesian animals on 3 occasions: approximately 2 wk before calving, within 24 h after calving, and approximately 2 wk after calving. Quantitative PCR was used to measure the expression of a selected set of cytokines and receptors by peripheral blood leukocytes. Additional analyses included hemoglobin concentration, red cell, platelet and white cell counts (total and differentiated), and clinical diagnostic biochemical profiles. Total leukocyte counts, neutrophils, and lymphocytes were higher in heifers than cows before calving and within 24 h after calving. Alkaline phosphatase was consistently higher in heifers than cows and several significant differences were observed between the 2 groups with regards to cytokine and cytokine-receptor mRNA expression. The results warrant further investigation from the perspective of identifying risk factors for metabolic and parturient disease in dairy cattle. [ABSTRACT FROM AUTHOR]
- Published
- 2013
- Full Text
- View/download PDF
20. BREEDING AND GENETICS SYMPOSIUM: Building single nucleotide polymorphism-derived gene regulatory networks: Towards functional genomewide association studies.
- Author
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Reverter, A. and Fortes, M. R. S.
- Subjects
- *
ANIMAL genetics , *ANIMAL breeding , *SINGLE nucleotide polymorphisms , *GENE regulatory networks , *GENOMES , *CATTLE breeding , *CONFERENCES & conventions - Abstract
The advent of economically viable high-throughput genetic and genomic techniques has equipped animal geneticists with an unprecedented ability to generate massive amounts of molecular data. As a result, large lists of genes differentially expressed in many experimental conditions of interests have been reported and, likewise, the association of an ever growing number of DNA variants with phenotypes of importance is now a routine endeavor. Although these studies have greatly improved our understanding of the genetic basis of complex phenotypes, they have also revealed the difficulty in explaining more than a fraction of the genetic variance. Inspired by this data-rich and knowledge-poor dichotomy, systems biology aims at the formal integration of seemingly disparate datasets allowing for a holistic view where key properties of the systems emerge as an intuitive feature and enable the generation of testable hypotheses. Herein, we present 2 examples of integrating molecular data anchored in the power of gene network inference. The first example is concerned with the onset of puberty in Bos indicus-influenced cows bred in Australia. Using the results from genomewide association studies across a range of phenotypes, we developed what we termed an association weight matrix to generate a gene network underlying phenotypes of puberty in cattle. The network was mined for the minimal set of transcription factor genes whose predicted target spanned the majority of the topology of the entire network. The second example deals with piebald, a pigmentation phenotype in Merino sheep. Two networks were developed: a regulatory network and an epistatic network. The former is inferred based on promoter sequence analysis of differentially expressed genes. The epistatic network is built from 2-locus models among all pairwise associated polymorphisms. At the intersection between these 2 networks, we revealed a set of genes and gene-gene interactions of validated and de novo predicted relevance to the piebald phenotype. We argue that these new approaches are holistic and therefore more appropriate than traditional approaches for investigating genetic mechanisms underlying complex phenotypes of importance in livestock species. [ABSTRACT FROM AUTHOR]
- Published
- 2013
- Full Text
- View/download PDF
21. BREEDING AND GENETICS SYMPOSIUM: Networks and pathways to guide genomic selection.
- Author
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Snelling, W. M., Cushman, R. A., Keele, J. W., Maltecca, C., Thomas, M. G., Fortes, M. R. S., and Reverter, A.
