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Rossi UA, Hasenauer FC, Caffaro ME, Neumann R, Salatin A, Poli MA, Rossetti CA. A haplotype at intron 8 of PTPRT gene is associated with resistance to Brucella infection in Argentinian creole goats. Vet Microbiol 2017; 207:133-137. [DOI: 10.1016/j.vetmic.2017.06.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 05/31/2017] [Accepted: 06/01/2017] [Indexed: 11/25/2022]
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Cha TS, Anne-Marie K, Chuah TS. Identification and characterization of RAPD-SCAR markers linked to glyphosate-susceptible and -resistant biotypes of Eleusine indica (L.) Gaertn. Mol Biol Rep 2014; 41:823-31. [PMID: 24374894 DOI: 10.1007/s11033-013-2922-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 12/18/2013] [Indexed: 10/25/2022]
Abstract
Eleusine indica is one of the most common weed species found in agricultural land worldwide. Although herbicide-glyphosate provides good control of the weed, its frequent uses has led to abundant reported cases of resistance. Hence, the development of genetic markers for quick detection of glyphosate-resistance in E. indica population is imperative for the control and management of the weed. In this study, a total of 14 specific random amplified polymorphic DNA (RAPD) markers were identified and two of the markers, namely S4R727 and S26R6976 were further sequence characterized. Sequence alignment revealed that marker S4R727 showing a 12-bp nucleotides deletion in resistant biotypes, while marker S26R6976 contained a 167-bp nucleotides insertion in the resistant biotypes. Based on these sequence differences, three pairs of new sequence characterized amplified region (SCAR) primers were developed. The specificity of these primer pairs were further validated with genomic DNA extracted from ten individual plants of one glyphosate-susceptible and five glyphosate-resistant (R2, R4, R6, R8 and R11) populations. The resulting RAPD-SCAR markers provided the basis for assessing genetic diversity between glyphosate-susceptible and -resistant E. indica biotypes, as well for the identification of genetic locus link to glyphosate-resistance event in the species.
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Affiliation(s)
- Thye San Cha
- School of Fundamental Science, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Terengganu, Malaysia,
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Effects of genetic variants for the bovine calpain gene on meat tenderness. Mol Biol Rep 2014; 41:2963-70. [DOI: 10.1007/s11033-014-3152-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 01/13/2014] [Indexed: 10/25/2022]
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Liao X, Peng F, Forni S, McLaren D, Plastow G, Stothard P. Whole genome sequencing of Gir cattle for identifying polymorphisms and loci under selection. Genome 2013; 56:592-8. [DOI: 10.1139/gen-2013-0082] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Genetic variation in Gir cattle (Bos indicus) has so far not been well characterized. In this study, we used whole genome sequencing of three Gir bulls and a pooled sample from another 11 bulls to identify polymorphisms and loci under selection. A total of 9 990 733 single nucleotide polymorphisms (SNPs) and 604 308 insertion/deletions (indels) were discovered in Gir samples, of which 62.34% and 83.62%, respectively, are previously unknown. Moreover, we detected 79 putative selective sweeps using the sequence data of the pooled sample. One of the most striking sweeps harbours several genes belonging to the cathelicidin gene family, such as CAMP, CATHL1, CATHL2, and CATHL3, which are related to pathogen- and parasite-resistance. Another interesting region harbours genes encoding mitogen-activated protein kinases, which are involved in directing cellular responses to a variety of stimuli, such as osmotic stress and heat shock. These findings are particularly interesting because Gir is resistant to hot temperatures and tropical diseases. This initial selective sweep analysis of Gir cattle has revealed a number of loci that could be important for their adaptation to tropical climates.
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Affiliation(s)
- Xiaoping Liao
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G2P5, Canada
| | - Fred Peng
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G2P5, Canada
| | - Selma Forni
- Genus plc, 100 Bluegrass Commons Boulevard, Suite 2200, Hendersonville, TN 37075, USA
| | | | - Graham Plastow
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G2P5, Canada
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G2P5, Canada
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Hasenauer FC, Caffaro ME, Czibener C, Comerci D, Poli MA, Rossetti CA. Genetic analysis of the 3' untranslated region of the bovine SLC11A1 gene reveals novel polymorphisms. Mol Biol Rep 2012; 40:545-52. [PMID: 23065223 DOI: 10.1007/s11033-012-2091-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Accepted: 10/03/2012] [Indexed: 12/01/2022]
Abstract
Polymorphisms in microsatellites at the 3' untranslated region (3'UTR) of the SLC11A1 (solute carrier family 11 member A1) gene have been associated with natural resistance to Brucella abortus and Mycobacterium bovis infection in livestock species. Here, we carried out an individual genetic analysis of the two microsatellites present at the 3'UTR SLC11A1 gene in 254 Bos taurus purebred, 125 B. indicus purebred and 54 B. taurus × B. indicus crossbred cattle. The genotyping by capillary electrophoresis showed the presence of four alleles (157, 159, 161 and 163) for the first microsatellite (MS1) and six alleles (175, 177, 179, 181, 183 and 185) for the second microsatellite (MS2). The alleles 159 and 175 were the most frequent in all breeds analyzed. B. taurus showed the most homogeneous haplotype and genotype for both microsatellites, whereas B. indicus showed the most heterogeneous haplotype and genotype. Two novel variants (alleles 161 and 163) within the MS1 are reported as well as novel variants in MS2 in Holstein breed. The knowledge of the polymorphisms distribution in both microsatellites at the 3'UTR of the SLC11A1 gene in cattle breeds is useful for future experimental design to evaluate the association between reported genotypes and natural resistance to pathogens infection.
