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Islam S, Reddy UK, Natarajan P, Abburi VL, Bajwa AA, Imran M, Zahoor MY, Abdullah M, Bukhari AM, Iqbal S, Ashraf K, Nadeem A, Rehman H, Rashid I, Shehzad W. Population demographic history and population structure for Pakistani Nili-Ravi breeding bulls based on SNP genotyping to identify genomic regions associated with male effects for milk yield and body weight. PLoS One 2020; 15:e0242500. [PMID: 33232358 PMCID: PMC7685427 DOI: 10.1371/journal.pone.0242500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 11/03/2020] [Indexed: 11/20/2022] Open
Abstract
The domestic Nili-Ravi water buffalo (Bubalus bubalis) is the best dairy animal contributing 68% to total milk production in Pakistan. In this study, we identified genome-wide single nucleotide polymorphisms (SNPs) to estimate various population genetic parameters such as diversity, pairwise population differentiation, linkage disequilibrium (LD) distribution and for genome-wide association study for milk yield and body weight traits in the Nili-Ravi dairy bulls that they may pass on to their daughters who are retained for milking purposes. The genotyping by sequencing approach revealed 13,039 reference genome-anchored SNPs with minor allele frequency of 0.05 among 167 buffalos. Population structure analysis revealed that the bulls were grouped into two clusters (K = 2), which indicates the presence of two different lineages in the Pakistani Nili-Ravi water buffalo population, and we showed the extent of admixture of these two lineages in our bull collection. LD analysis revealed 4169 significant SNP associations, with an average LD decay of 90 kb for these buffalo genome. Genome-wide association study involved a multi-locus mixed linear model for milk yield and body weight to identify genome-wide male effects. Our study further illustrates the utility of the genotyping by sequencing approach for identifying genomic regions to uncover additional demographic complexity and to improve the complex dairy traits of the Pakistani Nili-Ravi water buffalo population that would provide the lot of economic benefits to dairy industry.
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Affiliation(s)
- Saher Islam
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Umesh K. Reddy
- Department of Biology, West Virginia State University, Institute, West Virginia, United States of America
| | - Purushothaman Natarajan
- Department of Biology, West Virginia State University, Institute, West Virginia, United States of America
| | - Venkata Lakshmi Abburi
- Department of Biology, West Virginia State University, Institute, West Virginia, United States of America
| | - Amna Arshad Bajwa
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muhammad Imran
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muhammad Yasir Zahoor
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muhammad Abdullah
- Department of Livestock Production, University of Veterinary and Animal Sciences, Pattoki, Pakistan
| | - Aamir Mehmood Bukhari
- Semen Production Unit, Qadirabad, District Sahiwal, Pakistan
- Livestock and Dairy Development Department, Government of the Punjab, Lahore, Pakistan
| | - Sajid Iqbal
- Semen Production Unit, Qadirabad, District Sahiwal, Pakistan
- Livestock and Dairy Development Department, Government of the Punjab, Lahore, Pakistan
| | - Kamran Ashraf
- Department of Parasitology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Asif Nadeem
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Habibur Rehman
- Department of Physiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Imran Rashid
- Department of Parasitology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Wasim Shehzad
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
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Guan D, Landi V, Luigi-Sierra MG, Delgado JV, Such X, Castelló A, Cabrera B, Mármol-Sánchez E, Fernández-Alvarez J, de la Torre Casañas JLR, Martínez A, Jordana J, Amills M. Analyzing the genomic and transcriptomic architecture of milk traits in Murciano-Granadina goats. J Anim Sci Biotechnol 2020; 11:35. [PMID: 32175082 PMCID: PMC7065321 DOI: 10.1186/s40104-020-00435-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 02/17/2020] [Indexed: 12/19/2022] Open
Abstract
Background In this study, we aimed to investigate the molecular basis of lactation as well as to identify the genetic factors that influence milk yield and composition in goats. To achieve these two goals, we have analyzed how the mRNA profile of the mammary gland changes in seven Murciano-Granadina goats at each of three different time points, i.e. 78 d (T1, early lactation), 216 d (T2, late lactation) and 285 d (T3, dry period) after parturition. Moreover, we have performed a genome-wide association study (GWAS) for seven dairy traits recorded in the 1st lactation of 822 Murciano-Granadina goats. Results The expression profiles of the mammary gland in the early (T1) and late (T2) lactation were quite similar (42 differentially expressed genes), while strong transcriptomic differences (more than one thousand differentially expressed genes) were observed between the lactating (T1/T2) and non-lactating (T3) mammary glands. A large number of differentially expressed genes were involved in pathways related with the biosynthesis of amino acids, cholesterol, triglycerides and steroids as well as with glycerophospholipid metabolism, adipocytokine signaling, lipid binding, regulation of ion transmembrane transport, calcium ion binding, metalloendopeptidase activity and complement and coagulation cascades. With regard to the second goal of the study, the performance of the GWAS allowed us to detect 24 quantitative trait loci (QTLs), including three genome-wide significant associations: QTL1 (chromosome 2, 130.72-131.01 Mb) for lactose percentage, QTL6 (chromosome 6, 78.90-93.48 Mb) for protein percentage and QTL17 (chromosome 17, 11.20 Mb) for both protein and dry matter percentages. Interestingly, QTL6 shows positional coincidence with the casein genes, which encode 80% of milk proteins. Conclusions The abrogation of lactation involves dramatic changes in the expression of genes participating in a broad array of physiological processes such as protein, lipid and carbohydrate metabolism, calcium homeostasis, cell death and tissue remodeling, as well as immunity. We also conclude that genetic variation at the casein genes has a major impact on the milk protein content of Murciano-Granadina goats.