- Subjects
ANIMAL breeding ,ANIMAL genetics ,GENOMICS ,SINGLE nucleotide polymorphisms ,PHENOTYPES ,CONFERENCES & conventions - Abstract
Many traits affecting profitability and sustainability of meat, milk, and fiber production are polygenic, with no single gene having an overwhelming influence on observed variation. No knowledge of the specific genes controlling these traits has been needed to make substantial improvement through selection. Significant gains have been made through phenotypic selection enhanced by pedigree relationships and continually improving statistical methodology. Genomic selection, recently enabled by assays for dense SNP located throughout the genome, promises to increase selection accuracy and accelerate genetic improvement by emphasizing the SNP most strongly correlated to phenotype although the genes and sequence variants affecting phenotype remain largely unknown. These genomic predictions theoretically rely on linkage disequilibrium (LD) between genotyped SNP and unknown functional variants, but familial linkage may increase effectiveness when predicting individuals related to those in the training data. Genomic selection with functional SNP genotypes should be less reliant on LD patterns shared by training and target populations, possibly allowing robust prediction across unrelated populations. Although the specific variants causing polygenic variation may never be known with certainty, a number of tools and resources can be used to identify those most likely to affect phenotype. Associations of dense SNP genotypes with phenotype provide a 1-dimensional approach for identifying genes affecting specific traits; in contrast, associations with multiple traits allow defining networks of genes interacting to affect correlated traits. Such networks are especially compelling when corroborated by existing functional annotation and established molecular pathways. The SNP occurring within network genes, obtained from public databases or derived from genome and transcriptome sequences, may be classified according to expected effects on gene products. As illustrated by functionally informed genomic predictions being more accurate than naive whole-genome predictions of beef tenderness, coupling evidence from livestock genotypes, phenotypes, gene expression, and genomic variants with existing knowledge of gene functions and interactions may provide greater insight into the genes and genomic mechanisms affecting polygenic traits and facilitate functional genomic selection for economically important traits. [ABSTRACT FROM AUTHOR]
- Published
- 2013
- Full Text
- View/download PDF
22. Gene network analyses of first service conception in Brangus heifers: Use of genome and trait associations, hypothalamic-transcriptome information, and transcription factors.
- Author
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Fortes, M. R. S., Snelling, W. M., Reverter, A., Nagaraj, S. H., Lehnert, S. A., Hawken, R. J., DeAtley, K. L., Peters, S. O., Silver, G. A., Rincon, G., Medrano, J. F., Islas-Trejo, A., and Thomas, M. G.
- Subjects
- *
GENE regulatory networks , *HEIFERS , *ANIMAL genome mapping , *HYPOTHALAMIC hormones , *TRANSCRIPTION factors , *SINGLE nucleotide polymorphisms , *HERITABILITY - Abstract
Measures of heifer fertility are economi-cally 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 heif-ers (3/8 Brahman x 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 con-ception (FSC). These fertility traits were collected from controlled breeding seasons initiated with estrous syn-chronization and Al 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 associ-ated 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 hypothala-mus of a prepubertal and a postpubertal Brangus heifer. The remaining hypothalamic-influenced network con-tained 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. [ABSTRACT FROM AUTHOR]
- Published
- 2012
- Full Text
- View/download PDF
23. Genome-wide association studies of female reproduction in tropically adapted beef cattle.
- Author
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Hawken, R. J., Zhang, Y. D., Fortes, M. R. S., Collis, E., Barris, W. C., Corbet, N. J., Williams, P. J., Fordyce, G., Holroyd, R. G., J. R. W. Walkley, Barendse, W., Johnston, D. J., Prayaga, K. C., Tier, B., Reverter, A., and Lehnert, S. A.