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Affiliation(s)
- F C Hasenauer
- Instituto de Patobiología, CICVyA-CNIA, INTA, Nicolás Repetto y de Los Reseros s/n, Hurlingham, Buenos Aires B1686, Argentina
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Zhao C, Tian F, Yu Y, Luo J, Mitra A, Zhan F, Hou Y, Liu G, Zan L, Updike MS, Song J. Functional genomic analysis of variation on beef tenderness induced by acute stress in angus cattle. Comp Funct Genomics 2012; 2012:756284. [PMID: 22566754 PMCID: PMC3332163 DOI: 10.1155/2012/756284] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Accepted: 01/19/2012] [Indexed: 11/18/2022] Open
Abstract
Beef is one of the leading sources of protein, B vitamins, iron, and zinc in human food. Beef palatability is based on three general criteria: tenderness, juiciness, and flavor, of which tenderness is thought to be the most important factor. In this study, we found that beef tenderness, measured by the Warner-Bratzler shear force (WBSF), was dramatically increased by acute stress. Microarray analysis and qPCR identified a variety of genes that were differentially expressed. Pathway analysis showed that these genes were involved in immune response and regulation of metabolism process as activators or repressors. Further analysis identified that these changes may be related with CpG methylation of several genes. Therefore, the results from this study provide an enhanced understanding of the mechanisms that genetic and epigenetic regulations control meat quality and beef tenderness.
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Affiliation(s)
- Chunping Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Department of Animal & Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Fei Tian
- Department of Animal & Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Ying Yu
- Department of Animal & Avian Sciences, University of Maryland, College Park, MD 20742, USA
- Department of Animal Breeding and Genetics, College of Animal Sciences, China Agricultural University, Beijing 100193, China
| | - Juan Luo
- Department of Animal & Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Apratim Mitra
- Department of Animal & Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Fei Zhan
- Department of Animal & Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Yali Hou
- Department of Animal & Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - George Liu
- Bovine Functional Genomic Laboratory, Animal and Natural Resources Institute, USDA-Agricultural Research Service, Beltsville, MD 20705, USA
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - M. Scott Updike
- Department of Animal & Avian Sciences, University of Maryland, College Park, MD 20742, USA
- Standerds Division, USDA-Agricultural Marketing Service-National Organic Program, Washington, DC 20250, USA
| | - Jiuzhou Song
- Department of Animal & Avian Sciences, University of Maryland, College Park, MD 20742, USA
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Zhao C, Tian F, Yu Y, Luo J, Hu Q, Bequette BJ, Baldwin Vi RL, Liu G, Zan L, Scott Updike M, Song J. Muscle transcriptomic analyses in Angus cattle with divergent tenderness. Mol Biol Rep 2011; 39:4185-93. [PMID: 21901422 DOI: 10.1007/s11033-011-1203-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 07/11/2011] [Indexed: 11/25/2022]
Abstract
Beef tenderness contributes significantly to variation of beef palatability, and is largely influenced by various genetic and environmental factors. To identify candidate genes and pathways related to beef tenderness, we analyzed the longissimus dorsi (LD) muscle of Angus cattle that had different degrees of tenderness, measured by Warner-Bratzler shear force (WBSF). Microarray and RT-PCR analyses identified 53 genes that were differentially expressed in LD samples categorized as either tough or tender, including myosin, heavy chain 3 skeletal muscle embryonic (MYH3), myosin heavy chain 8 skeletal muscle perinatal (MYH8), guanylate binding protein 5 (GBP5), fatty acid binding protein 4 (FABP4), Stearoyl-coenzyme A desaturase (SCD), Fatty acid synthase (FASN), ubiquitin-like with PHD and ring finger domains 1 (UHRF1). Most of these genes are involved in lipid metabolism and skeletal muscle contraction. Employing Gene ontology (GO) and Ingenuity Pathway Analysis (IPA), several GO terms and pathways were found to be related to hydrolase, peptidase and GTPase activity, lipid metabolism, small molecule biochemistry, molecular transport, and tissue development. Overall, this analysis provides insight into the metabolic relationships between muscle biology and beef quality.
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Affiliation(s)
- Chunping Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
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Molecular characterization, expression pattern, polymorphism and association analysis of bovine ADAMTSL3 gene. Mol Biol Rep 2011; 39:1551-60. [DOI: 10.1007/s11033-011-0894-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Accepted: 05/17/2011] [Indexed: 10/18/2022]
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Chung HY, Davis ME. Effects of calpain genotypes on meat tenderness and carcass traits of Angus bulls. Mol Biol Rep 2010; 38:4575-81. [DOI: 10.1007/s11033-010-0589-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Accepted: 11/20/2010] [Indexed: 12/01/2022]
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