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Affiliation(s)
- Dailu Guan
- 1Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Vincenzo Landi
- 2Departamento de Genética, Universidad de Córdoba, 14071 Córdoba, Spain
| | - María Gracia Luigi-Sierra
- 1Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | | | - Xavier Such
- 3Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Anna Castelló
- 1Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.,3Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Betlem Cabrera
- 1Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.,3Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Emilio Mármol-Sánchez
- 1Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Javier Fernández-Alvarez
- Asociación Nacional de Criadores de Caprino de Raza Murciano-Granadina (CAPRIGRAN), 18340 Granada, Spain
| | | | - Amparo Martínez
- 2Departamento de Genética, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Jordi Jordana
- 3Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Marcel Amills
- 1Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.,3Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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Identification of the complete coding cDNAs and expression analysis of B4GALT1, LALBA, ST3GAL5, ST6GAL1 in the colostrum and milk of the Garganica and Maltese goat breeds to reveal possible implications for oligosaccharide biosynthesis. BMC Vet Res 2019; 15:457. [PMID: 31852463 PMCID: PMC6921551 DOI: 10.1186/s12917-019-2206-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 12/04/2019] [Indexed: 12/11/2022] Open
Abstract
Background Milk sialylated oligosaccharides (SOS) play crucial roles in many biological processes. The most abundant free SOS in goat’s milk are 3’sialyllactose (3′-SL), 6’sialyllactose (6′-SL) and disialyllactose (DSL). The production of these molecules is determined genetically by the expression of glycosyltransferases and by the availability of nucleotide sugar substrates, but the precise mechanisms regulating the differential patterns of milk oligosaccharides are not known. We aimed to identify the complete cDNAs of candidate genes implicated in SOS biosynthesis (B4GALT1, LALBA, ST3GAL5, ST6GAL1) and to analyse their expression during lactation in the Garganica and Maltese goat breeds. Moreover, we analysed the colostrum and milk contents of 3′-SL, 6′-SL and disialyllactose (DSL) and the possible correlations between expressed genes and SOS. Results We identified the complete coding cDNAs of B4GALT1 (HQ700335.1), ST3GAL5 (KF055858.2), and ST6GAL1 (HQ709167.1), the single nucleotide polymorphism (SNPs) of these genes and 2 splicing variants of the ST6GAL1 cDNA. RT-qPCR analysis showed that LALBA and ST6GAL1 were the genes with the highest and lowest expression in both breeds, respectively. The interaction effects of the breeds and sampling times were associated with higher levels of B4GALT1 and ST3GAL5 gene expression in Garganica than in Maltese goats at kidding. B4GALT1, LALBA, and ST3GAL5 gene expression changed from kidding to 60 and 120 days in Maltese goats, while in Garganica goats, a difference was observed only for the LALBA gene. Breed and lactation effects were also found for SOS contents. Positive correlations of B4GALT1, LALBA, ST3GAL5, and ST6GAL1 with 3′-SL/6′SL and DSL were found. Conclusions The genetic effect on the oligosaccharide content of milk was previously highlighted in bovines, and this study is the first to investigate this effect in two goat breeds (Garganica and Maltese) during lactation. The genetic variability of candidate genes involved in SOS biosynthesis highlights their potential role in affecting gene expression and ultimately biological function. The investigation of gene regulatory regions as well as the examination of other sialyltransferase genes will be needed to identify the genetic pattern leading to a higher SOS content in the autochtonous Garganica breed and to protect it using a focused breeding strategy.