- Subjects
CATTLE genetics ,BEEF cattle ,BEEF cattle reproduction ,PUERPERIUM ,HERITABILITY ,GENETIC pleiotropy ,SINGLE nucleotide polymorphisms ,ANIMAL genetics ,CATTLE - Abstract
The genetics of reproduction is poorly understood because the heritabilities of traits currently recorded are low. To elucidate the genetics underlying reproduction in beef cattle, we performed a genome-wide association study using the bovine SNP50 chip in 2 tropically adapted beef cattle breeds, Brahman and Tropical Composite. Here we present the results for 3 female reproduction traits: 1) age at puberty, defined as age in days at first observed corpus luteum (CL) after frequent ovarian ultrasound scans (AGECL); 2) the postpartum anestrous interval, measured as the number of days from calving to first ovulation postpartum (first rebreeding interval, PPAI); and 3) the occurrence of the first postpartum ovulation before weaning in the first rebreeding period (PW), defined from PPAI. In addition, correlated traits such as BW, height, serum IGF1 concentration, condition score, and fatness were also examined. In the Brahman and Tropical Composite cattle, 169 [false positive rate (FPR) = 0.262] and 84 (FPR = 0.581) SNP, respectively, were significant (P < 0.001) for AGECL. In Brahman, 41% of these significant markers mapped to a single chromosomal region on BTA14. In Tropical Composites, 16% of these significant markers were located on BTA5. For PPAI, 66 (FPR = 0.67) and 113 (FPR = 0.432) SNP were significant (P < 0.001) in Brahman and Tropical Composite, respectively, whereas for PW, 68 (FPR = 0.64) and 113 (FPR = 0.432) SNP were significant (P < 0.01). In Tropical Composites, the largest concentration of PPAI markers were located on BTA5 [19% (PPAI) and 23% (PW)], and BTA16 [17% (PPAI) and 18% (PW)]. In Brahman cattle, the largest concentration of markers for postpartum anestrus was located on BTA3 (14% for PPAI and PW) and BTA14 (17% PPAI). Very few of the significant markers for female reproduction traits for the Brahman and Tropical Composite breeds were located in the same chromosomal regions. However, fatness and BW traits as well as serum IGF1 concentration were found to be associated with similar genome regions within and between breeds. Clusters of SNP associated with multiple traits were located on BTA14 in Brahman and BTA5 in Tropical Composites. [ABSTRACT FROM AUTHOR]
- Published
- 2012
- Full Text
- View/download PDF
24. PHYSIOLOGY AND ENDOCRINOLOGY SYMPOSIUM: How single nucleotide polymorphism chips will advance our knowledge of factors controlling puberty and aid in selecting replacement beef females.
- Author
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Snelling, W. M., Cushman, R. A., Fortes, M. R. S., Reverter, A., Bennett, G. L., Keele, J. W., Kuehn, L. A., McDaneld, T. G., Thallman, R. M., and Thomas, M. G.
- Subjects
SINGLE nucleotide polymorphisms ,DNA ,PUBERTY ,FERTILITY ,PREGNANCY - Abstract
The promise of genomic selection is accurate prediction of the genetic potential of animals from their genotypes. Simple DNA tests might replace low-accuracy predictions for expensive or lowly heritable measures of puberty and fertility based on performance and pedigree. Knowing with some certainty which DNA variants (e.g., SNP) affect puberty and fertility is the best way to fulfill the promise. Several SNP from the BovineSNP50 assay have tentatively been associated with reproductive traits including age at puberty, antral follicle count, and pregnancy observed on different sets of heifers. However, sample sizes are too small and SNP density is too sparse to definitively determine genomic regions harboring causal variants affecting reproductive success. Additionally, associations between individual SNP and similar phenotypes are inconsistent across data sets, and genomic predictions do not appear to be globally applicable to cattle of different breeds. Discrepancies may be a result of different QTL segregating in the sampled populations, differences in linkage disequilibrium (LD) patterns such that the same SNP are not correlated with the same QTL, and spurious correlations with phenotype. Several approaches can be used independently or in combination to improve detection of genomic factors affecting heifer puberty and fertility. Larger samples and denser SNP will increase power to detect real associations with SNP having more consistent LD with underlying QTL. Meta-analysis combining results from different studies can also be used to effectively increase sample size. High-density genotyping with heifers pooled by pregnancy status or early and late puberty can be a cost-effective means to sample large numbers. Networks of genes, implicated by associations with multiple traits correlated with puberty and fertility, could provide insight into the complex nature of these traits, especially if corroborated by functional annotation, established gene interaction pathways, and transcript expression. Example analyses are provided to demonstrate how integrating information about gene function and regulation with statistical associations from whole-genome SNP genotyping assays might enhance knowledge of genomic mechanisms affecting puberty and fertility, enabling reliable DNA tests to guide heifer selection decisions. [ABSTRACT FROM AUTHOR]
- Published
- 2012
- Full Text
- View/download PDF
25. A single nucleotide polymorphism-derived regulatory gene network underlying puberty in 2 tropical breeds of beef cattle.
- Author
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Fortes, M. R. S., Reverter, A., Nagaraj, S. H., Zhang, Y., Jonsson, N. N., Barris, W., Lehnert, S., Boe-Hansen, G. B., and Hawken, R. J.
- Subjects
- *
GENETIC polymorphisms , *CATTLE breeding , *ACCLIMATIZATION , *CORPUS luteum , *NATURAL immunity , *CATTLE breeds - Abstract
Harsh tropical environments impose serious challenges on poorly adapted species. In beef cattle, tropical adaptation in the form of temperature and disease resistance, coupled with acclimatization to seasonal and limited forage, comes at a cost to production efficiency. Prominent among these costs is delayed onset of puberty, a challenging phenotype to manipulate through traditional breeding mechanisms. Recently, system biology approaches, including gene networks, have been applied to the genetic dissection of complex phenotypes. We aimed at developing and studying gene networks underlying cattle puberty. Our starting material comprises the association results of ~50,000 SNP on 22 traits, including age at puberty, and 2 cattle breed populations: Brahman (n = 843) and Tropical Composite (n = 866). We defined age at puberty as the age at first corpus luteum (AGECL). By capturing the genes harboring mutations minimally associated (P < 0.05) to AGECL or to a set of traits related with AGECL, we derived a gene network for each breed separately and a third network for the combined data set. At the intersection of the 3 networks, we identified candidate genes and pathways that were common to both breeds. Resulting from these analyses, we identified an enrichment of genes involved in axon guidance, cell adhesion, ErbB signaling, and glutamate activity, pathways that are known to affect pulsatile release of GnRH, which is necessary for the onset of puberty. Furthermore, we employed network connectivity and centrality parameters along with a regulatory impact factor metric to identify the key transcription factors (TF) responsible for the molecular regulation of puberty. As a novel finding, we report 5 TF (HIVEP3, TOX, EYA1, NCOA2, and ZFHX4) located in the network intersecting both breeds and interacting with other TF, forming a regulatory network that harmonizes with the recent literature of puberty. Finally, we support our network predictions with evidence derived from gene expression in hypothalamic tissue of adult cows. [ABSTRACT FROM AUTHOR]
- Published
- 2011
- Full Text
- View/download PDF
26. Real-time PCR genotyping and frequency of the myostatin F94L mutation in beef cattle breeds.
- Author
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Vankan, D. M., Waine, D. R., and Fortes, M. R. S.
- Subjects
DNA polymerases ,GENE frequency ,ANIMAL carcasses ,SIMMENTAL cattle ,DROUGHTMASTER cattle ,LIMOUSIN cattle ,CHAROLAIS cattle - Abstract
This research developed two real-time PCR assays, employing high-resolution melt and allele-specific analysis to accurately genotype the F94L mutation in cattle. This mutation (g.433C>A) in the growth differentiation factor 8 or myostatin gene has recently been shown to be functionally associated with increased muscle mass and carcass yield in cattle. The F94L mutation is not, like other myostatin mutations, associated with reduced fertility and dystocia. It is therefore a candidate for introgression into other breeds to improve retail beef yield and the development of a simple and accurate test to genotype this specific mutation is warranted. Variations in the efficiency of enzyme cleavage compromised the accuracy of genotyping by published methods, potentially resulting in an overestimation of the frequency of the mutant allele. The frequency of the F94L mutation was determined by real-time PCR in 1140 animals from 15 breeds of cattle in Australia. The mutation was present in Simmental (0.8%), Piedmontese (2%), Droughtmaster (4%) and Limousin (94.2%) but not found in Salers, Angus, Poll Hereford, Hereford, Gelbvieh, Charolais, Jersey, Brahman, Holstein, Shorthorn or Maine Anjou. The low prevalence of F94L in all beef breeds except Limousin indicates the significant potential for this mutation to improve retail yield in Australian beef cattle. [ABSTRACT FROM AUTHOR]
- Published
- 2010
- Full Text
- View/download PDF
27. Genome-wide association study and annotating candidate gene networks affecting age at first calving in Nellore cattle.