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Figueroa-Lozano S, de Vos P. Relationship Between Oligosaccharides and Glycoconjugates Content in Human Milk and the Development of the Gut Barrier. Compr Rev Food Sci Food Saf 2018; 18:121-139. [DOI: 10.1111/1541-4337.12400] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 09/17/2018] [Accepted: 09/18/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Susana Figueroa-Lozano
- Immunoendocrinology, Div. of Medical Biology, Dept. of Pathology and Medical Biology; Univ. of Groningen and University Medical Center Groningen; Groningen The Netherlands
| | - Paul de Vos
- Immunoendocrinology, Div. of Medical Biology, Dept. of Pathology and Medical Biology; Univ. of Groningen and University Medical Center Groningen; Groningen The Netherlands
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Song S, Ou-Yang Y, Huo J, Zhang Y, Yu C, Liu M, Teng X, Miao Y. Molecular cloning, sequence characterization, and tissue expression analysis
of three water buffalo (<i>Bubalus bubalis</i>) genes – <i>ST6GAL1</i>,
<i>ST8SIA4</i>, and <i>SLC35C1</i>. Arch Anim Breed 2016. [DOI: 10.5194/aab-59-363-2016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract. Recent studies have shown that ST6 beta-galactosamide alpha-2,6-sialyltransferase 1 (ST6GAL1), ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4 (ST8SIA4), and solute carrier family 35, member C1 (SLC35C1) play essential roles in the metabolism of milk glycoconjugates in mammals. However, studies on their coding genes in water buffalo have not been reported. In the present study, cloning and sequencing showed that the coding sequences (CDSs) of buffalo ST6GAL1, ST8SIA4, and SLC35C1 were 1218, 1080, and 1095 bp in length, which encoded a precursor protein composed of 405, 359, and 364 amino acids, respectively. The deduced sequences of these three proteins in turn showed 97.6–98.5, 98.6–99.7, and 97.8–99.2 % similarities with other bovine species. Both buffalo ST6GAL1 and ST8SIA4 were predicted to be a member of glycosyltransferase family 29 and were all hydrophilicity proteins functioning in the Golgi apparatus. Buffalo SLC35C1 was a hydrophobic membrane protein located in the Golgi membrane, containing a TPT domain that is found in a number of sugar phosphate transporters. In addition, semi-quantitative RT-PCR analysis in 13 lactating buffalo tissues revealed that the ST6GAL1 and ST8SIA4 were expressed in 9 tissues, while SLC35C1 was expressed in 11 tissues. The expression levels of these three genes in the mammary gland were significantly higher in lactating than in non-lactating stage. Collectively, our data indicate that ST6GAL1, ST8SIA4, and SLC35C1 are potentially involved in the process of buffalo lactation.
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Liu Z, Moate P, Cocks B, Rochfort S. Simple liquid chromatography-mass spectrometry method for quantification of major free oligosaccharides in bovine milk. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:11568-11574. [PMID: 25365143 DOI: 10.1021/jf5037849] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Free oligosaccharides (OS) are a significant functional component of milk that are difficult to quantitate. A simple method for quantitative analysis of the major free OS in bovine milk is described. Following a defatting step, protein elimination was performed by ultrafiltration. OS were separated by hydrophilic interaction liquid chromatography (HILIC) and detected by an Orbitrap mass analyzer in negative mode. The method is sensitive [with a limit of detection (LOD) for all representative OS of <0.1 ng] and reproducible, enabling simultaneous quantification of 13 major OS within a single run. Application of this method to the quantification of major OS in 32 milk samples collected after three different feeding treatments allowed us to reveal the relative abundance of different OS species, the variation of the OS content between individual cows, and the correlations between some of the major OS.
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Affiliation(s)
- Zhiqian Liu
- Biosciences Research Division, Department of Environment and Primary Industries, AgriBio , 5 Ring Road, Bundoora, Victoria 3083, Australia
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Park JJ, Lee M. Increasing the α 2, 6 sialylation of glycoproteins may contribute to metastatic spread and therapeutic resistance in colorectal cancer. Gut Liver 2013; 7:629-41. [PMID: 24312702 PMCID: PMC3848550 DOI: 10.5009/gnl.2013.7.6.629] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 10/02/2013] [Accepted: 10/02/2013] [Indexed: 12/13/2022] Open
Abstract
Abnormal glycosylation due to dysregulated glycosyltransferases and glycosidases is a key phenomenon of many malignancies, including colorectal cancer (CRC). In particular, increased ST6 Gal I (β-galactoside α 2, 6 sialyltransferase) and subsequently elevated levels of cell-surface α 2, 6-linked sialic acids have been associated with metastasis and therapeutic failure in CRC. As many CRC patients experience metastasis to the liver or lung and fail to respond to curative therapies, intensive research efforts have sought to identify the molecular changes underlying CRC metastasis. ST6 Gal I has been shown to facilitate CRC metastasis, and we believe that additional investigations into the involvement of ST6 Gal I in CRC could facilitate the development of new diagnostic and therapeutic targets. This review summarizes how ST6 Gal I has been implicated in the altered expression of sialylated glycoproteins, which have been linked to CRC metastasis, radioresistance, and chemoresistance.
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Affiliation(s)
- Jung-Jin Park
- Division of Life Science, Korea University College of Life Sciences and Biotechnology, Seoul, Korea
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Kuruppath S, Bisana S, Sharp JA, Lefevre C, Kumar S, Nicholas KR. Monotremes and marsupials: comparative models to better understand the function of milk. J Biosci 2013; 37:581-8. [PMID: 22922184 DOI: 10.1007/s12038-012-9247-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Sanjana Kuruppath
- Centre for Biotechnology, Chemistry and Systems Biology, Deakin University, Geelong 3217 VIC, Australia.
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