- Author
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Mota RR, Guimarães SEF, Fortes MRS, Hayes B, Silva FF, Verardo LL, Kelly MJ, de Campos CF, Guimarães JD, Wenceslau RR, Penitente-Filho JM, Garcia JF, and Moore S
- Subjects
- Animals, Breeding, Cattle physiology, Female, Genotype, Phenotype, Quantitative Trait Loci, Aging physiology, Cattle genetics, Fertility, Gene Regulatory Networks, Genome-Wide Association Study, Polymorphism, Single Nucleotide
- Abstract
We performed a genome-wide mapping for the age at first calving (AFC) with the goal of annotating candidate genes that regulate fertility in Nellore cattle. Phenotypic data from 762 cows and 777k SNP genotypes from 2,992 bulls and cows were used. Single nucleotide polymorphism (SNP) effects based on the single-step GBLUP methodology were blocked into adjacent windows of 1 Megabase (Mb) to explain the genetic variance. SNP windows explaining more than 0.40% of the AFC genetic variance were identified on chromosomes 2, 8, 9, 14, 16 and 17. From these windows, we identified 123 coding protein genes that were used to build gene networks. From the association study and derived gene networks, putative candidate genes (e.g., PAPPA, PREP, FER1L6, TPR, NMNAT1, ACAD10, PCMTD1, CRH, OPKR1, NPBWR1 and NCOA2) and transcription factors (TF) (STAT1, STAT3, RELA, E2F1 and EGR1) were strongly associated with female fertility (e.g., negative regulation of luteinizing hormone secretion, folliculogenesis and establishment of uterine receptivity). Evidence suggests that AFC inheritance is complex and controlled by multiple loci across the genome. As several windows explaining higher proportion of the genetic variance were identified on chromosome 14, further studies investigating the interaction across haplotypes to better understand the molecular architecture behind AFC in Nellore cattle should be undertaken., (© 2017 Blackwell Verlag GmbH.)
- Published
- 2017
- Full Text
- View/download PDF
28. SNP detection using RNA-sequences of candidate genes associated with puberty in cattle.
- Author
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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 MR, Nguyen LT, Venus B, Diaz IS, Souza FR, Fonseca LF, Baldi F, Albuquerque LG, Thomas MG, and Oliveira HN
- Subjects
- Animals, Base Sequence, Cattle, Female, Fertility genetics, Genome, Male, Polymorphism, Single Nucleotide, Pregnancy, RNA genetics, Selection, Genetic, Sequence Analysis, RNA methods, Sexual Maturation, Puberty genetics
- 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.
- Published
- 2017
- Full Text
- View/download PDF
29. A marker-derived gene network reveals the regulatory role of PPARGC1A, HNF4G, and FOXP3 in intramuscular fat deposition of beef cattle.
- Author
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Ramayo-Caldas Y, Fortes MR, Hudson NJ, Porto-Neto LR, Bolormaa S, Barendse W, Kelly M, Moore SS, Goddard ME, Lehnert SA, and Reverter A
- Subjects
- Adiposity physiology, Animals, Cattle anatomy & histology, Cattle physiology, Forkhead Transcription Factors physiology, Gene Expression Regulation genetics, Gene Expression Regulation physiology, Genetic Markers genetics, Genome-Wide Association Study veterinary, Hepatocyte Nuclear Factor 4 physiology, Meat standards, Quantitative Trait, Heritable, Transcription Factors physiology, Adiposity genetics, Cattle genetics, Forkhead Transcription Factors genetics, Gene Regulatory Networks genetics, Hepatocyte Nuclear Factor 4 genetics, Muscle, Skeletal physiology, Transcription Factors genetics
- Abstract
High intramuscular fat (IMF) awards price premiums to beef producers and is associated with meat quality and flavor. Studying gene interactions and pathways that affect IMF might unveil causative physiological mechanisms and inform genomic selection, leading to increased accuracy of predictions of breeding value. To study gene interactions and pathways, a gene network was derived from genetic markers associated with direct measures of IMF, other fat phenotypes, feedlot performance, and a number of meat quality traits relating to body conformation, development, and metabolism that might be plausibly expected to interact with IMF biology. Marker associations were inferred from genomewide association studies (GWAS) based on high density genotypes and 29 traits measured on 10,181 beef cattle animals from 3 breed types. For the network inference, SNP pairs were assessed according to the strength of the correlation between their additive association effects across the 29 traits. The co-association inferred network was formed by 2,434 genes connected by 28,283 edges. Topological network parameters suggested a highly cohesive network, in which the genes are strongly functionally interconnected. Pathway and network analyses pointed towards a trio of transcription factors (TF) as key regulators of carcass IMF: PPARGC1A, HNF4G, and FOXP3. Importantly, none of these genes would have been deemed as significantly associated with IMF from the GWAS. Instead, a total of 313 network genes show significant co-association with the 3 TF. These genes belong to a wide variety of biological functions, canonical pathways, and genetic networks linked to IMF-related phenotypes. In summary, our GWAS and network predictions are supported by the current literature and suggest a cooperative role for the 3 TF and other interacting genes including CAPN6, STC2, MAP2K4, EYA1, COPS5, XKR4, NR2E1, TOX, ATF1, ASPH, TGS1, and TTPA as modulators of carcass and meat quality traits in beef cattle.
- Published
- 2014
- Full Text
- View/download PDF
30. The integrity of sperm chromatin in young tropical composite bulls.
- Author
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Fortes MR, Holroyd RG, Reverter A, Venus BK, Satake N, and Boe-Hansen GB
- Subjects
- Animals, DNA Fragmentation, Fertility, Infertility, Male, Male, Tropical Climate, Cattle genetics, Cattle physiology, Chromatin physiology, Spermatozoa cytology
- Abstract
Sperm chromatin fragmentation is associated with subfertility, but its relationship with age progression in young bulls is poorly understood. The objective was to assess sperm chromatin fragmentation during the early post-pubertal development of 20 tropical composite bulls, using a sperm chromatin structure assay (SCSA) and sperm-bos-halomax (SBH). Bulls were subjected to bull breeding soundness evaluation (BBSE) at mean ages of 13, 18, and 24 mo. Traits measured included liveweight (WT), body condition score (BCS) and scrotal circumference (SC). Semen samples were collected by electroejaculation and assessed for mass activity (MA), motility (Mot), concentration (conc), sperm morphology and chromatin fragmentation. Concentration (r=0.34, P=0.0076), Mot (r=0.36, P=0.0041) and percentage of morphologic normal sperm (percent normal sperm (PNS); r=0.31, P=0.0132) were positively correlated with age. The percentage of sperm with proximal droplets (PD) was negatively correlated with age (r=-0.28, P=0.0348), whereas neither SCSA nor SBH results were significantly correlated with age. The percentage of sperm with chromatin fragmentation using SCSA was correlated with PNS (r=-0.53, P<0.0001), the percentage of sperm with head abnormalities (r=0.68, P<0.0001) and the percentage of intact sperm (Int) with SBH (r=-0.26, P=0.0456). In summary, for assessment of sperm chromatin fragmentation, samples could be equally collected at 13, 18 or 24 mo of age, as results did not vary with age., (Copyright © 2012 Elsevier Inc. All rights reserved.)
- Published
- 2012
- Full Text
- View/download PDF
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